Starting phenix.real_space_refine on Sun Dec 29 16:01:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f3d_28846/12_2024/8f3d_28846.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f3d_28846/12_2024/8f3d_28846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f3d_28846/12_2024/8f3d_28846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f3d_28846/12_2024/8f3d_28846.map" model { file = "/net/cci-nas-00/data/ceres_data/8f3d_28846/12_2024/8f3d_28846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f3d_28846/12_2024/8f3d_28846.cif" } resolution = 3.4 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= 0.000 sd= 0.004 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 306 5.16 5 C 36504 2.51 5 N 10254 2.21 5 O 10782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 57846 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4350 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "B" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4350 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "C" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4350 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "D" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4350 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "E" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4350 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "F" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4350 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "H" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5276 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain: "I" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5276 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain: "J" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5276 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain: "K" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5276 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain: "L" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5276 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain: "M" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5276 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 23.86, per 1000 atoms: 0.41 Number of scatterers: 57846 At special positions: 0 Unit cell: (155.1, 166.1, 232.1, 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 306 16.00 O 10782 8.00 N 10254 7.00 C 36504 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.01 Conformation dependent library (CDL) restraints added in 6.1 seconds 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13596 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 60 sheets defined 34.0% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.65 Creating SS restraints... Processing helix chain 'A' and resid 161 through 176 Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.771A pdb=" N VAL A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 219 removed outlier: 3.602A pdb=" N ASP A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.734A pdb=" N GLU A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 311 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 337 through 351 removed outlier: 3.728A pdb=" N ILE A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.586A pdb=" N ALA A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 395 removed outlier: 4.191A pdb=" N LEU A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 440 removed outlier: 3.575A pdb=" N ASN A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 451 removed outlier: 4.466A pdb=" N HIS A 446 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 466 through 471 removed outlier: 3.846A pdb=" N PHE A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 466 through 471' Processing helix chain 'A' and resid 484 through 492 Processing helix chain 'A' and resid 530 through 548 Processing helix chain 'A' and resid 563 through 569 Processing helix chain 'A' and resid 570 through 585 Processing helix chain 'A' and resid 601 through 606 removed outlier: 3.596A pdb=" N MET A 605 " --> pdb=" O GLY A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 611 Processing helix chain 'A' and resid 629 through 638 removed outlier: 3.729A pdb=" N THR A 633 " --> pdb=" O THR A 629 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 637 " --> pdb=" O THR A 633 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 638 " --> pdb=" O VAL A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 653 Processing helix chain 'A' and resid 653 through 664 removed outlier: 3.902A pdb=" N GLU A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 696 removed outlier: 3.651A pdb=" N VAL A 688 " --> pdb=" O ASP A 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 176 Processing helix chain 'B' and resid 177 through 186 removed outlier: 3.774A pdb=" N VAL B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG B 183 " --> pdb=" O ARG B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 removed outlier: 3.602A pdb=" N ASP B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 removed outlier: 3.735A pdb=" N GLU B 229 " --> pdb=" O ARG B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 311 Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 337 through 351 removed outlier: 3.728A pdb=" N ILE B 341 " --> pdb=" O HIS B 337 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.586A pdb=" N ALA B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 395 removed outlier: 4.190A pdb=" N LEU B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 440 removed outlier: 3.577A pdb=" N ASN B 440 " --> pdb=" O ARG B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 451 removed outlier: 4.465A pdb=" N HIS B 446 " --> pdb=" O ASN B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 466 through 471 removed outlier: 3.846A pdb=" N PHE B 470 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 466 through 471' Processing helix chain 'B' and resid 484 through 492 Processing helix chain 'B' and resid 530 through 548 Processing helix chain 'B' and resid 563 through 569 Processing helix chain 'B' and resid 570 through 585 Processing helix chain 'B' and resid 601 through 606 removed outlier: 3.595A pdb=" N MET B 605 " --> pdb=" O GLY B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 611 Processing helix chain 'B' and resid 629 through 638 removed outlier: 3.729A pdb=" N THR B 633 " --> pdb=" O THR B 629 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 637 " --> pdb=" O THR B 633 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 638 " --> pdb=" O VAL B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 653 Processing helix chain 'B' and resid 653 through 664 removed outlier: 3.901A pdb=" N GLU B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 696 removed outlier: 3.651A pdb=" N VAL B 688 " --> pdb=" O ASP B 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 176 Processing helix chain 'C' and resid 177 through 186 removed outlier: 3.772A pdb=" N VAL C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG C 183 " --> pdb=" O ARG C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 219 removed outlier: 3.603A pdb=" N ASP C 209 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 3.735A pdb=" N GLU C 229 " --> pdb=" O ARG C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 311 Processing helix chain 'C' and resid 327 through 332 Processing helix chain 'C' and resid 337 through 351 removed outlier: 3.728A pdb=" N ILE C 341 " --> pdb=" O HIS C 337 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.586A pdb=" N ALA C 372 " --> pdb=" O ALA C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 395 removed outlier: 4.191A pdb=" N LEU C 395 " --> pdb=" O PRO C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 440 removed outlier: 3.575A pdb=" N ASN C 440 " --> pdb=" O ARG C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 451 removed outlier: 4.465A pdb=" N HIS C 446 " --> pdb=" O ASN C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 466 through 471 removed outlier: 3.847A pdb=" N PHE C 470 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE C 471 " --> pdb=" O LEU C 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 466 through 471' Processing helix chain 'C' and resid 484 through 492 Processing helix chain 'C' and resid 530 through 548 Processing helix chain 'C' and resid 563 through 569 Processing helix chain 'C' and resid 570 through 585 Processing helix chain 'C' and resid 601 through 606 removed outlier: 3.596A pdb=" N MET C 605 " --> pdb=" O GLY C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 611 Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.729A pdb=" N THR C 633 " --> pdb=" O THR C 629 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 637 " --> pdb=" O THR C 633 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR C 638 " --> pdb=" O VAL C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 653 Processing helix chain 'C' and resid 653 through 664 removed outlier: 3.901A pdb=" N GLU C 664 " --> pdb=" O LYS C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 696 removed outlier: 3.653A pdb=" N VAL C 688 " --> pdb=" O ASP C 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 176 Processing helix chain 'D' and resid 177 through 186 removed outlier: 3.773A pdb=" N VAL D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 219 removed outlier: 3.602A pdb=" N ASP D 209 " --> pdb=" O SER D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 removed outlier: 3.734A pdb=" N GLU D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 311 Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 337 through 351 removed outlier: 3.728A pdb=" N ILE D 341 " --> pdb=" O HIS D 337 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER D 349 " --> pdb=" O GLU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.586A pdb=" N ALA D 372 " --> pdb=" O ALA D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 395 removed outlier: 4.192A pdb=" N LEU D 395 " --> pdb=" O PRO D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 440 removed outlier: 3.576A pdb=" N ASN D 440 " --> pdb=" O ARG D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 451 removed outlier: 4.464A pdb=" N HIS D 446 " --> pdb=" O ASN D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 465 No H-bonds generated for 'chain 'D' and resid 463 through 465' Processing helix chain 'D' and resid 466 through 471 removed outlier: 3.847A pdb=" N PHE D 470 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE D 471 " --> pdb=" O LEU D 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 466 through 471' Processing helix chain 'D' and resid 484 through 492 Processing helix chain 'D' and resid 530 through 548 Processing helix chain 'D' and resid 563 through 569 Processing helix chain 'D' and resid 570 through 585 Processing helix chain 'D' and resid 601 through 606 removed outlier: 3.595A pdb=" N MET D 605 " --> pdb=" O GLY D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 611 Processing helix chain 'D' and resid 629 through 638 removed outlier: 3.728A pdb=" N THR D 633 " --> pdb=" O THR D 629 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 637 " --> pdb=" O THR D 633 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR D 638 " --> pdb=" O VAL D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 653 Processing helix chain 'D' and resid 653 through 664 removed outlier: 3.903A pdb=" N GLU D 664 " --> pdb=" O LYS D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 696 removed outlier: 3.652A pdb=" N VAL D 688 " --> pdb=" O ASP D 684 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 176 Processing helix chain 'E' and resid 177 through 186 removed outlier: 3.772A pdb=" N VAL E 182 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG E 183 " --> pdb=" O ARG E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 219 removed outlier: 3.602A pdb=" N ASP E 209 " --> pdb=" O SER E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 232 removed outlier: 3.734A pdb=" N GLU E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 311 Processing helix chain 'E' and resid 327 through 332 Processing helix chain 'E' and resid 337 through 351 removed outlier: 3.729A pdb=" N ILE E 341 " --> pdb=" O HIS E 337 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE E 342 " --> pdb=" O PHE E 338 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER E 349 " --> pdb=" O GLU E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.586A pdb=" N ALA E 372 " --> pdb=" O ALA E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 removed outlier: 4.192A pdb=" N LEU E 395 " --> pdb=" O PRO E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 440 removed outlier: 3.576A pdb=" N ASN E 440 " --> pdb=" O ARG E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 451 removed outlier: 4.465A pdb=" N HIS E 446 " --> pdb=" O ASN E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 465 No H-bonds generated for 'chain 'E' and resid 463 through 465' Processing helix chain 'E' and resid 466 through 471 removed outlier: 3.848A pdb=" N PHE E 470 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE E 471 " --> pdb=" O LEU E 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 466 through 471' Processing helix chain 'E' and resid 484 through 492 Processing helix chain 'E' and resid 530 through 548 Processing helix chain 'E' and resid 563 through 569 Processing helix chain 'E' and resid 570 through 585 Processing helix chain 'E' and resid 601 through 606 removed outlier: 3.596A pdb=" N MET E 605 " --> pdb=" O GLY E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 607 through 611 Processing helix chain 'E' and resid 629 through 638 removed outlier: 3.729A pdb=" N THR E 633 " --> pdb=" O THR E 629 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU E 637 " --> pdb=" O THR E 633 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR E 638 " --> pdb=" O VAL E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 645 through 653 Processing helix chain 'E' and resid 653 through 664 removed outlier: 3.902A pdb=" N GLU E 664 " --> pdb=" O LYS E 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 696 removed outlier: 3.653A pdb=" N VAL E 688 " --> pdb=" O ASP E 684 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 176 Processing helix chain 'F' and resid 177 through 186 removed outlier: 3.773A pdb=" N VAL F 182 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 219 removed outlier: 3.603A pdb=" N ASP F 209 " --> pdb=" O SER F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 232 removed outlier: 3.734A pdb=" N GLU F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 311 Processing helix chain 'F' and resid 327 through 332 Processing helix chain 'F' and resid 337 through 351 removed outlier: 3.727A pdb=" N ILE F 341 " --> pdb=" O HIS F 337 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE F 342 " --> pdb=" O PHE F 338 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER F 349 " --> pdb=" O GLU F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.585A pdb=" N ALA F 372 " --> pdb=" O ALA F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 removed outlier: 4.191A pdb=" N LEU F 395 " --> pdb=" O PRO F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 440 removed outlier: 3.576A pdb=" N ASN F 440 " --> pdb=" O ARG F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 451 removed outlier: 4.464A pdb=" N HIS F 446 " --> pdb=" O ASN F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 465 No H-bonds generated for 'chain 'F' and resid 463 through 465' Processing helix chain 'F' and resid 466 through 471 removed outlier: 3.847A pdb=" N PHE F 470 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE F 471 " --> pdb=" O LEU F 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 466 through 471' Processing helix chain 'F' and resid 484 through 492 Processing helix chain 'F' and resid 530 through 548 Processing helix chain 'F' and resid 563 through 569 Processing helix chain 'F' and resid 570 through 585 Processing helix chain 'F' and resid 601 through 606 removed outlier: 3.595A pdb=" N MET F 605 " --> pdb=" O GLY F 601 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 611 Processing helix chain 'F' and resid 629 through 638 removed outlier: 3.729A pdb=" N THR F 633 " --> pdb=" O THR F 629 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU F 637 " --> pdb=" O THR F 633 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR F 638 " --> pdb=" O VAL F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 645 through 653 Processing helix chain 'F' and resid 653 through 664 removed outlier: 3.901A pdb=" N GLU F 664 " --> pdb=" O LYS F 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 696 removed outlier: 3.652A pdb=" N VAL F 688 " --> pdb=" O ASP F 684 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 35 removed outlier: 3.629A pdb=" N THR H 31 " --> pdb=" O ARG H 27 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS H 32 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG H 33 " --> pdb=" O PHE H 29 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU H 34 " --> pdb=" O ARG H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 55 Processing helix chain 'H' and resid 73 through 84 Processing helix chain 'H' and resid 94 through 98 removed outlier: 4.461A pdb=" N GLU H 98 " --> pdb=" O PHE H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 110 Processing helix chain 'H' and resid 117 through 126 removed outlier: 3.893A pdb=" N SER H 126 " --> pdb=" O SER H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 138 Processing helix chain 'H' and resid 151 through 160 removed outlier: 3.661A pdb=" N LEU H 155 " --> pdb=" O ASN H 151 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA H 156 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS H 160 " --> pdb=" O ALA H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 200 Processing helix chain 'H' and resid 259 through 278 Processing helix chain 'H' and resid 308 through 314 removed outlier: 3.642A pdb=" N THR H 312 " --> pdb=" O GLU H 308 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU H 314 " --> pdb=" O PRO H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 335 removed outlier: 3.528A pdb=" N LEU H 328 " --> pdb=" O ASP H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 432 Processing helix chain 'H' and resid 440 through 450 removed outlier: 3.916A pdb=" N THR H 450 " --> pdb=" O ARG H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 456 removed outlier: 3.904A pdb=" N ARG H 455 " --> pdb=" O GLU H 452 " (cutoff:3.500A) Processing helix chain 'H' and resid 461 through 466 removed outlier: 3.925A pdb=" N GLU H 465 " --> pdb=" O ASN H 461 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS H 466 " --> pdb=" O PHE H 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 461 through 466' Processing helix chain 'H' and resid 477 through 491 removed outlier: 3.728A pdb=" N ALA H 481 " --> pdb=" O THR H 477 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA H 482 " --> pdb=" O PRO H 478 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU H 489 " --> pdb=" O ALA H 485 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 35 removed outlier: 3.630A pdb=" N THR I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS I 32 " --> pdb=" O VAL I 28 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG I 33 " --> pdb=" O PHE I 29 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU I 34 " --> pdb=" O ARG I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 55 Processing helix chain 'I' and resid 73 through 84 Processing helix chain 'I' and resid 94 through 98 removed outlier: 4.461A pdb=" N GLU I 98 " --> pdb=" O PHE I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 110 Processing helix chain 'I' and resid 117 through 126 removed outlier: 3.892A pdb=" N SER I 126 " --> pdb=" O SER I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 138 Processing helix chain 'I' and resid 151 through 160 removed outlier: 3.662A pdb=" N LEU I 155 " --> pdb=" O ASN I 151 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA I 156 " --> pdb=" O VAL I 152 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS I 160 " --> pdb=" O ALA I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 200 Processing helix chain 'I' and resid 259 through 278 Processing helix chain 'I' and resid 308 through 314 removed outlier: 3.642A pdb=" N THR I 312 " --> pdb=" O GLU I 308 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU I 314 " --> pdb=" O PRO I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 324 through 335 removed outlier: 3.528A pdb=" N LEU I 328 " --> pdb=" O ASP I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 417 through 432 Processing helix chain 'I' and resid 440 through 450 removed outlier: 3.915A pdb=" N THR I 450 " --> pdb=" O ARG I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 452 through 456 removed outlier: 3.904A pdb=" N ARG I 455 " --> pdb=" O GLU I 452 " (cutoff:3.500A) Processing helix chain 'I' and resid 461 through 466 removed outlier: 3.925A pdb=" N GLU I 465 " --> pdb=" O ASN I 461 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS I 466 " --> pdb=" O PHE I 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 461 through 466' Processing helix chain 'I' and resid 477 through 491 removed outlier: 3.727A pdb=" N ALA I 481 " --> pdb=" O THR I 477 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA I 482 " --> pdb=" O PRO I 478 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU I 489 " --> pdb=" O ALA I 485 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 35 removed outlier: 3.629A pdb=" N THR J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS J 32 " --> pdb=" O VAL J 28 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG J 33 " --> pdb=" O PHE J 29 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU J 34 " --> pdb=" O ARG J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 55 Processing helix chain 'J' and resid 73 through 84 Processing helix chain 'J' and resid 94 through 98 removed outlier: 4.461A pdb=" N GLU J 98 " --> pdb=" O PHE J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 110 Processing helix chain 'J' and resid 117 through 126 removed outlier: 3.893A pdb=" N SER J 126 " --> pdb=" O SER J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 138 Processing helix chain 'J' and resid 151 through 160 removed outlier: 3.661A pdb=" N LEU J 155 " --> pdb=" O ASN J 151 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA J 156 " --> pdb=" O VAL J 152 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS J 160 " --> pdb=" O ALA J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 200 Processing helix chain 'J' and resid 259 through 278 Processing helix chain 'J' and resid 308 through 314 removed outlier: 3.642A pdb=" N THR J 312 " --> pdb=" O GLU J 308 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU J 314 " --> pdb=" O PRO J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 335 removed outlier: 3.527A pdb=" N LEU J 328 " --> pdb=" O ASP J 324 " (cutoff:3.500A) Processing helix chain 'J' and resid 417 through 432 Processing helix chain 'J' and resid 440 through 450 removed outlier: 3.916A pdb=" N THR J 450 " --> pdb=" O ARG J 446 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 456 removed outlier: 3.904A pdb=" N ARG J 455 " --> pdb=" O GLU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 466 removed outlier: 3.926A pdb=" N GLU J 465 " --> pdb=" O ASN J 461 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS J 466 " --> pdb=" O PHE J 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 461 through 466' Processing helix chain 'J' and resid 477 through 491 removed outlier: 3.727A pdb=" N ALA J 481 " --> pdb=" O THR J 477 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA J 482 " --> pdb=" O PRO J 478 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU J 489 " --> pdb=" O ALA J 485 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 35 removed outlier: 3.630A pdb=" N THR K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS K 32 " --> pdb=" O VAL K 28 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG K 33 " --> pdb=" O PHE K 29 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU K 34 " --> pdb=" O ARG K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 55 Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 94 through 98 removed outlier: 4.461A pdb=" N GLU K 98 " --> pdb=" O PHE K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 110 Processing helix chain 'K' and resid 117 through 126 removed outlier: 3.892A pdb=" N SER K 126 " --> pdb=" O SER K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 138 Processing helix chain 'K' and resid 151 through 160 removed outlier: 3.661A pdb=" N LEU K 155 " --> pdb=" O ASN K 151 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA K 156 " --> pdb=" O VAL K 152 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS K 160 " --> pdb=" O ALA K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 200 Processing helix chain 'K' and resid 259 through 278 Processing helix chain 'K' and resid 308 through 314 removed outlier: 3.643A pdb=" N THR K 312 " --> pdb=" O GLU K 308 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU K 314 " --> pdb=" O PRO K 310 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 335 removed outlier: 3.528A pdb=" N LEU K 328 " --> pdb=" O ASP K 324 " (cutoff:3.500A) Processing helix chain 'K' and resid 417 through 432 Processing helix chain 'K' and resid 440 through 450 removed outlier: 3.915A pdb=" N THR K 450 " --> pdb=" O ARG K 446 " (cutoff:3.500A) Processing helix chain 'K' and resid 452 through 456 removed outlier: 3.903A pdb=" N ARG K 455 " --> pdb=" O GLU K 452 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 466 removed outlier: 3.925A pdb=" N GLU K 465 " --> pdb=" O ASN K 461 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS K 466 " --> pdb=" O PHE K 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 461 through 466' Processing helix chain 'K' and resid 477 through 491 removed outlier: 3.728A pdb=" N ALA K 481 " --> pdb=" O THR K 477 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA K 482 " --> pdb=" O PRO K 478 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU K 489 " --> pdb=" O ALA K 485 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 35 removed outlier: 3.630A pdb=" N THR L 31 " --> pdb=" O ARG L 27 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS L 32 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG L 33 " --> pdb=" O PHE L 29 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU L 34 " --> pdb=" O ARG L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 55 Processing helix chain 'L' and resid 73 through 84 Processing helix chain 'L' and resid 94 through 98 removed outlier: 4.461A pdb=" N GLU L 98 " --> pdb=" O PHE L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 110 Processing helix chain 'L' and resid 117 through 126 removed outlier: 3.892A pdb=" N SER L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 138 Processing helix chain 'L' and resid 151 through 160 removed outlier: 3.661A pdb=" N LEU L 155 " --> pdb=" O ASN L 151 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA L 156 " --> pdb=" O VAL L 152 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS L 160 " --> pdb=" O ALA L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 190 through 200 Processing helix chain 'L' and resid 259 through 278 Processing helix chain 'L' and resid 308 through 314 removed outlier: 3.643A pdb=" N THR L 312 " --> pdb=" O GLU L 308 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU L 314 " --> pdb=" O PRO L 310 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 335 removed outlier: 3.528A pdb=" N LEU L 328 " --> pdb=" O ASP L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 417 through 432 Processing helix chain 'L' and resid 440 through 450 removed outlier: 3.915A pdb=" N THR L 450 " --> pdb=" O ARG L 446 " (cutoff:3.500A) Processing helix chain 'L' and resid 452 through 456 removed outlier: 3.904A pdb=" N ARG L 455 " --> pdb=" O GLU L 452 " (cutoff:3.500A) Processing helix chain 'L' and resid 461 through 466 removed outlier: 3.924A pdb=" N GLU L 465 " --> pdb=" O ASN L 461 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS L 466 " --> pdb=" O PHE L 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 461 through 466' Processing helix chain 'L' and resid 477 through 491 removed outlier: 3.727A pdb=" N ALA L 481 " --> pdb=" O THR L 477 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA L 482 " --> pdb=" O PRO L 478 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU L 489 " --> pdb=" O ALA L 485 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 removed outlier: 3.629A pdb=" N THR M 31 " --> pdb=" O ARG M 27 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS M 32 " --> pdb=" O VAL M 28 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG M 33 " --> pdb=" O PHE M 29 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU M 34 " --> pdb=" O ARG M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 55 Processing helix chain 'M' and resid 73 through 84 Processing helix chain 'M' and resid 94 through 98 removed outlier: 4.462A pdb=" N GLU M 98 " --> pdb=" O PHE M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 110 Processing helix chain 'M' and resid 117 through 126 removed outlier: 3.892A pdb=" N SER M 126 " --> pdb=" O SER M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 138 Processing helix chain 'M' and resid 151 through 160 removed outlier: 3.662A pdb=" N LEU M 155 " --> pdb=" O ASN M 151 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA M 156 " --> pdb=" O VAL M 152 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS M 160 " --> pdb=" O ALA M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 200 Processing helix chain 'M' and resid 259 through 278 Processing helix chain 'M' and resid 308 through 314 removed outlier: 3.642A pdb=" N THR M 312 " --> pdb=" O GLU M 308 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU M 314 " --> pdb=" O PRO M 310 " (cutoff:3.500A) Processing helix chain 'M' and resid 324 through 335 removed outlier: 3.527A pdb=" N LEU M 328 " --> pdb=" O ASP M 324 " (cutoff:3.500A) Processing helix chain 'M' and resid 417 through 432 Processing helix chain 'M' and resid 440 through 450 removed outlier: 3.915A pdb=" N THR M 450 " --> pdb=" O ARG M 446 " (cutoff:3.500A) Processing helix chain 'M' and resid 452 through 456 removed outlier: 3.903A pdb=" N ARG M 455 " --> pdb=" O GLU M 452 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 466 removed outlier: 3.925A pdb=" N GLU M 465 " --> pdb=" O ASN M 461 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS M 466 " --> pdb=" O PHE M 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 461 through 466' Processing helix chain 'M' and resid 477 through 491 removed outlier: 3.727A pdb=" N ALA M 481 " --> pdb=" O THR M 477 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA M 482 " --> pdb=" O PRO M 478 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU M 489 " --> pdb=" O ALA M 485 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 273 removed outlier: 3.701A pdb=" N VAL A 380 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 424 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 498 through 499 removed outlier: 3.526A pdb=" N ASP A 498 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 511 " --> pdb=" O ILE A 522 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A 551 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N VAL A 592 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE A 553 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LYS A 589 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N PHE A 616 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR A 591 " --> pdb=" O PHE A 616 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 266 through 273 removed outlier: 3.702A pdb=" N VAL B 380 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 424 " --> pdb=" O ILE B 379 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 498 through 499 removed outlier: 3.524A pdb=" N ASP B 498 " --> pdb=" O PHE B 512 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 511 " --> pdb=" O ILE B 522 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU B 551 " --> pdb=" O VAL B 590 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N VAL B 592 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE B 553 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LYS B 589 " --> pdb=" O PHE B 614 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N PHE B 616 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR B 591 " --> pdb=" O PHE B 616 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 266 through 273 removed outlier: 3.703A pdb=" N VAL C 380 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 424 " --> pdb=" O ILE C 379 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 498 through 499 removed outlier: 3.526A pdb=" N ASP C 498 " --> pdb=" O PHE C 512 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY C 511 " --> pdb=" O ILE C 522 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 551 " --> pdb=" O VAL C 590 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL C 592 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE C 553 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LYS C 589 " --> pdb=" O PHE C 614 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N PHE C 616 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR C 591 " --> pdb=" O PHE C 616 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 266 through 273 removed outlier: 3.701A pdb=" N VAL D 380 " --> pdb=" O VAL D 359 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 424 " --> pdb=" O ILE D 379 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 498 through 499 removed outlier: 3.525A pdb=" N ASP D 498 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY D 511 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU D 551 " --> pdb=" O VAL D 590 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL D 592 " --> pdb=" O LEU D 551 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE D 553 " --> pdb=" O VAL D 592 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LYS D 589 " --> pdb=" O PHE D 614 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N PHE D 616 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR D 591 " --> pdb=" O PHE D 616 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 266 through 273 removed outlier: 3.700A pdb=" N VAL E 380 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA E 424 " --> pdb=" O ILE E 379 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 498 through 499 removed outlier: 3.525A pdb=" N ASP E 498 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY E 511 " --> pdb=" O ILE E 522 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU E 551 " --> pdb=" O VAL E 590 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N VAL E 592 " --> pdb=" O LEU E 551 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE E 553 " --> pdb=" O VAL E 592 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS E 589 " --> pdb=" O PHE E 614 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N PHE E 616 " --> pdb=" O LYS E 589 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR E 591 " --> pdb=" O PHE E 616 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 266 through 273 removed outlier: 3.701A pdb=" N VAL F 380 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F 424 " --> pdb=" O ILE F 379 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 498 through 499 removed outlier: 3.526A pdb=" N ASP F 498 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY F 511 " --> pdb=" O ILE F 522 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU F 551 " --> pdb=" O VAL F 590 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL F 592 " --> pdb=" O LEU F 551 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE F 553 " --> pdb=" O VAL F 592 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS F 589 " --> pdb=" O PHE F 614 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N PHE F 616 " --> pdb=" O LYS F 589 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR F 591 " --> pdb=" O PHE F 616 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 59 through 61 removed outlier: 6.870A pdb=" N LEU H 16 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N LEU H 42 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N VAL H 18 " --> pdb=" O LEU H 42 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS H 15 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N HIS H 90 " --> pdb=" O LYS H 15 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU H 17 " --> pdb=" O HIS H 90 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE H 89 " --> pdb=" O GLU H 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 218 through 226 removed outlier: 7.390A pdb=" N THR H 284 " --> pdb=" O MET H 301 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N MET H 301 " --> pdb=" O THR H 284 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU H 286 " --> pdb=" O MET H 299 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET H 299 " --> pdb=" O GLU H 286 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 239 through 244 removed outlier: 7.408A pdb=" N CYS H 240 " --> pdb=" O GLU H 251 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLU H 251 " --> pdb=" O CYS H 240 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL H 242 " --> pdb=" O VAL H 249 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL H 249 " --> pdb=" O VAL H 242 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL H 249 " --> pdb=" O ARG H 355 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA H 409 " --> pdb=" O VAL H 356 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 321 through 322 Processing sheet with id=AB8, first strand: chain 'H' and resid 374 through 375 removed outlier: 3.752A pdb=" N PHE H 374 " --> pdb=" O ALA H 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 507 through 514 Processing sheet with id=AC1, first strand: chain 'H' and resid 532 through 537 removed outlier: 4.244A pdb=" N ILE H 561 " --> pdb=" O ALA H 581 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN H 563 " --> pdb=" O ALA H 579 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU H 578 " --> pdb=" O ILE H 589 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE H 589 " --> pdb=" O LEU H 578 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL H 580 " --> pdb=" O THR H 587 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR H 587 " --> pdb=" O VAL H 580 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 664 through 666 Processing sheet with id=AC3, first strand: chain 'I' and resid 59 through 61 removed outlier: 6.870A pdb=" N LEU I 16 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N LEU I 42 " --> pdb=" O LEU I 16 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL I 18 " --> pdb=" O LEU I 42 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS I 15 " --> pdb=" O ALA I 88 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N HIS I 90 " --> pdb=" O LYS I 15 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU I 17 " --> pdb=" O HIS I 90 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE I 89 " --> pdb=" O GLU I 112 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 218 through 226 removed outlier: 7.390A pdb=" N THR I 284 " --> pdb=" O MET I 301 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N MET I 301 " --> pdb=" O THR I 284 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU I 286 " --> pdb=" O MET I 299 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET I 299 " --> pdb=" O GLU I 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 239 through 244 removed outlier: 7.408A pdb=" N CYS I 240 " --> pdb=" O GLU I 251 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLU I 251 " --> pdb=" O CYS I 240 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL I 242 " --> pdb=" O VAL I 249 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL I 249 " --> pdb=" O VAL I 242 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL I 249 " --> pdb=" O ARG I 355 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA I 409 " --> pdb=" O VAL I 356 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 321 through 322 Processing sheet with id=AC7, first strand: chain 'I' and resid 374 through 375 removed outlier: 3.753A pdb=" N PHE I 374 " --> pdb=" O ALA I 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 507 through 514 Processing sheet with id=AC9, first strand: chain 'I' and resid 532 through 537 removed outlier: 4.243A pdb=" N ILE I 561 " --> pdb=" O ALA I 581 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN I 563 " --> pdb=" O ALA I 579 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU I 578 " --> pdb=" O ILE I 589 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE I 589 " --> pdb=" O LEU I 578 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL I 580 " --> pdb=" O THR I 587 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR I 587 " --> pdb=" O VAL I 580 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 664 through 666 Processing sheet with id=AD2, first strand: chain 'J' and resid 59 through 61 removed outlier: 6.871A pdb=" N LEU J 16 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N LEU J 42 " --> pdb=" O LEU J 16 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL J 18 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS J 15 " --> pdb=" O ALA J 88 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N HIS J 90 " --> pdb=" O LYS J 15 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU J 17 " --> pdb=" O HIS J 90 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE J 89 " --> pdb=" O GLU J 112 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 218 through 226 removed outlier: 7.390A pdb=" N THR J 284 " --> pdb=" O MET J 301 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N MET J 301 " --> pdb=" O THR J 284 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU J 286 " --> pdb=" O MET J 299 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET J 299 " --> pdb=" O GLU J 286 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 239 through 244 removed outlier: 7.407A pdb=" N CYS J 240 " --> pdb=" O GLU J 251 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N GLU J 251 " --> pdb=" O CYS J 240 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL J 242 " --> pdb=" O VAL J 249 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL J 249 " --> pdb=" O VAL J 242 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL J 249 " --> pdb=" O ARG J 355 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA J 409 " --> pdb=" O VAL J 356 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 321 through 322 Processing sheet with id=AD6, first strand: chain 'J' and resid 374 through 375 removed outlier: 3.753A pdb=" N PHE J 374 " --> pdb=" O ALA J 435 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 507 through 514 Processing sheet with id=AD8, first strand: chain 'J' and resid 532 through 537 removed outlier: 4.243A pdb=" N ILE J 561 " --> pdb=" O ALA J 581 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN J 563 " --> pdb=" O ALA J 579 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU J 578 " --> pdb=" O ILE J 589 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE J 589 " --> pdb=" O LEU J 578 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL J 580 " --> pdb=" O THR J 587 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR J 587 " --> pdb=" O VAL J 580 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 664 through 666 Processing sheet with id=AE1, first strand: chain 'K' and resid 59 through 61 removed outlier: 6.870A pdb=" N LEU K 16 " --> pdb=" O VAL K 40 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N LEU K 42 " --> pdb=" O LEU K 16 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL K 18 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS K 15 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N HIS K 90 " --> pdb=" O LYS K 15 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU K 17 " --> pdb=" O HIS K 90 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE K 89 " --> pdb=" O GLU K 112 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 218 through 226 removed outlier: 7.390A pdb=" N THR K 284 " --> pdb=" O MET K 301 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N MET K 301 " --> pdb=" O THR K 284 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU K 286 " --> pdb=" O MET K 299 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET K 299 " --> pdb=" O GLU K 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 239 through 244 removed outlier: 7.408A pdb=" N CYS K 240 " --> pdb=" O GLU K 251 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N GLU K 251 " --> pdb=" O CYS K 240 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL K 242 " --> pdb=" O VAL K 249 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL K 249 " --> pdb=" O VAL K 242 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL K 249 " --> pdb=" O ARG K 355 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA K 409 " --> pdb=" O VAL K 356 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 321 through 322 Processing sheet with id=AE5, first strand: chain 'K' and resid 374 through 375 removed outlier: 3.752A pdb=" N PHE K 374 " --> pdb=" O ALA K 435 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 507 through 514 Processing sheet with id=AE7, first strand: chain 'K' and resid 532 through 537 removed outlier: 4.244A pdb=" N ILE K 561 " --> pdb=" O ALA K 581 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN K 563 " --> pdb=" O ALA K 579 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU K 578 " --> pdb=" O ILE K 589 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE K 589 " --> pdb=" O LEU K 578 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL K 580 " --> pdb=" O THR K 587 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR K 587 " --> pdb=" O VAL K 580 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 664 through 666 Processing sheet with id=AE9, first strand: chain 'L' and resid 59 through 61 removed outlier: 6.871A pdb=" N LEU L 16 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N LEU L 42 " --> pdb=" O LEU L 16 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL L 18 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS L 15 " --> pdb=" O ALA L 88 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N HIS L 90 " --> pdb=" O LYS L 15 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU L 17 " --> pdb=" O HIS L 90 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE L 89 " --> pdb=" O GLU L 112 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 218 through 226 removed outlier: 7.390A pdb=" N THR L 284 " --> pdb=" O MET L 301 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N MET L 301 " --> pdb=" O THR L 284 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU L 286 " --> pdb=" O MET L 299 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET L 299 " --> pdb=" O GLU L 286 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 239 through 244 removed outlier: 7.408A pdb=" N CYS L 240 " --> pdb=" O GLU L 251 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLU L 251 " --> pdb=" O CYS L 240 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL L 242 " --> pdb=" O VAL L 249 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL L 249 " --> pdb=" O VAL L 242 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL L 249 " --> pdb=" O ARG L 355 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA L 409 " --> pdb=" O VAL L 356 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 321 through 322 Processing sheet with id=AF4, first strand: chain 'L' and resid 374 through 375 removed outlier: 3.752A pdb=" N PHE L 374 " --> pdb=" O ALA L 435 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 507 through 514 Processing sheet with id=AF6, first strand: chain 'L' and resid 532 through 537 removed outlier: 4.244A pdb=" N ILE L 561 " --> pdb=" O ALA L 581 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN L 563 " --> pdb=" O ALA L 579 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU L 578 " --> pdb=" O ILE L 589 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE L 589 " --> pdb=" O LEU L 578 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL L 580 " --> pdb=" O THR L 587 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR L 587 " --> pdb=" O VAL L 580 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 664 through 666 Processing sheet with id=AF8, first strand: chain 'M' and resid 59 through 61 removed outlier: 6.870A pdb=" N LEU M 16 " --> pdb=" O VAL M 40 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N LEU M 42 " --> pdb=" O LEU M 16 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL M 18 " --> pdb=" O LEU M 42 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS M 15 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N HIS M 90 " --> pdb=" O LYS M 15 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU M 17 " --> pdb=" O HIS M 90 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE M 89 " --> pdb=" O GLU M 112 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 218 through 226 removed outlier: 7.390A pdb=" N THR M 284 " --> pdb=" O MET M 301 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N MET M 301 " --> pdb=" O THR M 284 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU M 286 " --> pdb=" O MET M 299 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET M 299 " --> pdb=" O GLU M 286 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 239 through 244 removed outlier: 7.407A pdb=" N CYS M 240 " --> pdb=" O GLU M 251 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N GLU M 251 " --> pdb=" O CYS M 240 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL M 242 " --> pdb=" O VAL M 249 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL M 249 " --> pdb=" O VAL M 242 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL M 249 " --> pdb=" O ARG M 355 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA M 409 " --> pdb=" O VAL M 356 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 321 through 322 Processing sheet with id=AG3, first strand: chain 'M' and resid 374 through 375 removed outlier: 3.753A pdb=" N PHE M 374 " --> pdb=" O ALA M 435 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 507 through 514 Processing sheet with id=AG5, first strand: chain 'M' and resid 532 through 537 removed outlier: 4.243A pdb=" N ILE M 561 " --> pdb=" O ALA M 581 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN M 563 " --> pdb=" O ALA M 579 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU M 578 " --> pdb=" O ILE M 589 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE M 589 " --> pdb=" O LEU M 578 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL M 580 " --> pdb=" O THR M 587 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR M 587 " --> pdb=" O VAL M 580 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 664 through 666 1992 hydrogen bonds defined for protein. 5616 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: 26.39 Time building geometry restraints manager: 14.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18910 1.34 - 1.46: 9055 1.46 - 1.58: 30559 1.58 - 1.70: 0 1.70 - 1.82: 486 Bond restraints: 59010 Sorted by residual: bond pdb=" CA LEU E 178 " pdb=" C LEU E 178 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.24e-02 6.50e+03 1.33e+01 bond pdb=" CA LEU A 178 " pdb=" C LEU A 178 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.24e-02 6.50e+03 1.33e+01 bond pdb=" CA LEU B 178 " pdb=" C LEU B 178 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.24e-02 6.50e+03 1.32e+01 bond pdb=" CA LEU D 178 " pdb=" C LEU D 178 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.24e-02 6.50e+03 1.31e+01 bond pdb=" CA GLU A 143 " pdb=" C GLU A 143 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.34e-02 5.57e+03 1.30e+01 ... (remaining 59005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 78072 2.77 - 5.54: 1480 5.54 - 8.31: 173 8.31 - 11.08: 33 11.08 - 13.85: 18 Bond angle restraints: 79776 Sorted by residual: angle pdb=" N ARG D 144 " pdb=" CA ARG D 144 " pdb=" C ARG D 144 " ideal model delta sigma weight residual 111.71 97.86 13.85 1.15e+00 7.56e-01 1.45e+02 angle pdb=" N ARG C 144 " pdb=" CA ARG C 144 " pdb=" C ARG C 144 " ideal model delta sigma weight residual 111.71 97.91 13.80 1.15e+00 7.56e-01 1.44e+02 angle pdb=" N ARG F 144 " pdb=" CA ARG F 144 " pdb=" C ARG F 144 " ideal model delta sigma weight residual 111.71 97.92 13.79 1.15e+00 7.56e-01 1.44e+02 angle pdb=" N ARG B 144 " pdb=" CA ARG B 144 " pdb=" C ARG B 144 " ideal model delta sigma weight residual 111.71 97.92 13.79 1.15e+00 7.56e-01 1.44e+02 angle pdb=" N ARG E 144 " pdb=" CA ARG E 144 " pdb=" C ARG E 144 " ideal model delta sigma weight residual 111.71 97.92 13.79 1.15e+00 7.56e-01 1.44e+02 ... (remaining 79771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 31910 16.05 - 32.09: 2905 32.09 - 48.14: 603 48.14 - 64.19: 144 64.19 - 80.23: 24 Dihedral angle restraints: 35586 sinusoidal: 14322 harmonic: 21264 Sorted by residual: dihedral pdb=" CA GLU C 499 " pdb=" C GLU C 499 " pdb=" N PHE C 500 " pdb=" CA PHE C 500 " ideal model delta harmonic sigma weight residual 180.00 156.21 23.79 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLU F 499 " pdb=" C GLU F 499 " pdb=" N PHE F 500 " pdb=" CA PHE F 500 " ideal model delta harmonic sigma weight residual 180.00 156.26 23.74 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLU D 499 " pdb=" C GLU D 499 " pdb=" N PHE D 500 " pdb=" CA PHE D 500 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 35583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 6485 0.048 - 0.096: 1710 0.096 - 0.145: 558 0.145 - 0.193: 54 0.193 - 0.241: 19 Chirality restraints: 8826 Sorted by residual: chirality pdb=" CA GLU M 362 " pdb=" N GLU M 362 " pdb=" C GLU M 362 " pdb=" CB GLU M 362 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA GLU I 362 " pdb=" N GLU I 362 " pdb=" C GLU I 362 " pdb=" CB GLU I 362 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA GLU H 362 " pdb=" N GLU H 362 " pdb=" C GLU H 362 " pdb=" CB GLU H 362 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 8823 not shown) Planarity restraints: 10464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTI D 801 " 0.015 2.00e-02 2.50e+03 3.64e-02 1.99e+01 pdb=" C4 BTI D 801 " -0.043 2.00e-02 2.50e+03 pdb=" C5 BTI D 801 " -0.011 2.00e-02 2.50e+03 pdb=" N2 BTI D 801 " 0.053 2.00e-02 2.50e+03 pdb=" N3 BTI D 801 " 0.031 2.00e-02 2.50e+03 pdb=" O3 BTI D 801 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTI B 801 " -0.015 2.00e-02 2.50e+03 3.60e-02 1.95e+01 pdb=" C4 BTI B 801 " 0.042 2.00e-02 2.50e+03 pdb=" C5 BTI B 801 " 0.011 2.00e-02 2.50e+03 pdb=" N2 BTI B 801 " -0.052 2.00e-02 2.50e+03 pdb=" N3 BTI B 801 " -0.031 2.00e-02 2.50e+03 pdb=" O3 BTI B 801 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTI F 801 " 0.014 2.00e-02 2.50e+03 3.59e-02 1.94e+01 pdb=" C4 BTI F 801 " -0.043 2.00e-02 2.50e+03 pdb=" C5 BTI F 801 " -0.011 2.00e-02 2.50e+03 pdb=" N2 BTI F 801 " 0.052 2.00e-02 2.50e+03 pdb=" N3 BTI F 801 " 0.031 2.00e-02 2.50e+03 pdb=" O3 BTI F 801 " -0.044 2.00e-02 2.50e+03 ... (remaining 10461 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 144 2.41 - 3.03: 37520 3.03 - 3.65: 86490 3.65 - 4.28: 127563 4.28 - 4.90: 205528 Nonbonded interactions: 457245 Sorted by model distance: nonbonded pdb=" CE MET M 650 " pdb=" CD LYS M 651 " model vdw 1.784 3.860 nonbonded pdb=" CE MET L 650 " pdb=" CD LYS L 651 " model vdw 1.784 3.860 nonbonded pdb=" CE MET H 650 " pdb=" CD LYS H 651 " model vdw 1.784 3.860 nonbonded pdb=" CE MET J 650 " pdb=" CD LYS J 651 " model vdw 1.785 3.860 nonbonded pdb=" CE MET K 650 " pdb=" CD LYS K 651 " model vdw 1.785 3.860 ... (remaining 457240 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.980 Check model and map are aligned: 0.350 Set scattering table: 0.450 Process input model: 107.010 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.390 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: 0.020 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 59010 Z= 0.346 Angle : 0.930 13.854 79776 Z= 0.586 Chirality : 0.049 0.241 8826 Planarity : 0.005 0.091 10464 Dihedral : 13.028 80.234 21990 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.39 % Allowed : 2.60 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.29 (0.10), residues: 7440 helix: 0.03 (0.11), residues: 2256 sheet: 0.89 (0.17), residues: 1008 loop : -1.89 (0.09), residues: 4176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 488 HIS 0.012 0.002 HIS F 311 PHE 0.022 0.002 PHE C 500 TYR 0.037 0.002 TYR D 504 ARG 0.006 0.001 ARG F 608 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1544 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 1520 time to evaluate : 7.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 ILE cc_start: 0.8151 (mt) cc_final: 0.7828 (mt) REVERT: A 557 ILE cc_start: 0.5210 (pt) cc_final: 0.4988 (pt) REVERT: A 626 MET cc_start: 0.5473 (ttp) cc_final: 0.5115 (ttp) REVERT: A 655 ASP cc_start: 0.5949 (t70) cc_final: 0.5260 (m-30) REVERT: B 171 MET cc_start: 0.6208 (tpp) cc_final: 0.5835 (mmm) REVERT: B 222 MET cc_start: 0.5605 (mtp) cc_final: 0.5330 (mtm) REVERT: B 298 LYS cc_start: 0.7593 (ttmt) cc_final: 0.7252 (tttt) REVERT: B 360 MET cc_start: 0.6838 (mtp) cc_final: 0.6610 (mtt) REVERT: B 433 LEU cc_start: 0.7744 (mt) cc_final: 0.7506 (mt) REVERT: B 541 ILE cc_start: 0.7965 (mt) cc_final: 0.7732 (mt) REVERT: C 142 TYR cc_start: 0.6376 (m-10) cc_final: 0.6077 (m-10) REVERT: C 153 LEU cc_start: 0.7262 (pp) cc_final: 0.6696 (mp) REVERT: C 222 MET cc_start: 0.5770 (mtp) cc_final: 0.5230 (mtm) REVERT: C 392 PRO cc_start: 0.7880 (Cg_endo) cc_final: 0.7675 (Cg_exo) REVERT: C 541 ILE cc_start: 0.7987 (mt) cc_final: 0.7748 (mt) REVERT: D 376 GLU cc_start: 0.6704 (mm-30) cc_final: 0.6439 (mt-10) REVERT: D 514 ARG cc_start: 0.7196 (mmm160) cc_final: 0.6853 (mtp85) REVERT: D 626 MET cc_start: 0.4940 (ttp) cc_final: 0.4641 (ttp) REVERT: D 655 ASP cc_start: 0.6080 (t70) cc_final: 0.5308 (m-30) REVERT: E 168 MET cc_start: 0.6483 (tpp) cc_final: 0.5911 (tpp) REVERT: E 198 LYS cc_start: 0.6292 (tptp) cc_final: 0.6002 (ptpt) REVERT: E 514 ARG cc_start: 0.7427 (mmm160) cc_final: 0.7064 (mtp85) REVERT: E 655 ASP cc_start: 0.5697 (t70) cc_final: 0.5220 (m-30) REVERT: F 198 LYS cc_start: 0.6345 (tptp) cc_final: 0.5842 (ptpt) REVERT: F 305 LYS cc_start: 0.7594 (tptt) cc_final: 0.7370 (ttpt) REVERT: F 376 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6709 (mt-10) REVERT: F 514 ARG cc_start: 0.7529 (mmm160) cc_final: 0.7179 (mtp85) REVERT: F 655 ASP cc_start: 0.5674 (t70) cc_final: 0.5268 (m-30) REVERT: H 134 MET cc_start: 0.5209 (mpp) cc_final: 0.4960 (mmp) REVERT: H 228 LYS cc_start: 0.6026 (mtmm) cc_final: 0.5781 (ttmm) REVERT: H 412 ILE cc_start: 0.6627 (mp) cc_final: 0.5940 (mp) REVERT: H 483 MET cc_start: 0.5404 (mpp) cc_final: 0.4986 (mtm) REVERT: H 588 VAL cc_start: 0.7493 (m) cc_final: 0.7197 (p) REVERT: I 11 ARG cc_start: 0.4880 (mmm160) cc_final: 0.4197 (ptm160) REVERT: I 134 MET cc_start: 0.5521 (mpp) cc_final: 0.5302 (mmp) REVERT: I 191 MET cc_start: 0.3213 (ppp) cc_final: 0.2579 (tmm) REVERT: I 296 PHE cc_start: 0.5011 (p90) cc_final: 0.4344 (p90) REVERT: I 342 GLN cc_start: 0.5930 (tm-30) cc_final: 0.5727 (tp40) REVERT: I 407 MET cc_start: 0.4699 (tpt) cc_final: 0.4383 (tpt) REVERT: I 412 ILE cc_start: 0.6535 (mp) cc_final: 0.5715 (mp) REVERT: I 483 MET cc_start: 0.5585 (mpp) cc_final: 0.4339 (mtt) REVERT: I 533 ILE cc_start: 0.7550 (mt) cc_final: 0.7258 (tt) REVERT: I 609 SER cc_start: 0.4674 (m) cc_final: 0.4436 (p) REVERT: I 648 GLU cc_start: 0.5788 (mp0) cc_final: 0.5229 (mm-30) REVERT: J 11 ARG cc_start: 0.4855 (mmm160) cc_final: 0.4373 (ptm160) REVERT: J 124 MET cc_start: 0.5441 (mmm) cc_final: 0.4244 (ttm) REVERT: J 134 MET cc_start: 0.5467 (mpp) cc_final: 0.5069 (mmp) REVERT: J 191 MET cc_start: 0.3150 (ppp) cc_final: 0.2774 (tmm) REVERT: J 342 GLN cc_start: 0.6030 (tm-30) cc_final: 0.5728 (tp40) REVERT: J 407 MET cc_start: 0.5110 (tpt) cc_final: 0.4806 (tpt) REVERT: J 483 MET cc_start: 0.5349 (mpp) cc_final: 0.3993 (mtt) REVERT: K 47 GLU cc_start: 0.4176 (mm-30) cc_final: 0.3811 (mt-10) REVERT: K 52 HIS cc_start: 0.5000 (p-80) cc_final: 0.4557 (p90) REVERT: K 191 MET cc_start: 0.3153 (ppp) cc_final: 0.2786 (ppp) REVERT: K 296 PHE cc_start: 0.5172 (p90) cc_final: 0.4854 (p90) REVERT: K 331 LYS cc_start: 0.7013 (mttt) cc_final: 0.6611 (mmtp) REVERT: K 407 MET cc_start: 0.5565 (tpt) cc_final: 0.4526 (tmm) REVERT: K 412 ILE cc_start: 0.6424 (mp) cc_final: 0.5800 (mp) REVERT: K 444 LEU cc_start: 0.7226 (mm) cc_final: 0.7010 (mp) REVERT: K 483 MET cc_start: 0.5440 (mpp) cc_final: 0.4830 (mtm) REVERT: L 134 MET cc_start: 0.5603 (mpp) cc_final: 0.5283 (mmp) REVERT: L 179 MET cc_start: 0.2906 (mtm) cc_final: 0.2467 (tmm) REVERT: L 192 LEU cc_start: 0.4998 (pp) cc_final: 0.4651 (mt) REVERT: L 290 ASP cc_start: 0.4622 (t0) cc_final: 0.3752 (m-30) REVERT: L 295 GLU cc_start: 0.4352 (pt0) cc_final: 0.3212 (mm-30) REVERT: L 376 ARG cc_start: 0.4681 (mmm160) cc_final: 0.4277 (mmm-85) REVERT: L 483 MET cc_start: 0.5995 (mpp) cc_final: 0.4942 (mtt) REVERT: L 596 GLN cc_start: 0.6144 (pp30) cc_final: 0.5832 (pp30) REVERT: L 633 LYS cc_start: 0.3188 (tptp) cc_final: 0.2978 (mmmt) REVERT: M 52 HIS cc_start: 0.5197 (p-80) cc_final: 0.4883 (p90) REVERT: M 133 ILE cc_start: 0.6282 (mm) cc_final: 0.5561 (mm) REVERT: M 192 LEU cc_start: 0.5174 (pp) cc_final: 0.4847 (mt) REVERT: M 376 ARG cc_start: 0.4862 (mmm160) cc_final: 0.4469 (mmm-85) REVERT: M 412 ILE cc_start: 0.6605 (mp) cc_final: 0.6075 (mp) REVERT: M 470 LEU cc_start: 0.7746 (mt) cc_final: 0.7345 (mt) REVERT: M 483 MET cc_start: 0.5985 (mpp) cc_final: 0.4752 (mtt) REVERT: M 513 TYR cc_start: 0.4760 (t80) cc_final: 0.4550 (t80) REVERT: M 609 SER cc_start: 0.5385 (m) cc_final: 0.4946 (p) outliers start: 24 outliers final: 2 residues processed: 1532 average time/residue: 0.6336 time to fit residues: 1542.3222 Evaluate side-chains 714 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 712 time to evaluate : 5.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain M residue 233 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 623 optimal weight: 5.9990 chunk 559 optimal weight: 7.9990 chunk 310 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 377 optimal weight: 7.9990 chunk 298 optimal weight: 9.9990 chunk 578 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 351 optimal weight: 30.0000 chunk 430 optimal weight: 20.0000 chunk 670 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 HIS A 442 ASN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 GLN A 574 ASN B 186 GLN B 300 HIS ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 ASN C 186 GLN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 HIS D 186 GLN D 300 HIS D 442 ASN D 446 HIS D 525 ASN D 546 GLN D 574 ASN E 186 GLN E 300 HIS ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 GLN F 300 HIS F 383 ASN ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 HIS H 219 HIS H 306 GLN H 466 HIS ** H 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 517 HIS I 36 HIS I 306 GLN I 466 HIS ** I 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 511 HIS J 36 HIS ** J 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 GLN J 427 GLN J 466 HIS ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 306 GLN K 466 HIS ** K 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 517 HIS L 36 HIS L 52 HIS L 219 HIS L 306 GLN ** L 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 36 HIS ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 517 HIS M 642 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 59010 Z= 0.395 Angle : 0.854 12.791 79776 Z= 0.447 Chirality : 0.053 0.320 8826 Planarity : 0.007 0.072 10464 Dihedral : 5.913 42.832 8294 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.50 % Allowed : 12.45 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.09), residues: 7440 helix: 0.03 (0.10), residues: 2268 sheet: 0.44 (0.16), residues: 1002 loop : -2.05 (0.09), residues: 4170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 538 HIS 0.015 0.002 HIS A 216 PHE 0.032 0.003 PHE B 500 TYR 0.045 0.003 TYR D 504 ARG 0.011 0.001 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 732 time to evaluate : 5.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 TYR cc_start: 0.5528 (m-80) cc_final: 0.5200 (m-80) REVERT: A 617 MET cc_start: 0.6020 (ttm) cc_final: 0.5509 (mtp) REVERT: A 655 ASP cc_start: 0.5718 (t70) cc_final: 0.5074 (m-30) REVERT: B 142 TYR cc_start: 0.6226 (OUTLIER) cc_final: 0.5956 (m-80) REVERT: B 298 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7670 (tttt) REVERT: B 395 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7104 (mt) REVERT: B 442 ASN cc_start: 0.7662 (m110) cc_final: 0.7434 (m110) REVERT: C 142 TYR cc_start: 0.6268 (OUTLIER) cc_final: 0.5937 (m-80) REVERT: D 171 MET cc_start: 0.5485 (tpp) cc_final: 0.5218 (mmm) REVERT: E 373 MET cc_start: 0.4975 (mtm) cc_final: 0.4747 (mtm) REVERT: F 140 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7265 (tp) REVERT: H 52 HIS cc_start: 0.5048 (p-80) cc_final: 0.4686 (p-80) REVERT: H 249 VAL cc_start: 0.5132 (t) cc_final: 0.4882 (t) REVERT: H 334 MET cc_start: 0.6691 (mmt) cc_final: 0.6228 (mmm) REVERT: H 407 MET cc_start: 0.4879 (tpt) cc_final: 0.4399 (tpt) REVERT: H 483 MET cc_start: 0.6662 (mpp) cc_final: 0.5944 (mpp) REVERT: H 513 TYR cc_start: 0.4490 (t80) cc_final: 0.4261 (t80) REVERT: H 677 ASP cc_start: 0.5462 (m-30) cc_final: 0.4871 (t70) REVERT: I 249 VAL cc_start: 0.5669 (t) cc_final: 0.5349 (t) REVERT: I 407 MET cc_start: 0.4995 (tpt) cc_final: 0.4429 (tpt) REVERT: I 648 GLU cc_start: 0.6454 (mp0) cc_final: 0.5868 (mm-30) REVERT: I 685 GLU cc_start: 0.2919 (tp30) cc_final: 0.2549 (tm-30) REVERT: J 249 VAL cc_start: 0.5195 (t) cc_final: 0.4931 (t) REVERT: J 301 MET cc_start: 0.4589 (ttt) cc_final: 0.4334 (ttt) REVERT: J 407 MET cc_start: 0.4992 (tpt) cc_final: 0.4664 (tpt) REVERT: J 513 TYR cc_start: 0.4343 (t80) cc_final: 0.4064 (t80) REVERT: J 609 SER cc_start: 0.5186 (m) cc_final: 0.4764 (p) REVERT: J 661 ASP cc_start: 0.6353 (m-30) cc_final: 0.5903 (p0) REVERT: J 685 GLU cc_start: 0.3103 (tp30) cc_final: 0.2430 (tm-30) REVERT: K 52 HIS cc_start: 0.5347 (p-80) cc_final: 0.5066 (p90) REVERT: K 272 GLN cc_start: 0.6703 (mt0) cc_final: 0.6472 (tm-30) REVERT: K 301 MET cc_start: 0.4255 (ttt) cc_final: 0.4025 (ttt) REVERT: K 407 MET cc_start: 0.5042 (tpt) cc_final: 0.4126 (tmm) REVERT: K 483 MET cc_start: 0.6694 (mpp) cc_final: 0.5947 (mpp) REVERT: K 513 TYR cc_start: 0.4198 (t80) cc_final: 0.3932 (t80) REVERT: K 540 HIS cc_start: 0.5801 (OUTLIER) cc_final: 0.5346 (t-90) REVERT: K 652 MET cc_start: 0.5211 (tpp) cc_final: 0.4968 (tpp) REVERT: K 677 ASP cc_start: 0.5485 (m-30) cc_final: 0.5095 (t70) REVERT: L 179 MET cc_start: 0.3026 (mtm) cc_final: 0.2278 (tmm) REVERT: L 290 ASP cc_start: 0.5284 (t0) cc_final: 0.4405 (m-30) REVERT: L 295 GLU cc_start: 0.4690 (pt0) cc_final: 0.4375 (tm-30) REVERT: L 376 ARG cc_start: 0.4587 (mmm160) cc_final: 0.4044 (tpp-160) REVERT: L 407 MET cc_start: 0.5056 (tpt) cc_final: 0.4335 (tpt) REVERT: L 483 MET cc_start: 0.6654 (mpp) cc_final: 0.6150 (mpp) REVERT: L 609 SER cc_start: 0.5565 (m) cc_final: 0.5169 (p) REVERT: L 631 LEU cc_start: 0.3483 (OUTLIER) cc_final: 0.3193 (tp) REVERT: L 643 VAL cc_start: 0.4782 (p) cc_final: 0.4194 (t) REVERT: M 124 MET cc_start: 0.6460 (mmm) cc_final: 0.6242 (tpp) REVERT: M 192 LEU cc_start: 0.5305 (pp) cc_final: 0.4946 (mt) REVERT: M 260 MET cc_start: 0.6929 (tpt) cc_final: 0.6054 (mmm) REVERT: M 287 PHE cc_start: 0.6966 (m-80) cc_final: 0.6690 (m-10) REVERT: M 407 MET cc_start: 0.4655 (tpt) cc_final: 0.4083 (tpt) REVERT: M 642 GLN cc_start: 0.5364 (OUTLIER) cc_final: 0.4589 (tm-30) REVERT: M 661 ASP cc_start: 0.5970 (m-30) cc_final: 0.5512 (p0) REVERT: M 677 ASP cc_start: 0.5112 (m-30) cc_final: 0.4631 (t0) outliers start: 214 outliers final: 117 residues processed: 894 average time/residue: 0.6196 time to fit residues: 923.1452 Evaluate side-chains 675 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 551 time to evaluate : 5.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 591 THR Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 314 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 591 THR Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain H residue 219 HIS Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 578 LEU Chi-restraints excluded: chain H residue 650 MET Chi-restraints excluded: chain H residue 674 VAL Chi-restraints excluded: chain H residue 679 VAL Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 314 GLU Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 602 LEU Chi-restraints excluded: chain I residue 665 SER Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 674 VAL Chi-restraints excluded: chain J residue 679 VAL Chi-restraints excluded: chain K residue 219 HIS Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 540 HIS Chi-restraints excluded: chain K residue 578 LEU Chi-restraints excluded: chain K residue 588 VAL Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 219 HIS Chi-restraints excluded: chain L residue 345 VAL Chi-restraints excluded: chain L residue 365 PHE Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 674 VAL Chi-restraints excluded: chain L residue 679 VAL Chi-restraints excluded: chain M residue 219 HIS Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain M residue 269 VAL Chi-restraints excluded: chain M residue 285 VAL Chi-restraints excluded: chain M residue 345 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain M residue 573 MET Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 642 GLN Chi-restraints excluded: chain M residue 674 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 372 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 557 optimal weight: 9.9990 chunk 456 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 671 optimal weight: 8.9990 chunk 725 optimal weight: 4.9990 chunk 597 optimal weight: 20.0000 chunk 665 optimal weight: 7.9990 chunk 228 optimal weight: 4.9990 chunk 538 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS A 283 ASN ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 HIS B 283 ASN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 HIS C 283 ASN C 525 ASN C 539 HIS C 574 ASN D 300 HIS ** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 539 HIS E 283 ASN ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 HIS E 574 ASN F 283 ASN ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 539 HIS F 574 ASN H 469 GLN ** H 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 257 HIS ** I 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 257 HIS ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 HIS K 219 HIS K 469 GLN ** K 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 HIS ** L 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS M 219 HIS ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 642 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 59010 Z= 0.370 Angle : 0.812 16.421 79776 Z= 0.423 Chirality : 0.051 0.273 8826 Planarity : 0.007 0.101 10464 Dihedral : 6.132 39.515 8292 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 5.25 % Allowed : 16.41 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.73 (0.09), residues: 7440 helix: -0.00 (0.10), residues: 2208 sheet: 0.35 (0.16), residues: 1014 loop : -2.29 (0.09), residues: 4218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 247 HIS 0.037 0.002 HIS L 219 PHE 0.043 0.003 PHE F 500 TYR 0.038 0.003 TYR A 504 ARG 0.013 0.001 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 321 poor density : 628 time to evaluate : 5.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 GLU cc_start: 0.5562 (OUTLIER) cc_final: 0.5354 (mp0) REVERT: A 168 MET cc_start: 0.6263 (tpp) cc_final: 0.5803 (tpt) REVERT: A 617 MET cc_start: 0.6063 (ttm) cc_final: 0.5598 (mtp) REVERT: B 298 LYS cc_start: 0.7792 (ttmt) cc_final: 0.7573 (tttt) REVERT: B 395 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7191 (mt) REVERT: B 474 MET cc_start: 0.3168 (OUTLIER) cc_final: 0.2413 (mtp) REVERT: B 674 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.5901 (mp) REVERT: C 239 LEU cc_start: 0.7955 (tp) cc_final: 0.7677 (tt) REVERT: C 298 LYS cc_start: 0.7856 (ttmt) cc_final: 0.7632 (tttt) REVERT: C 474 MET cc_start: 0.2921 (OUTLIER) cc_final: 0.2196 (mtp) REVERT: C 496 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6793 (mtt90) REVERT: C 674 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.5909 (mp) REVERT: D 168 MET cc_start: 0.6321 (tpp) cc_final: 0.5967 (tpt) REVERT: D 423 TYR cc_start: 0.5489 (m-80) cc_final: 0.5253 (m-80) REVERT: E 143 GLU cc_start: 0.5715 (OUTLIER) cc_final: 0.5438 (mp0) REVERT: E 674 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6432 (mp) REVERT: F 168 MET cc_start: 0.5755 (tpp) cc_final: 0.5517 (tpp) REVERT: F 674 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6397 (mp) REVERT: H 52 HIS cc_start: 0.5160 (p-80) cc_final: 0.4896 (p-80) REVERT: H 124 MET cc_start: 0.6121 (tpp) cc_final: 0.5774 (tpp) REVERT: H 334 MET cc_start: 0.6792 (mmt) cc_final: 0.6366 (mmm) REVERT: H 407 MET cc_start: 0.4282 (tpt) cc_final: 0.3734 (tpt) REVERT: H 442 GLU cc_start: 0.6576 (tm-30) cc_final: 0.5837 (pm20) REVERT: H 483 MET cc_start: 0.6684 (mpp) cc_final: 0.5857 (mtt) REVERT: H 495 ASN cc_start: 0.6291 (m110) cc_final: 0.6019 (t0) REVERT: H 513 TYR cc_start: 0.4451 (t80) cc_final: 0.4244 (t80) REVERT: H 677 ASP cc_start: 0.5335 (m-30) cc_final: 0.4954 (t70) REVERT: H 685 GLU cc_start: 0.3784 (OUTLIER) cc_final: 0.3077 (tm-30) REVERT: I 58 GLU cc_start: 0.6087 (OUTLIER) cc_final: 0.5832 (pm20) REVERT: I 407 MET cc_start: 0.4677 (tpt) cc_final: 0.4063 (tpt) REVERT: I 450 THR cc_start: 0.5407 (m) cc_final: 0.5073 (p) REVERT: I 483 MET cc_start: 0.6851 (mpp) cc_final: 0.6110 (mtt) REVERT: I 648 GLU cc_start: 0.6287 (mp0) cc_final: 0.6021 (mm-30) REVERT: I 650 MET cc_start: 0.5544 (OUTLIER) cc_final: 0.5288 (tpp) REVERT: I 665 SER cc_start: 0.3146 (OUTLIER) cc_final: 0.2842 (t) REVERT: I 685 GLU cc_start: 0.3028 (OUTLIER) cc_final: 0.2566 (tm-30) REVERT: J 123 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7189 (tt) REVERT: J 221 GLU cc_start: 0.4243 (OUTLIER) cc_final: 0.3816 (mp0) REVERT: J 257 HIS cc_start: 0.6129 (OUTLIER) cc_final: 0.5691 (m90) REVERT: J 407 MET cc_start: 0.4869 (tpt) cc_final: 0.4178 (tpt) REVERT: J 483 MET cc_start: 0.6861 (mpp) cc_final: 0.6125 (mtt) REVERT: J 685 GLU cc_start: 0.3375 (OUTLIER) cc_final: 0.2650 (tm-30) REVERT: K 52 HIS cc_start: 0.5247 (p-80) cc_final: 0.5022 (p-80) REVERT: K 220 ILE cc_start: 0.6771 (mt) cc_final: 0.6526 (mm) REVERT: K 407 MET cc_start: 0.4481 (tpt) cc_final: 0.3999 (tpt) REVERT: K 483 MET cc_start: 0.6836 (mpp) cc_final: 0.5987 (mtt) REVERT: K 513 TYR cc_start: 0.4289 (t80) cc_final: 0.3974 (t80) REVERT: K 652 MET cc_start: 0.5405 (tpp) cc_final: 0.5161 (tpp) REVERT: K 677 ASP cc_start: 0.5493 (m-30) cc_final: 0.4923 (t70) REVERT: L 52 HIS cc_start: 0.5327 (OUTLIER) cc_final: 0.5009 (p90) REVERT: L 179 MET cc_start: 0.2447 (mtm) cc_final: 0.1832 (tmm) REVERT: L 407 MET cc_start: 0.4771 (tpt) cc_final: 0.4120 (tpt) REVERT: L 422 LEU cc_start: 0.6356 (tt) cc_final: 0.6140 (mt) REVERT: L 643 VAL cc_start: 0.4417 (p) cc_final: 0.4186 (t) REVERT: L 685 GLU cc_start: 0.3145 (OUTLIER) cc_final: 0.2438 (tm-30) REVERT: M 52 HIS cc_start: 0.5220 (p-80) cc_final: 0.4821 (p90) REVERT: M 179 MET cc_start: -0.0039 (tpp) cc_final: -0.0258 (tpp) REVERT: M 192 LEU cc_start: 0.5306 (pp) cc_final: 0.4946 (mt) REVERT: M 260 MET cc_start: 0.6837 (tpt) cc_final: 0.6035 (mmp) REVERT: M 287 PHE cc_start: 0.6944 (m-80) cc_final: 0.6539 (m-10) REVERT: M 299 MET cc_start: 0.6620 (tmm) cc_final: 0.6412 (ttp) REVERT: M 407 MET cc_start: 0.4091 (tpt) cc_final: 0.3508 (tpt) REVERT: M 677 ASP cc_start: 0.5170 (m-30) cc_final: 0.4907 (t70) REVERT: M 685 GLU cc_start: 0.3767 (OUTLIER) cc_final: 0.2832 (tm-30) outliers start: 321 outliers final: 210 residues processed: 875 average time/residue: 0.5806 time to fit residues: 861.4108 Evaluate side-chains 749 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 517 time to evaluate : 5.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 314 CYS Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 598 TYR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 591 THR Chi-restraints excluded: chain D residue 598 TYR Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 655 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 591 THR Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 314 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 509 VAL Chi-restraints excluded: chain F residue 587 VAL Chi-restraints excluded: chain F residue 591 THR Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 655 ASP Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 219 HIS Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 562 VAL Chi-restraints excluded: chain H residue 578 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 594 LEU Chi-restraints excluded: chain H residue 604 ASP Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 650 MET Chi-restraints excluded: chain H residue 673 VAL Chi-restraints excluded: chain H residue 674 VAL Chi-restraints excluded: chain H residue 685 GLU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 519 VAL Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 562 VAL Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 589 ILE Chi-restraints excluded: chain I residue 602 LEU Chi-restraints excluded: chain I residue 604 ASP Chi-restraints excluded: chain I residue 650 MET Chi-restraints excluded: chain I residue 665 SER Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain I residue 685 GLU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 128 SER Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 221 GLU Chi-restraints excluded: chain J residue 257 HIS Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 589 ILE Chi-restraints excluded: chain J residue 596 GLN Chi-restraints excluded: chain J residue 604 ASP Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 674 VAL Chi-restraints excluded: chain J residue 685 GLU Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 219 HIS Chi-restraints excluded: chain K residue 258 LEU Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 444 LEU Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 578 LEU Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain K residue 604 ASP Chi-restraints excluded: chain K residue 631 LEU Chi-restraints excluded: chain K residue 673 VAL Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 52 HIS Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 218 ARG Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 269 VAL Chi-restraints excluded: chain L residue 345 VAL Chi-restraints excluded: chain L residue 365 PHE Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 562 VAL Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 ASP Chi-restraints excluded: chain L residue 674 VAL Chi-restraints excluded: chain L residue 685 GLU Chi-restraints excluded: chain M residue 32 CYS Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 269 VAL Chi-restraints excluded: chain M residue 285 VAL Chi-restraints excluded: chain M residue 345 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 422 LEU Chi-restraints excluded: chain M residue 444 LEU Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 521 VAL Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 562 VAL Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 588 VAL Chi-restraints excluded: chain M residue 604 ASP Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 674 VAL Chi-restraints excluded: chain M residue 685 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 663 optimal weight: 1.9990 chunk 504 optimal weight: 8.9990 chunk 348 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 320 optimal weight: 0.9980 chunk 450 optimal weight: 10.0000 chunk 673 optimal weight: 0.3980 chunk 713 optimal weight: 10.0000 chunk 352 optimal weight: 30.0000 chunk 638 optimal weight: 20.0000 chunk 192 optimal weight: 6.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS A 283 ASN A 300 HIS ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 HIS C 283 ASN D 137 HIS D 283 ASN D 324 ASN ** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 HIS ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 HIS H 469 GLN ** H 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN J 219 HIS J 257 HIS ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 HIS ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 59010 Z= 0.261 Angle : 0.700 10.677 79776 Z= 0.364 Chirality : 0.047 0.234 8826 Planarity : 0.005 0.058 10464 Dihedral : 5.741 39.743 8292 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.84 % Allowed : 17.81 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.48 (0.09), residues: 7440 helix: 0.31 (0.11), residues: 2244 sheet: 0.56 (0.16), residues: 978 loop : -2.22 (0.09), residues: 4218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 251 HIS 0.027 0.002 HIS L 52 PHE 0.022 0.002 PHE M 298 TYR 0.035 0.002 TYR A 504 ARG 0.013 0.001 ARG F 465 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 296 poor density : 586 time to evaluate : 5.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 LEU cc_start: 0.6150 (OUTLIER) cc_final: 0.5937 (tp) REVERT: A 617 MET cc_start: 0.5958 (ttm) cc_final: 0.5533 (mtp) REVERT: B 395 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7392 (mt) REVERT: B 474 MET cc_start: 0.3124 (OUTLIER) cc_final: 0.2360 (mtp) REVERT: C 239 LEU cc_start: 0.7962 (tp) cc_final: 0.7679 (tt) REVERT: C 496 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6858 (mtt90) REVERT: C 608 ARG cc_start: 0.7540 (tpp80) cc_final: 0.7320 (tpp80) REVERT: D 171 MET cc_start: 0.5546 (tpp) cc_final: 0.5155 (mmm) REVERT: D 272 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.5842 (tp) REVERT: D 288 LYS cc_start: 0.1972 (mptt) cc_final: 0.1478 (mppt) REVERT: D 360 MET cc_start: 0.6184 (mtp) cc_final: 0.5933 (mtt) REVERT: E 288 LYS cc_start: 0.2265 (mptt) cc_final: 0.1598 (mppt) REVERT: E 373 MET cc_start: 0.5059 (mtm) cc_final: 0.4605 (ttp) REVERT: E 483 ASP cc_start: 0.5137 (OUTLIER) cc_final: 0.4830 (m-30) REVERT: E 674 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6150 (mp) REVERT: F 288 LYS cc_start: 0.2564 (mptt) cc_final: 0.2037 (mptt) REVERT: F 474 MET cc_start: 0.3530 (OUTLIER) cc_final: 0.2943 (mtp) REVERT: F 674 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.5892 (mp) REVERT: H 124 MET cc_start: 0.6112 (tpp) cc_final: 0.5706 (tpp) REVERT: H 220 ILE cc_start: 0.6949 (mt) cc_final: 0.5968 (tp) REVERT: H 260 MET cc_start: 0.6824 (mmp) cc_final: 0.6450 (mmm) REVERT: H 286 GLU cc_start: 0.5896 (tp30) cc_final: 0.5660 (tp30) REVERT: H 298 PHE cc_start: 0.6390 (t80) cc_final: 0.6190 (t80) REVERT: H 334 MET cc_start: 0.6779 (mmt) cc_final: 0.6416 (mmm) REVERT: H 442 GLU cc_start: 0.6533 (tm-30) cc_final: 0.5847 (pm20) REVERT: H 483 MET cc_start: 0.6659 (mpp) cc_final: 0.5844 (mtt) REVERT: H 495 ASN cc_start: 0.6193 (m110) cc_final: 0.5909 (t0) REVERT: H 642 GLN cc_start: 0.5023 (OUTLIER) cc_final: 0.4417 (tm-30) REVERT: H 677 ASP cc_start: 0.5364 (m-30) cc_final: 0.5135 (t70) REVERT: H 685 GLU cc_start: 0.3627 (OUTLIER) cc_final: 0.2820 (tm-30) REVERT: I 407 MET cc_start: 0.4506 (tpt) cc_final: 0.3870 (tpt) REVERT: I 483 MET cc_start: 0.6828 (mpp) cc_final: 0.6135 (mtt) REVERT: I 648 GLU cc_start: 0.6263 (mp0) cc_final: 0.6027 (mm-30) REVERT: I 665 SER cc_start: 0.3122 (OUTLIER) cc_final: 0.2856 (t) REVERT: I 685 GLU cc_start: 0.3117 (OUTLIER) cc_final: 0.2588 (tm-30) REVERT: J 58 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.6097 (pm20) REVERT: J 123 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7096 (tt) REVERT: J 179 MET cc_start: 0.3131 (mtp) cc_final: 0.1969 (tmm) REVERT: J 407 MET cc_start: 0.4712 (tpt) cc_final: 0.4021 (tpt) REVERT: J 450 THR cc_start: 0.5101 (m) cc_final: 0.4825 (p) REVERT: J 483 MET cc_start: 0.6820 (mpp) cc_final: 0.6185 (mtt) REVERT: J 642 GLN cc_start: 0.4674 (OUTLIER) cc_final: 0.4014 (tm-30) REVERT: J 665 SER cc_start: 0.3736 (OUTLIER) cc_final: 0.3305 (t) REVERT: J 685 GLU cc_start: 0.3318 (OUTLIER) cc_final: 0.2579 (tm-30) REVERT: K 407 MET cc_start: 0.4392 (tpt) cc_final: 0.3947 (tpt) REVERT: K 483 MET cc_start: 0.6677 (mpp) cc_final: 0.5859 (mtt) REVERT: K 513 TYR cc_start: 0.4377 (t80) cc_final: 0.4039 (t80) REVERT: K 642 GLN cc_start: 0.5237 (OUTLIER) cc_final: 0.4250 (tm-30) REVERT: K 677 ASP cc_start: 0.5235 (m-30) cc_final: 0.4898 (t70) REVERT: L 165 PRO cc_start: 0.1537 (Cg_exo) cc_final: 0.1224 (Cg_endo) REVERT: L 179 MET cc_start: 0.2456 (mtm) cc_final: 0.1913 (tmm) REVERT: L 407 MET cc_start: 0.4729 (tpt) cc_final: 0.4069 (tpt) REVERT: L 642 GLN cc_start: 0.4216 (OUTLIER) cc_final: 0.3830 (tm-30) REVERT: L 643 VAL cc_start: 0.4280 (OUTLIER) cc_final: 0.3717 (t) REVERT: M 52 HIS cc_start: 0.4998 (p-80) cc_final: 0.4492 (p90) REVERT: M 124 MET cc_start: 0.6197 (mmm) cc_final: 0.5949 (mmm) REVERT: M 133 ILE cc_start: 0.6849 (mm) cc_final: 0.6439 (mm) REVERT: M 165 PRO cc_start: 0.2043 (Cg_exo) cc_final: 0.1719 (Cg_endo) REVERT: M 192 LEU cc_start: 0.5463 (pp) cc_final: 0.5114 (mt) REVERT: M 260 MET cc_start: 0.6641 (tpt) cc_final: 0.5995 (mmp) REVERT: M 287 PHE cc_start: 0.6861 (m-80) cc_final: 0.6357 (m-80) REVERT: M 299 MET cc_start: 0.6623 (tmm) cc_final: 0.6404 (ttp) REVERT: M 407 MET cc_start: 0.4062 (tpt) cc_final: 0.3424 (tpt) REVERT: M 469 GLN cc_start: 0.5405 (tm-30) cc_final: 0.4950 (pt0) REVERT: M 677 ASP cc_start: 0.5130 (m-30) cc_final: 0.4853 (t70) REVERT: M 685 GLU cc_start: 0.3974 (tp30) cc_final: 0.2822 (tm-30) outliers start: 296 outliers final: 204 residues processed: 814 average time/residue: 0.5456 time to fit residues: 752.7791 Evaluate side-chains 753 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 528 time to evaluate : 5.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 314 CYS Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 591 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 617 MET Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 655 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 625 VAL Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 314 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 587 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 629 THR Chi-restraints excluded: chain F residue 655 ASP Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 562 VAL Chi-restraints excluded: chain H residue 578 LEU Chi-restraints excluded: chain H residue 642 GLN Chi-restraints excluded: chain H residue 650 MET Chi-restraints excluded: chain H residue 661 ASP Chi-restraints excluded: chain H residue 674 VAL Chi-restraints excluded: chain H residue 685 GLU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 52 HIS Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 314 GLU Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 665 SER Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain I residue 673 VAL Chi-restraints excluded: chain I residue 685 GLU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 519 VAL Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 562 VAL Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 602 LEU Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain J residue 642 GLN Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 674 VAL Chi-restraints excluded: chain J residue 685 GLU Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 219 HIS Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 301 MET Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 444 LEU Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 578 LEU Chi-restraints excluded: chain K residue 588 VAL Chi-restraints excluded: chain K residue 642 GLN Chi-restraints excluded: chain K residue 656 VAL Chi-restraints excluded: chain K residue 661 ASP Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 52 HIS Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 219 HIS Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 271 LEU Chi-restraints excluded: chain L residue 345 VAL Chi-restraints excluded: chain L residue 365 PHE Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 562 VAL Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 589 ILE Chi-restraints excluded: chain L residue 594 LEU Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 642 GLN Chi-restraints excluded: chain L residue 643 VAL Chi-restraints excluded: chain L residue 674 VAL Chi-restraints excluded: chain M residue 32 CYS Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 269 VAL Chi-restraints excluded: chain M residue 285 VAL Chi-restraints excluded: chain M residue 345 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 422 LEU Chi-restraints excluded: chain M residue 444 LEU Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 588 VAL Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 673 VAL Chi-restraints excluded: chain M residue 674 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 594 optimal weight: 0.6980 chunk 404 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 531 optimal weight: 20.0000 chunk 294 optimal weight: 10.0000 chunk 608 optimal weight: 1.9990 chunk 493 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 364 optimal weight: 10.0000 chunk 640 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 HIS C 283 ASN ** C 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS D 283 ASN ** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS E 300 HIS ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 HIS H 219 HIS ** H 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 342 GLN K 469 GLN ** L 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 59010 Z= 0.357 Angle : 0.790 13.504 79776 Z= 0.413 Chirality : 0.050 0.255 8826 Planarity : 0.007 0.075 10464 Dihedral : 6.245 54.796 8292 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.60 % Favored : 90.39 % Rotamer: Outliers : 6.70 % Allowed : 17.53 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.09), residues: 7440 helix: -0.09 (0.10), residues: 2250 sheet: 0.42 (0.15), residues: 1068 loop : -2.45 (0.09), residues: 4122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 251 HIS 0.043 0.002 HIS D 137 PHE 0.024 0.002 PHE E 500 TYR 0.035 0.003 TYR A 142 ARG 0.009 0.001 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 410 poor density : 589 time to evaluate : 5.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 LEU cc_start: 0.6086 (OUTLIER) cc_final: 0.5883 (tp) REVERT: A 288 LYS cc_start: 0.2242 (mptt) cc_final: 0.1545 (mppt) REVERT: A 497 PHE cc_start: 0.5781 (OUTLIER) cc_final: 0.5274 (t80) REVERT: A 617 MET cc_start: 0.5905 (ttm) cc_final: 0.5501 (mtp) REVERT: B 395 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7522 (mt) REVERT: B 474 MET cc_start: 0.3443 (OUTLIER) cc_final: 0.2655 (mtp) REVERT: C 168 MET cc_start: 0.6061 (tpt) cc_final: 0.5733 (tpt) REVERT: C 474 MET cc_start: 0.3180 (OUTLIER) cc_final: 0.2451 (mtp) REVERT: C 496 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6821 (mtt90) REVERT: D 137 HIS cc_start: 0.5028 (p90) cc_final: 0.4805 (p-80) REVERT: D 272 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5887 (tp) REVERT: D 288 LYS cc_start: 0.2346 (mptt) cc_final: 0.1857 (mppt) REVERT: D 360 MET cc_start: 0.6244 (mtp) cc_final: 0.5859 (mtt) REVERT: D 436 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6053 (tpm170) REVERT: E 436 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6816 (tpm170) REVERT: E 483 ASP cc_start: 0.4858 (OUTLIER) cc_final: 0.4524 (m-30) REVERT: E 674 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.6197 (mp) REVERT: F 288 LYS cc_start: 0.2902 (mptt) cc_final: 0.2604 (mptt) REVERT: F 436 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6709 (tpm170) REVERT: F 474 MET cc_start: 0.3899 (OUTLIER) cc_final: 0.3355 (mtp) REVERT: F 483 ASP cc_start: 0.5267 (OUTLIER) cc_final: 0.5023 (m-30) REVERT: F 508 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7634 (tt) REVERT: F 674 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6297 (mp) REVERT: H 124 MET cc_start: 0.6273 (tpp) cc_final: 0.5711 (tpp) REVERT: H 220 ILE cc_start: 0.7424 (mt) cc_final: 0.6963 (tp) REVERT: H 260 MET cc_start: 0.6785 (mmp) cc_final: 0.6432 (mmm) REVERT: H 334 MET cc_start: 0.6410 (mmt) cc_final: 0.6051 (mtt) REVERT: H 392 THR cc_start: 0.6903 (OUTLIER) cc_final: 0.6605 (p) REVERT: H 407 MET cc_start: 0.4266 (tpt) cc_final: 0.3437 (tpt) REVERT: H 483 MET cc_start: 0.6748 (mpp) cc_final: 0.5940 (mtt) REVERT: H 642 GLN cc_start: 0.5270 (OUTLIER) cc_final: 0.4347 (tm-30) REVERT: H 643 VAL cc_start: 0.4819 (p) cc_final: 0.4287 (t) REVERT: H 685 GLU cc_start: 0.3922 (OUTLIER) cc_final: 0.2866 (tm-30) REVERT: I 298 PHE cc_start: 0.5526 (t80) cc_final: 0.5322 (t80) REVERT: I 342 GLN cc_start: 0.6921 (tm-30) cc_final: 0.6692 (tp-100) REVERT: I 383 ARG cc_start: 0.2745 (OUTLIER) cc_final: 0.2364 (ptt90) REVERT: I 407 MET cc_start: 0.4445 (tpt) cc_final: 0.3772 (tpt) REVERT: I 483 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6072 (mtt) REVERT: I 642 GLN cc_start: 0.4653 (OUTLIER) cc_final: 0.4103 (tm-30) REVERT: I 665 SER cc_start: 0.3363 (OUTLIER) cc_final: 0.3110 (t) REVERT: I 685 GLU cc_start: 0.3027 (OUTLIER) cc_final: 0.2509 (tm-30) REVERT: J 58 GLU cc_start: 0.6224 (OUTLIER) cc_final: 0.5983 (pm20) REVERT: J 123 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7085 (tt) REVERT: J 179 MET cc_start: 0.2830 (mtp) cc_final: 0.1651 (tmm) REVERT: J 407 MET cc_start: 0.4693 (tpt) cc_final: 0.3992 (tpt) REVERT: J 450 THR cc_start: 0.5906 (m) cc_final: 0.5601 (p) REVERT: J 483 MET cc_start: 0.6898 (mpp) cc_final: 0.5986 (mtt) REVERT: J 642 GLN cc_start: 0.5112 (OUTLIER) cc_final: 0.4292 (tm-30) REVERT: J 665 SER cc_start: 0.3789 (OUTLIER) cc_final: 0.3398 (t) REVERT: J 685 GLU cc_start: 0.3314 (OUTLIER) cc_final: 0.2414 (tm-30) REVERT: K 12 LYS cc_start: 0.5530 (mtpt) cc_final: 0.5329 (ptpp) REVERT: K 124 MET cc_start: 0.6324 (tpp) cc_final: 0.5942 (tpp) REVERT: K 260 MET cc_start: 0.6423 (mmp) cc_final: 0.6128 (mmm) REVERT: K 392 THR cc_start: 0.6840 (OUTLIER) cc_final: 0.6502 (p) REVERT: K 513 TYR cc_start: 0.4285 (t80) cc_final: 0.4061 (t80) REVERT: K 642 GLN cc_start: 0.5337 (OUTLIER) cc_final: 0.4472 (tm-30) REVERT: L 165 PRO cc_start: 0.2082 (Cg_exo) cc_final: 0.1720 (Cg_endo) REVERT: L 179 MET cc_start: 0.2587 (mtm) cc_final: 0.1977 (tmm) REVERT: L 407 MET cc_start: 0.4657 (tpt) cc_final: 0.4031 (tpt) REVERT: L 642 GLN cc_start: 0.4724 (OUTLIER) cc_final: 0.4231 (tm-30) REVERT: M 52 HIS cc_start: 0.5799 (p-80) cc_final: 0.5424 (p-80) REVERT: M 55 GLU cc_start: 0.5639 (mt-10) cc_final: 0.5439 (mm-30) REVERT: M 71 TYR cc_start: 0.6373 (m-80) cc_final: 0.5793 (m-80) REVERT: M 124 MET cc_start: 0.6573 (mmm) cc_final: 0.6284 (mmm) REVERT: M 192 LEU cc_start: 0.5741 (pp) cc_final: 0.5444 (mt) REVERT: M 469 GLN cc_start: 0.5713 (tm-30) cc_final: 0.5161 (pt0) REVERT: M 677 ASP cc_start: 0.5121 (m-30) cc_final: 0.4781 (t70) REVERT: M 685 GLU cc_start: 0.4389 (OUTLIER) cc_final: 0.3684 (tp30) outliers start: 410 outliers final: 304 residues processed: 924 average time/residue: 0.5333 time to fit residues: 841.8228 Evaluate side-chains 850 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 337 poor density : 513 time to evaluate : 5.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 314 CYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 436 ARG Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 591 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 598 TYR Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 617 MET Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 655 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 436 ARG Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 591 THR Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 625 VAL Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 314 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 436 ARG Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 478 VAL Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 587 VAL Chi-restraints excluded: chain F residue 591 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 629 THR Chi-restraints excluded: chain F residue 655 ASP Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 36 HIS Chi-restraints excluded: chain H residue 52 HIS Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 345 VAL Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 450 THR Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 562 VAL Chi-restraints excluded: chain H residue 578 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 594 LEU Chi-restraints excluded: chain H residue 604 ASP Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 642 GLN Chi-restraints excluded: chain H residue 650 MET Chi-restraints excluded: chain H residue 661 ASP Chi-restraints excluded: chain H residue 668 VAL Chi-restraints excluded: chain H residue 674 VAL Chi-restraints excluded: chain H residue 685 GLU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 52 HIS Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 314 GLU Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain I residue 383 ARG Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 483 MET Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 519 VAL Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 562 VAL Chi-restraints excluded: chain I residue 578 LEU Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 589 ILE Chi-restraints excluded: chain I residue 596 GLN Chi-restraints excluded: chain I residue 602 LEU Chi-restraints excluded: chain I residue 604 ASP Chi-restraints excluded: chain I residue 617 THR Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 642 GLN Chi-restraints excluded: chain I residue 645 VAL Chi-restraints excluded: chain I residue 665 SER Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain I residue 669 LYS Chi-restraints excluded: chain I residue 673 VAL Chi-restraints excluded: chain I residue 685 GLU Chi-restraints excluded: chain J residue 52 HIS Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 128 SER Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 519 VAL Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 562 VAL Chi-restraints excluded: chain J residue 578 LEU Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 589 ILE Chi-restraints excluded: chain J residue 596 GLN Chi-restraints excluded: chain J residue 602 LEU Chi-restraints excluded: chain J residue 604 ASP Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain J residue 642 GLN Chi-restraints excluded: chain J residue 661 ASP Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 668 VAL Chi-restraints excluded: chain J residue 674 VAL Chi-restraints excluded: chain J residue 685 GLU Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 301 MET Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 444 LEU Chi-restraints excluded: chain K residue 450 THR Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 578 LEU Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain K residue 604 ASP Chi-restraints excluded: chain K residue 620 VAL Chi-restraints excluded: chain K residue 631 LEU Chi-restraints excluded: chain K residue 642 GLN Chi-restraints excluded: chain K residue 656 VAL Chi-restraints excluded: chain K residue 668 VAL Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 219 HIS Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 271 LEU Chi-restraints excluded: chain L residue 285 VAL Chi-restraints excluded: chain L residue 345 VAL Chi-restraints excluded: chain L residue 365 PHE Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 483 MET Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 562 VAL Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 589 ILE Chi-restraints excluded: chain L residue 594 LEU Chi-restraints excluded: chain L residue 604 ASP Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 642 GLN Chi-restraints excluded: chain L residue 643 VAL Chi-restraints excluded: chain L residue 674 VAL Chi-restraints excluded: chain L residue 685 GLU Chi-restraints excluded: chain M residue 32 CYS Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 269 VAL Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 285 VAL Chi-restraints excluded: chain M residue 325 LEU Chi-restraints excluded: chain M residue 345 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain M residue 422 LEU Chi-restraints excluded: chain M residue 434 VAL Chi-restraints excluded: chain M residue 444 LEU Chi-restraints excluded: chain M residue 483 MET Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 521 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 552 THR Chi-restraints excluded: chain M residue 562 VAL Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 588 VAL Chi-restraints excluded: chain M residue 589 ILE Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 604 ASP Chi-restraints excluded: chain M residue 617 THR Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 673 VAL Chi-restraints excluded: chain M residue 674 VAL Chi-restraints excluded: chain M residue 685 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 240 optimal weight: 2.9990 chunk 642 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 418 optimal weight: 20.0000 chunk 176 optimal weight: 8.9990 chunk 714 optimal weight: 7.9990 chunk 592 optimal weight: 20.0000 chunk 330 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 236 optimal weight: 10.0000 chunk 374 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN C 283 ASN ** C 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN ** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 ASN ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 ASN ** F 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 HIS ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 HIS H 257 HIS ** H 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 342 GLN ** I 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 257 HIS ** L 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.6448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 59010 Z= 0.414 Angle : 0.844 15.180 79776 Z= 0.444 Chirality : 0.053 0.288 8826 Planarity : 0.007 0.089 10464 Dihedral : 6.701 56.594 8292 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.46 % Favored : 89.52 % Rotamer: Outliers : 7.35 % Allowed : 18.17 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.23 (0.09), residues: 7440 helix: -0.45 (0.10), residues: 2238 sheet: 0.22 (0.15), residues: 1050 loop : -2.67 (0.08), residues: 4152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 251 HIS 0.037 0.002 HIS H 36 PHE 0.026 0.003 PHE B 500 TYR 0.031 0.003 TYR A 142 ARG 0.018 0.001 ARG L 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 450 poor density : 561 time to evaluate : 5.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5863 (tp) REVERT: A 288 LYS cc_start: 0.2097 (mptt) cc_final: 0.1524 (mppt) REVERT: A 436 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.5513 (tpt170) REVERT: A 497 PHE cc_start: 0.5803 (OUTLIER) cc_final: 0.5250 (t80) REVERT: A 617 MET cc_start: 0.5868 (ttm) cc_final: 0.5558 (mtp) REVERT: B 395 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7401 (mt) REVERT: B 474 MET cc_start: 0.3813 (OUTLIER) cc_final: 0.2993 (mtp) REVERT: C 153 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7209 (pp) REVERT: C 474 MET cc_start: 0.3626 (OUTLIER) cc_final: 0.2846 (mtp) REVERT: C 496 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6852 (mtt90) REVERT: D 143 GLU cc_start: 0.6275 (OUTLIER) cc_final: 0.5631 (pm20) REVERT: D 272 LEU cc_start: 0.6209 (OUTLIER) cc_final: 0.5914 (tp) REVERT: D 288 LYS cc_start: 0.2204 (mptt) cc_final: 0.1660 (mppt) REVERT: D 360 MET cc_start: 0.6455 (mtp) cc_final: 0.6070 (mtt) REVERT: D 436 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.5445 (tpt170) REVERT: E 143 GLU cc_start: 0.5911 (OUTLIER) cc_final: 0.5630 (mp0) REVERT: E 183 ARG cc_start: 0.6623 (OUTLIER) cc_final: 0.5726 (mtm-85) REVERT: E 483 ASP cc_start: 0.5096 (OUTLIER) cc_final: 0.4803 (m-30) REVERT: E 674 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6296 (mp) REVERT: F 483 ASP cc_start: 0.5034 (OUTLIER) cc_final: 0.4761 (m-30) REVERT: F 508 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7749 (tt) REVERT: F 674 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6337 (mp) REVERT: H 124 MET cc_start: 0.6315 (tpp) cc_final: 0.5658 (tpp) REVERT: H 145 TYR cc_start: 0.4439 (p90) cc_final: 0.4170 (p90) REVERT: H 209 ILE cc_start: 0.2587 (mm) cc_final: 0.2198 (mm) REVERT: H 220 ILE cc_start: 0.7552 (mt) cc_final: 0.7139 (tp) REVERT: H 260 MET cc_start: 0.6718 (mmp) cc_final: 0.6349 (mmm) REVERT: H 334 MET cc_start: 0.6614 (mmt) cc_final: 0.6381 (mtt) REVERT: H 392 THR cc_start: 0.6947 (OUTLIER) cc_final: 0.6649 (p) REVERT: H 642 GLN cc_start: 0.5227 (OUTLIER) cc_final: 0.4391 (tm-30) REVERT: H 685 GLU cc_start: 0.4068 (OUTLIER) cc_final: 0.2551 (tm-30) REVERT: I 298 PHE cc_start: 0.5703 (t80) cc_final: 0.5388 (t80) REVERT: I 383 ARG cc_start: 0.2821 (OUTLIER) cc_final: 0.2615 (ptt90) REVERT: I 483 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6529 (mpp) REVERT: I 642 GLN cc_start: 0.4590 (OUTLIER) cc_final: 0.4074 (tm-30) REVERT: I 665 SER cc_start: 0.3367 (OUTLIER) cc_final: 0.3143 (t) REVERT: I 685 GLU cc_start: 0.3013 (OUTLIER) cc_final: 0.2652 (tm-30) REVERT: J 58 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.6046 (pm20) REVERT: J 123 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7108 (tt) REVERT: J 179 MET cc_start: 0.2863 (OUTLIER) cc_final: 0.1603 (tmm) REVERT: J 407 MET cc_start: 0.4946 (tpt) cc_final: 0.4729 (tpt) REVERT: J 483 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6408 (mpp) REVERT: J 642 GLN cc_start: 0.5090 (OUTLIER) cc_final: 0.4390 (tm-30) REVERT: J 685 GLU cc_start: 0.3123 (OUTLIER) cc_final: 0.2461 (tm-30) REVERT: K 124 MET cc_start: 0.6540 (tpp) cc_final: 0.5971 (tpp) REVERT: K 180 LYS cc_start: 0.3758 (mmtt) cc_final: 0.3381 (mttm) REVERT: K 260 MET cc_start: 0.6362 (mmp) cc_final: 0.6057 (mmm) REVERT: K 392 THR cc_start: 0.6857 (OUTLIER) cc_final: 0.6555 (p) REVERT: K 540 HIS cc_start: 0.5824 (OUTLIER) cc_final: 0.5243 (t-90) REVERT: K 642 GLN cc_start: 0.5476 (OUTLIER) cc_final: 0.4434 (tm-30) REVERT: L 179 MET cc_start: 0.2437 (mtm) cc_final: 0.1921 (tmm) REVERT: L 642 GLN cc_start: 0.4742 (OUTLIER) cc_final: 0.4427 (tm-30) REVERT: M 52 HIS cc_start: 0.6006 (OUTLIER) cc_final: 0.5423 (p-80) REVERT: M 55 GLU cc_start: 0.5862 (mt-10) cc_final: 0.5639 (mm-30) REVERT: M 71 TYR cc_start: 0.6460 (m-80) cc_final: 0.5929 (m-80) REVERT: M 192 LEU cc_start: 0.5964 (pp) cc_final: 0.5716 (mt) REVERT: M 469 GLN cc_start: 0.5713 (tm-30) cc_final: 0.5151 (pt0) REVERT: M 483 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6468 (mpp) REVERT: M 677 ASP cc_start: 0.5106 (m-30) cc_final: 0.4847 (t70) REVERT: M 685 GLU cc_start: 0.4510 (OUTLIER) cc_final: 0.3713 (tp30) outliers start: 450 outliers final: 344 residues processed: 933 average time/residue: 0.5260 time to fit residues: 839.8356 Evaluate side-chains 898 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 383 poor density : 515 time to evaluate : 5.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 436 ARG Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 314 CYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 548 ASN Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 598 TYR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 436 ARG Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 591 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 598 TYR Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 617 MET Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 655 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 183 ARG Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 591 THR Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 625 VAL Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 168 MET Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 314 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 478 VAL Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 509 VAL Chi-restraints excluded: chain F residue 587 VAL Chi-restraints excluded: chain F residue 591 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 655 ASP Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain H residue 345 VAL Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 450 THR Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 562 VAL Chi-restraints excluded: chain H residue 566 THR Chi-restraints excluded: chain H residue 578 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 594 LEU Chi-restraints excluded: chain H residue 604 ASP Chi-restraints excluded: chain H residue 617 THR Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 642 GLN Chi-restraints excluded: chain H residue 643 VAL Chi-restraints excluded: chain H residue 650 MET Chi-restraints excluded: chain H residue 661 ASP Chi-restraints excluded: chain H residue 668 VAL Chi-restraints excluded: chain H residue 674 VAL Chi-restraints excluded: chain H residue 685 GLU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 52 HIS Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 154 PHE Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 314 GLU Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain I residue 383 ARG Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 483 MET Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 519 VAL Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 529 ASN Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 562 VAL Chi-restraints excluded: chain I residue 578 LEU Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 589 ILE Chi-restraints excluded: chain I residue 596 GLN Chi-restraints excluded: chain I residue 604 ASP Chi-restraints excluded: chain I residue 617 THR Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 642 GLN Chi-restraints excluded: chain I residue 645 VAL Chi-restraints excluded: chain I residue 665 SER Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain I residue 668 VAL Chi-restraints excluded: chain I residue 669 LYS Chi-restraints excluded: chain I residue 673 VAL Chi-restraints excluded: chain I residue 685 GLU Chi-restraints excluded: chain J residue 52 HIS Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 128 SER Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 179 MET Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 483 MET Chi-restraints excluded: chain J residue 486 THR Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 519 VAL Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 529 ASN Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 562 VAL Chi-restraints excluded: chain J residue 578 LEU Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 589 ILE Chi-restraints excluded: chain J residue 596 GLN Chi-restraints excluded: chain J residue 602 LEU Chi-restraints excluded: chain J residue 604 ASP Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain J residue 642 GLN Chi-restraints excluded: chain J residue 661 ASP Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 668 VAL Chi-restraints excluded: chain J residue 669 LYS Chi-restraints excluded: chain J residue 674 VAL Chi-restraints excluded: chain J residue 685 GLU Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 219 HIS Chi-restraints excluded: chain K residue 220 ILE Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 301 MET Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 444 LEU Chi-restraints excluded: chain K residue 450 THR Chi-restraints excluded: chain K residue 486 THR Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 540 HIS Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 578 LEU Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain K residue 604 ASP Chi-restraints excluded: chain K residue 620 VAL Chi-restraints excluded: chain K residue 631 LEU Chi-restraints excluded: chain K residue 642 GLN Chi-restraints excluded: chain K residue 656 VAL Chi-restraints excluded: chain K residue 668 VAL Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 219 HIS Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 271 LEU Chi-restraints excluded: chain L residue 285 VAL Chi-restraints excluded: chain L residue 325 LEU Chi-restraints excluded: chain L residue 345 VAL Chi-restraints excluded: chain L residue 365 PHE Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 460 THR Chi-restraints excluded: chain L residue 483 MET Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 562 VAL Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 589 ILE Chi-restraints excluded: chain L residue 594 LEU Chi-restraints excluded: chain L residue 604 ASP Chi-restraints excluded: chain L residue 617 THR Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 630 LEU Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 642 GLN Chi-restraints excluded: chain L residue 643 VAL Chi-restraints excluded: chain L residue 674 VAL Chi-restraints excluded: chain L residue 679 VAL Chi-restraints excluded: chain M residue 32 CYS Chi-restraints excluded: chain M residue 52 HIS Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 269 VAL Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 285 VAL Chi-restraints excluded: chain M residue 345 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain M residue 422 LEU Chi-restraints excluded: chain M residue 434 VAL Chi-restraints excluded: chain M residue 444 LEU Chi-restraints excluded: chain M residue 483 MET Chi-restraints excluded: chain M residue 521 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 562 VAL Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 588 VAL Chi-restraints excluded: chain M residue 589 ILE Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 599 LEU Chi-restraints excluded: chain M residue 604 ASP Chi-restraints excluded: chain M residue 617 THR Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 673 VAL Chi-restraints excluded: chain M residue 674 VAL Chi-restraints excluded: chain M residue 685 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 688 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 406 optimal weight: 5.9990 chunk 521 optimal weight: 9.9990 chunk 404 optimal weight: 10.0000 chunk 601 optimal weight: 5.9990 chunk 398 optimal weight: 8.9990 chunk 711 optimal weight: 9.9990 chunk 445 optimal weight: 1.9990 chunk 433 optimal weight: 6.9990 chunk 328 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN A 324 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 GLN B 283 ASN ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 HIS C 165 GLN C 283 ASN C 413 HIS D 283 ASN ** D 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 555 GLN E 324 ASN ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 HIS ** H 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 427 GLN ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.6578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 59010 Z= 0.316 Angle : 0.757 12.604 79776 Z= 0.396 Chirality : 0.049 0.246 8826 Planarity : 0.006 0.060 10464 Dihedral : 6.345 53.898 8292 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.97 % Favored : 90.01 % Rotamer: Outliers : 6.85 % Allowed : 19.28 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.09), residues: 7440 helix: -0.22 (0.10), residues: 2250 sheet: 0.23 (0.15), residues: 1068 loop : -2.62 (0.08), residues: 4122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 251 HIS 0.010 0.002 HIS K 52 PHE 0.025 0.002 PHE M 298 TYR 0.023 0.002 TYR A 142 ARG 0.008 0.001 ARG L 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 419 poor density : 580 time to evaluate : 5.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5696 (tp) REVERT: A 288 LYS cc_start: 0.1877 (mptt) cc_final: 0.1403 (mppt) REVERT: A 436 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.5678 (tpt170) REVERT: A 474 MET cc_start: 0.3760 (OUTLIER) cc_final: 0.3185 (mtp) REVERT: A 497 PHE cc_start: 0.5724 (OUTLIER) cc_final: 0.5207 (t80) REVERT: A 617 MET cc_start: 0.5948 (ttm) cc_final: 0.5713 (mtp) REVERT: B 153 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7052 (pp) REVERT: B 395 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7488 (mt) REVERT: B 474 MET cc_start: 0.3614 (OUTLIER) cc_final: 0.2726 (mtp) REVERT: C 153 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7074 (pp) REVERT: C 474 MET cc_start: 0.3527 (OUTLIER) cc_final: 0.2768 (mtp) REVERT: C 496 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6821 (mtt90) REVERT: D 143 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.5697 (pm20) REVERT: D 168 MET cc_start: 0.5777 (tpt) cc_final: 0.5447 (tpp) REVERT: D 272 LEU cc_start: 0.5847 (OUTLIER) cc_final: 0.5576 (tp) REVERT: E 183 ARG cc_start: 0.6635 (OUTLIER) cc_final: 0.5713 (mtm-85) REVERT: E 436 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6965 (mmm160) REVERT: E 598 TYR cc_start: 0.6538 (OUTLIER) cc_final: 0.6089 (p90) REVERT: E 674 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6439 (mp) REVERT: F 436 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6891 (mmm160) REVERT: F 598 TYR cc_start: 0.6461 (OUTLIER) cc_final: 0.5999 (p90) REVERT: F 674 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6489 (mp) REVERT: H 124 MET cc_start: 0.6297 (tpp) cc_final: 0.5626 (tpp) REVERT: H 209 ILE cc_start: 0.2616 (mm) cc_final: 0.2235 (mm) REVERT: H 220 ILE cc_start: 0.7807 (mt) cc_final: 0.7186 (tp) REVERT: H 251 GLU cc_start: 0.1319 (mp0) cc_final: 0.1013 (mp0) REVERT: H 260 MET cc_start: 0.6432 (mmp) cc_final: 0.6103 (mmm) REVERT: H 334 MET cc_start: 0.6494 (mmt) cc_final: 0.6142 (mtt) REVERT: H 407 MET cc_start: 0.4169 (tpt) cc_final: 0.3435 (tpt) REVERT: H 642 GLN cc_start: 0.5193 (OUTLIER) cc_final: 0.4325 (tm-30) REVERT: H 685 GLU cc_start: 0.3784 (OUTLIER) cc_final: 0.2838 (tm-30) REVERT: I 383 ARG cc_start: 0.2942 (OUTLIER) cc_final: 0.2486 (ptt90) REVERT: I 407 MET cc_start: 0.4766 (tpt) cc_final: 0.3809 (tpt) REVERT: I 483 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6363 (mtt) REVERT: I 642 GLN cc_start: 0.4664 (OUTLIER) cc_final: 0.4168 (tm-30) REVERT: I 665 SER cc_start: 0.3380 (OUTLIER) cc_final: 0.3168 (t) REVERT: I 685 GLU cc_start: 0.3021 (OUTLIER) cc_final: 0.2790 (tm-30) REVERT: J 52 HIS cc_start: 0.5757 (OUTLIER) cc_final: 0.5395 (p90) REVERT: J 58 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6130 (pm20) REVERT: J 179 MET cc_start: 0.2700 (OUTLIER) cc_final: 0.1470 (tmm) REVERT: J 483 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6138 (mtt) REVERT: J 642 GLN cc_start: 0.5139 (OUTLIER) cc_final: 0.4436 (tm-30) REVERT: J 665 SER cc_start: 0.3146 (OUTLIER) cc_final: 0.2815 (t) REVERT: J 685 GLU cc_start: 0.3397 (OUTLIER) cc_final: 0.2627 (tm-30) REVERT: K 124 MET cc_start: 0.6430 (tpp) cc_final: 0.5849 (tpp) REVERT: K 179 MET cc_start: -0.0009 (tpt) cc_final: -0.0467 (tmm) REVERT: K 180 LYS cc_start: 0.3691 (mmtt) cc_final: 0.2919 (mttm) REVERT: K 392 THR cc_start: 0.6799 (OUTLIER) cc_final: 0.6486 (p) REVERT: K 407 MET cc_start: 0.3944 (tpt) cc_final: 0.3204 (tpt) REVERT: K 642 GLN cc_start: 0.5478 (OUTLIER) cc_final: 0.4423 (tm-30) REVERT: L 179 MET cc_start: 0.2534 (mtm) cc_final: 0.1925 (tmm) REVERT: L 685 GLU cc_start: 0.3619 (OUTLIER) cc_final: 0.3062 (tp30) REVERT: M 52 HIS cc_start: 0.5955 (p-80) cc_final: 0.5510 (p90) REVERT: M 71 TYR cc_start: 0.6199 (m-80) cc_final: 0.5670 (m-80) REVERT: M 191 MET cc_start: 0.3707 (ppp) cc_final: 0.3076 (tmm) REVERT: M 192 LEU cc_start: 0.5747 (pp) cc_final: 0.5514 (mp) REVERT: M 469 GLN cc_start: 0.5669 (tm-30) cc_final: 0.5101 (pt0) REVERT: M 483 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6515 (mpp) REVERT: M 677 ASP cc_start: 0.5142 (m-30) cc_final: 0.4879 (t70) REVERT: M 685 GLU cc_start: 0.4451 (OUTLIER) cc_final: 0.3702 (tp30) outliers start: 419 outliers final: 323 residues processed: 914 average time/residue: 0.5235 time to fit residues: 817.7936 Evaluate side-chains 880 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 361 poor density : 519 time to evaluate : 5.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 436 ARG Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 314 CYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 548 ASN Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 555 GLN Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 591 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 598 TYR Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 617 MET Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 655 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 183 ARG Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 436 ARG Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 591 THR Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 598 TYR Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 625 VAL Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 314 CYS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 436 ARG Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 478 VAL Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 509 VAL Chi-restraints excluded: chain F residue 587 VAL Chi-restraints excluded: chain F residue 591 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 598 TYR Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 629 THR Chi-restraints excluded: chain F residue 655 ASP Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 221 GLU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 345 VAL Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 450 THR Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 483 MET Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 562 VAL Chi-restraints excluded: chain H residue 566 THR Chi-restraints excluded: chain H residue 578 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 594 LEU Chi-restraints excluded: chain H residue 596 GLN Chi-restraints excluded: chain H residue 604 ASP Chi-restraints excluded: chain H residue 617 THR Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain H residue 642 GLN Chi-restraints excluded: chain H residue 643 VAL Chi-restraints excluded: chain H residue 650 MET Chi-restraints excluded: chain H residue 674 VAL Chi-restraints excluded: chain H residue 685 GLU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 52 HIS Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 154 PHE Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 314 GLU Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain I residue 383 ARG Chi-restraints excluded: chain I residue 483 MET Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 519 VAL Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 562 VAL Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 596 GLN Chi-restraints excluded: chain I residue 604 ASP Chi-restraints excluded: chain I residue 617 THR Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 642 GLN Chi-restraints excluded: chain I residue 665 SER Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain I residue 668 VAL Chi-restraints excluded: chain I residue 669 LYS Chi-restraints excluded: chain I residue 685 GLU Chi-restraints excluded: chain J residue 52 HIS Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 179 MET Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 444 LEU Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 483 MET Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 519 VAL Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 562 VAL Chi-restraints excluded: chain J residue 578 LEU Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 596 GLN Chi-restraints excluded: chain J residue 602 LEU Chi-restraints excluded: chain J residue 604 ASP Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain J residue 642 GLN Chi-restraints excluded: chain J residue 661 ASP Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 668 VAL Chi-restraints excluded: chain J residue 669 LYS Chi-restraints excluded: chain J residue 674 VAL Chi-restraints excluded: chain J residue 685 GLU Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 219 HIS Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 301 MET Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 444 LEU Chi-restraints excluded: chain K residue 450 THR Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 566 THR Chi-restraints excluded: chain K residue 578 LEU Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain K residue 604 ASP Chi-restraints excluded: chain K residue 631 LEU Chi-restraints excluded: chain K residue 642 GLN Chi-restraints excluded: chain K residue 656 VAL Chi-restraints excluded: chain K residue 668 VAL Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 219 HIS Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 271 LEU Chi-restraints excluded: chain L residue 285 VAL Chi-restraints excluded: chain L residue 345 VAL Chi-restraints excluded: chain L residue 365 PHE Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 460 THR Chi-restraints excluded: chain L residue 483 MET Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 562 VAL Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 589 ILE Chi-restraints excluded: chain L residue 594 LEU Chi-restraints excluded: chain L residue 596 GLN Chi-restraints excluded: chain L residue 599 LEU Chi-restraints excluded: chain L residue 604 ASP Chi-restraints excluded: chain L residue 617 THR Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 630 LEU Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 643 VAL Chi-restraints excluded: chain L residue 674 VAL Chi-restraints excluded: chain L residue 685 GLU Chi-restraints excluded: chain M residue 32 CYS Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 269 VAL Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 285 VAL Chi-restraints excluded: chain M residue 345 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain M residue 422 LEU Chi-restraints excluded: chain M residue 444 LEU Chi-restraints excluded: chain M residue 483 MET Chi-restraints excluded: chain M residue 521 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 562 VAL Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 589 ILE Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 604 ASP Chi-restraints excluded: chain M residue 617 THR Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 674 VAL Chi-restraints excluded: chain M residue 678 HIS Chi-restraints excluded: chain M residue 685 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 440 optimal weight: 10.0000 chunk 284 optimal weight: 3.9990 chunk 424 optimal weight: 2.9990 chunk 214 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 137 optimal weight: 0.8980 chunk 452 optimal weight: 4.9990 chunk 484 optimal weight: 6.9990 chunk 351 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 559 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 283 ASN A 447 ASN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 GLN B 283 ASN ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN C 283 ASN D 283 ASN D 447 ASN ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 555 GLN ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 GLN F 324 ASN F 413 HIS ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 GLN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 ASN ** J 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 495 ASN ** M 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.6632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 59010 Z= 0.229 Angle : 0.683 10.117 79776 Z= 0.357 Chirality : 0.047 0.215 8826 Planarity : 0.005 0.057 10464 Dihedral : 5.840 51.519 8292 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 5.52 % Allowed : 20.83 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.71 (0.09), residues: 7440 helix: 0.30 (0.11), residues: 2208 sheet: 0.31 (0.16), residues: 1020 loop : -2.44 (0.09), residues: 4212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 251 HIS 0.010 0.001 HIS K 52 PHE 0.026 0.001 PHE M 298 TYR 0.029 0.002 TYR C 603 ARG 0.006 0.001 ARG C 465 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 338 poor density : 598 time to evaluate : 5.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5306 (pt0) REVERT: A 168 MET cc_start: 0.6040 (tpt) cc_final: 0.5631 (tpp) REVERT: A 288 LYS cc_start: 0.1220 (mptt) cc_final: 0.0826 (mmtm) REVERT: A 436 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.5642 (tpt170) REVERT: A 497 PHE cc_start: 0.5566 (OUTLIER) cc_final: 0.5140 (t80) REVERT: A 598 TYR cc_start: 0.6773 (OUTLIER) cc_final: 0.6550 (p90) REVERT: A 617 MET cc_start: 0.5762 (ttm) cc_final: 0.5537 (mtp) REVERT: B 288 LYS cc_start: 0.2331 (mptt) cc_final: 0.1398 (mmtm) REVERT: B 395 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7480 (mt) REVERT: B 474 MET cc_start: 0.3604 (OUTLIER) cc_final: 0.2705 (mtp) REVERT: B 496 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6901 (mtt90) REVERT: C 288 LYS cc_start: 0.1956 (mptt) cc_final: 0.0962 (mmtm) REVERT: C 474 MET cc_start: 0.3263 (OUTLIER) cc_final: 0.2485 (mtp) REVERT: C 496 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6803 (mtt90) REVERT: D 272 LEU cc_start: 0.5738 (OUTLIER) cc_final: 0.5507 (tp) REVERT: D 360 MET cc_start: 0.6576 (mtp) cc_final: 0.6295 (mtt) REVERT: D 436 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6959 (mmm160) REVERT: D 474 MET cc_start: 0.3407 (OUTLIER) cc_final: 0.3051 (mtt) REVERT: E 373 MET cc_start: 0.5133 (mtm) cc_final: 0.4841 (ttp) REVERT: E 436 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6893 (mmm160) REVERT: E 561 MET cc_start: 0.3648 (mmt) cc_final: 0.3350 (mmt) REVERT: E 598 TYR cc_start: 0.6727 (OUTLIER) cc_final: 0.6169 (p90) REVERT: E 674 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6295 (mp) REVERT: F 436 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6950 (mmm160) REVERT: F 508 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7759 (tt) REVERT: F 598 TYR cc_start: 0.6619 (OUTLIER) cc_final: 0.6123 (p90) REVERT: F 674 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6305 (mp) REVERT: H 124 MET cc_start: 0.6438 (tpp) cc_final: 0.5834 (tpp) REVERT: H 209 ILE cc_start: 0.2992 (mm) cc_final: 0.2671 (mm) REVERT: H 220 ILE cc_start: 0.7772 (mt) cc_final: 0.7168 (tp) REVERT: H 260 MET cc_start: 0.6402 (mmp) cc_final: 0.6061 (mmm) REVERT: H 407 MET cc_start: 0.4349 (tpt) cc_final: 0.3595 (tpt) REVERT: H 483 MET cc_start: 0.6496 (mpp) cc_final: 0.5716 (mtt) REVERT: H 642 GLN cc_start: 0.5281 (OUTLIER) cc_final: 0.4358 (tm-30) REVERT: H 685 GLU cc_start: 0.3687 (tp30) cc_final: 0.2807 (tm-30) REVERT: I 47 GLU cc_start: 0.5689 (mm-30) cc_final: 0.5435 (mm-30) REVERT: I 383 ARG cc_start: 0.2793 (OUTLIER) cc_final: 0.1444 (mtm110) REVERT: I 407 MET cc_start: 0.4849 (tpt) cc_final: 0.3791 (tpt) REVERT: I 483 MET cc_start: 0.7054 (mpp) cc_final: 0.6404 (mtt) REVERT: I 642 GLN cc_start: 0.4711 (OUTLIER) cc_final: 0.4161 (tm-30) REVERT: I 665 SER cc_start: 0.3123 (OUTLIER) cc_final: 0.2847 (t) REVERT: I 685 GLU cc_start: 0.3240 (OUTLIER) cc_final: 0.2680 (tm-30) REVERT: J 53 VAL cc_start: 0.5203 (OUTLIER) cc_final: 0.4958 (p) REVERT: J 179 MET cc_start: 0.2636 (OUTLIER) cc_final: 0.1453 (tmm) REVERT: J 407 MET cc_start: 0.5047 (tpt) cc_final: 0.4163 (tpt) REVERT: J 483 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6228 (mtt) REVERT: J 514 ILE cc_start: 0.6239 (mt) cc_final: 0.6006 (mt) REVERT: J 642 GLN cc_start: 0.4968 (OUTLIER) cc_final: 0.4256 (tm-30) REVERT: J 665 SER cc_start: 0.3393 (OUTLIER) cc_final: 0.3108 (t) REVERT: J 685 GLU cc_start: 0.3577 (OUTLIER) cc_final: 0.2582 (tm-30) REVERT: K 124 MET cc_start: 0.6539 (tpp) cc_final: 0.5934 (tpp) REVERT: K 179 MET cc_start: 0.0000 (tpt) cc_final: -0.0414 (tmm) REVERT: K 180 LYS cc_start: 0.3626 (mmtt) cc_final: 0.2933 (mttm) REVERT: K 392 THR cc_start: 0.6792 (OUTLIER) cc_final: 0.6435 (p) REVERT: K 407 MET cc_start: 0.4248 (tpt) cc_final: 0.3433 (tpt) REVERT: K 483 MET cc_start: 0.6577 (mpp) cc_final: 0.5801 (mtt) REVERT: K 540 HIS cc_start: 0.6066 (OUTLIER) cc_final: 0.5489 (t-90) REVERT: K 642 GLN cc_start: 0.5471 (OUTLIER) cc_final: 0.4459 (tm-30) REVERT: L 179 MET cc_start: 0.2663 (mtm) cc_final: 0.1873 (tmm) REVERT: L 685 GLU cc_start: 0.3544 (tp30) cc_final: 0.2497 (tm-30) REVERT: M 52 HIS cc_start: 0.5775 (p-80) cc_final: 0.5381 (p90) REVERT: M 71 TYR cc_start: 0.6210 (m-80) cc_final: 0.5749 (m-80) REVERT: M 124 MET cc_start: 0.6422 (mmm) cc_final: 0.6056 (tpp) REVERT: M 260 MET cc_start: 0.6554 (tpt) cc_final: 0.5850 (mmm) REVERT: M 483 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6461 (mpp) REVERT: M 685 GLU cc_start: 0.4449 (tp30) cc_final: 0.2908 (tm-30) outliers start: 338 outliers final: 250 residues processed: 867 average time/residue: 0.5295 time to fit residues: 783.9562 Evaluate side-chains 835 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 284 poor density : 551 time to evaluate : 7.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 436 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 314 CYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 436 ARG Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 555 GLN Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 591 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 617 MET Chi-restraints excluded: chain D residue 655 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 436 ARG Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 598 TYR Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 625 VAL Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 314 CYS Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 436 ARG Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 478 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 598 TYR Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 655 ASP Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 345 VAL Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 450 THR Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 562 VAL Chi-restraints excluded: chain H residue 566 THR Chi-restraints excluded: chain H residue 578 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 594 LEU Chi-restraints excluded: chain H residue 617 THR Chi-restraints excluded: chain H residue 642 GLN Chi-restraints excluded: chain H residue 650 MET Chi-restraints excluded: chain H residue 661 ASP Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 52 HIS Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 154 PHE Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 314 GLU Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain I residue 383 ARG Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 519 VAL Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 562 VAL Chi-restraints excluded: chain I residue 578 LEU Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 589 ILE Chi-restraints excluded: chain I residue 596 GLN Chi-restraints excluded: chain I residue 642 GLN Chi-restraints excluded: chain I residue 665 SER Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain I residue 668 VAL Chi-restraints excluded: chain I residue 669 LYS Chi-restraints excluded: chain I residue 685 GLU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 179 MET Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 444 LEU Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 483 MET Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 519 VAL Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 562 VAL Chi-restraints excluded: chain J residue 578 LEU Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 596 GLN Chi-restraints excluded: chain J residue 602 LEU Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain J residue 642 GLN Chi-restraints excluded: chain J residue 661 ASP Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 669 LYS Chi-restraints excluded: chain J residue 674 VAL Chi-restraints excluded: chain J residue 685 GLU Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 450 THR Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 540 HIS Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 566 THR Chi-restraints excluded: chain K residue 578 LEU Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain K residue 620 VAL Chi-restraints excluded: chain K residue 631 LEU Chi-restraints excluded: chain K residue 642 GLN Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 219 HIS Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 271 LEU Chi-restraints excluded: chain L residue 285 VAL Chi-restraints excluded: chain L residue 345 VAL Chi-restraints excluded: chain L residue 365 PHE Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 460 THR Chi-restraints excluded: chain L residue 483 MET Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 589 ILE Chi-restraints excluded: chain L residue 594 LEU Chi-restraints excluded: chain L residue 604 ASP Chi-restraints excluded: chain L residue 617 THR Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 643 VAL Chi-restraints excluded: chain L residue 674 VAL Chi-restraints excluded: chain M residue 32 CYS Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 269 VAL Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 285 VAL Chi-restraints excluded: chain M residue 345 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain M residue 444 LEU Chi-restraints excluded: chain M residue 483 MET Chi-restraints excluded: chain M residue 521 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 562 VAL Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 589 ILE Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 599 LEU Chi-restraints excluded: chain M residue 617 THR Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 674 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 647 optimal weight: 6.9990 chunk 681 optimal weight: 1.9990 chunk 621 optimal weight: 7.9990 chunk 662 optimal weight: 10.0000 chunk 398 optimal weight: 1.9990 chunk 288 optimal weight: 7.9990 chunk 520 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 598 optimal weight: 5.9990 chunk 626 optimal weight: 20.0000 chunk 660 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN A 413 HIS A 447 ASN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN C 283 ASN D 165 GLN D 283 ASN ** D 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 HIS ** I 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 529 ASN ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.6812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 59010 Z= 0.303 Angle : 0.750 11.312 79776 Z= 0.391 Chirality : 0.049 0.235 8826 Planarity : 0.006 0.065 10464 Dihedral : 6.097 54.109 8292 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.15 % Favored : 89.84 % Rotamer: Outliers : 5.75 % Allowed : 20.59 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.87 (0.09), residues: 7440 helix: 0.06 (0.11), residues: 2250 sheet: 0.28 (0.15), residues: 1068 loop : -2.56 (0.09), residues: 4122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 251 HIS 0.009 0.002 HIS K 52 PHE 0.026 0.002 PHE M 298 TYR 0.041 0.002 TYR C 603 ARG 0.007 0.001 ARG C 465 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 352 poor density : 552 time to evaluate : 5.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 GLU cc_start: 0.6155 (OUTLIER) cc_final: 0.5441 (pt0) REVERT: A 288 LYS cc_start: 0.1507 (mptt) cc_final: 0.0650 (mppt) REVERT: A 436 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.5619 (tpt170) REVERT: A 497 PHE cc_start: 0.5746 (OUTLIER) cc_final: 0.5207 (t80) REVERT: A 598 TYR cc_start: 0.6753 (OUTLIER) cc_final: 0.6538 (p90) REVERT: A 617 MET cc_start: 0.5932 (ttm) cc_final: 0.5724 (mtp) REVERT: B 153 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6892 (pp) REVERT: B 288 LYS cc_start: 0.2477 (mptt) cc_final: 0.1476 (mmtm) REVERT: B 395 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7329 (mt) REVERT: B 474 MET cc_start: 0.3709 (OUTLIER) cc_final: 0.2809 (mtp) REVERT: C 474 MET cc_start: 0.3361 (OUTLIER) cc_final: 0.2604 (mtp) REVERT: D 168 MET cc_start: 0.5781 (tpt) cc_final: 0.5553 (tpp) REVERT: D 272 LEU cc_start: 0.5914 (OUTLIER) cc_final: 0.5636 (tp) REVERT: D 288 LYS cc_start: 0.1906 (mptt) cc_final: 0.1234 (mppt) REVERT: D 436 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.5539 (tpt170) REVERT: D 474 MET cc_start: 0.3660 (OUTLIER) cc_final: 0.3187 (mtt) REVERT: E 143 GLU cc_start: 0.5740 (OUTLIER) cc_final: 0.5309 (mp0) REVERT: E 183 ARG cc_start: 0.6633 (OUTLIER) cc_final: 0.6404 (mtm-85) REVERT: E 436 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6894 (mmm160) REVERT: E 474 MET cc_start: 0.3644 (ttt) cc_final: 0.2956 (tpp) REVERT: E 561 MET cc_start: 0.3320 (mmt) cc_final: 0.3052 (mmt) REVERT: E 598 TYR cc_start: 0.6813 (OUTLIER) cc_final: 0.6366 (p90) REVERT: E 674 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6315 (mp) REVERT: F 288 LYS cc_start: 0.2407 (mptt) cc_final: 0.1967 (mmtm) REVERT: F 436 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6789 (tpm170) REVERT: F 508 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7687 (tt) REVERT: F 598 TYR cc_start: 0.6732 (OUTLIER) cc_final: 0.6328 (p90) REVERT: F 674 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6318 (mp) REVERT: H 124 MET cc_start: 0.6289 (tpp) cc_final: 0.5659 (tpp) REVERT: H 209 ILE cc_start: 0.3185 (mm) cc_final: 0.2870 (mm) REVERT: H 220 ILE cc_start: 0.7804 (mt) cc_final: 0.7181 (tp) REVERT: H 251 GLU cc_start: 0.1659 (mp0) cc_final: 0.1304 (mp0) REVERT: H 260 MET cc_start: 0.6387 (mmp) cc_final: 0.6052 (mmm) REVERT: H 407 MET cc_start: 0.4343 (tpt) cc_final: 0.3578 (tpt) REVERT: H 559 LYS cc_start: 0.5718 (tttm) cc_final: 0.4607 (tmmt) REVERT: H 642 GLN cc_start: 0.5155 (OUTLIER) cc_final: 0.4333 (tm-30) REVERT: H 685 GLU cc_start: 0.3600 (tp30) cc_final: 0.2795 (tm-30) REVERT: I 47 GLU cc_start: 0.5688 (mm-30) cc_final: 0.5441 (mm-30) REVERT: I 52 HIS cc_start: 0.5902 (OUTLIER) cc_final: 0.5469 (p90) REVERT: I 383 ARG cc_start: 0.2760 (OUTLIER) cc_final: 0.2413 (ptt90) REVERT: I 407 MET cc_start: 0.4826 (tpt) cc_final: 0.3750 (tpt) REVERT: I 483 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6290 (mtt) REVERT: I 642 GLN cc_start: 0.4520 (OUTLIER) cc_final: 0.4028 (tm-30) REVERT: I 665 SER cc_start: 0.3456 (OUTLIER) cc_final: 0.3209 (t) REVERT: I 685 GLU cc_start: 0.3192 (OUTLIER) cc_final: 0.2681 (tm-30) REVERT: J 52 HIS cc_start: 0.5772 (OUTLIER) cc_final: 0.5426 (p90) REVERT: J 179 MET cc_start: 0.2817 (mtp) cc_final: 0.1550 (tmm) REVERT: J 220 ILE cc_start: 0.7709 (mt) cc_final: 0.6987 (tp) REVERT: J 407 MET cc_start: 0.4938 (tpt) cc_final: 0.4043 (tpt) REVERT: J 483 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6239 (mtt) REVERT: J 642 GLN cc_start: 0.5016 (OUTLIER) cc_final: 0.4320 (tm-30) REVERT: J 665 SER cc_start: 0.2990 (OUTLIER) cc_final: 0.2688 (t) REVERT: J 685 GLU cc_start: 0.3617 (OUTLIER) cc_final: 0.2590 (tm-30) REVERT: K 124 MET cc_start: 0.6427 (tpp) cc_final: 0.5833 (tpp) REVERT: K 179 MET cc_start: -0.0134 (tpt) cc_final: -0.0468 (tmm) REVERT: K 180 LYS cc_start: 0.3647 (mmtt) cc_final: 0.2959 (mttm) REVERT: K 407 MET cc_start: 0.4109 (tpt) cc_final: 0.3332 (tpt) REVERT: K 540 HIS cc_start: 0.5738 (OUTLIER) cc_final: 0.5300 (t-90) REVERT: K 642 GLN cc_start: 0.5510 (OUTLIER) cc_final: 0.4470 (tm-30) REVERT: L 179 MET cc_start: 0.1997 (mtm) cc_final: 0.1498 (tmm) REVERT: L 191 MET cc_start: 0.3743 (ppp) cc_final: 0.2912 (tmm) REVERT: L 301 MET cc_start: 0.4735 (ttt) cc_final: 0.4471 (ttt) REVERT: L 407 MET cc_start: 0.4716 (tpt) cc_final: 0.3728 (tpt) REVERT: L 559 LYS cc_start: 0.5933 (tttm) cc_final: 0.4673 (tmmt) REVERT: L 685 GLU cc_start: 0.3401 (OUTLIER) cc_final: 0.2482 (tm-30) REVERT: M 52 HIS cc_start: 0.5795 (p-80) cc_final: 0.5388 (p90) REVERT: M 124 MET cc_start: 0.6424 (mmm) cc_final: 0.6057 (tpp) REVERT: M 483 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6459 (mpp) REVERT: M 685 GLU cc_start: 0.4459 (OUTLIER) cc_final: 0.2910 (tm-30) outliers start: 352 outliers final: 286 residues processed: 844 average time/residue: 0.5311 time to fit residues: 763.9689 Evaluate side-chains 856 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 323 poor density : 533 time to evaluate : 5.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 436 ARG Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 314 CYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 436 ARG Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 591 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 598 TYR Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 617 MET Chi-restraints excluded: chain D residue 655 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 183 ARG Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 436 ARG Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 591 THR Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 598 TYR Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 314 CYS Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 436 ARG Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 478 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 591 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 598 TYR Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 629 THR Chi-restraints excluded: chain F residue 655 ASP Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain H residue 345 VAL Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 450 THR Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 483 MET Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 562 VAL Chi-restraints excluded: chain H residue 566 THR Chi-restraints excluded: chain H residue 578 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 594 LEU Chi-restraints excluded: chain H residue 596 GLN Chi-restraints excluded: chain H residue 617 THR Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain H residue 642 GLN Chi-restraints excluded: chain H residue 650 MET Chi-restraints excluded: chain H residue 661 ASP Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 52 HIS Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 154 PHE Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 314 GLU Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain I residue 383 ARG Chi-restraints excluded: chain I residue 483 MET Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 519 VAL Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 562 VAL Chi-restraints excluded: chain I residue 578 LEU Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 589 ILE Chi-restraints excluded: chain I residue 596 GLN Chi-restraints excluded: chain I residue 604 ASP Chi-restraints excluded: chain I residue 642 GLN Chi-restraints excluded: chain I residue 665 SER Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain I residue 668 VAL Chi-restraints excluded: chain I residue 669 LYS Chi-restraints excluded: chain I residue 685 GLU Chi-restraints excluded: chain J residue 52 HIS Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 444 LEU Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 483 MET Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 519 VAL Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 529 ASN Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 562 VAL Chi-restraints excluded: chain J residue 578 LEU Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 589 ILE Chi-restraints excluded: chain J residue 596 GLN Chi-restraints excluded: chain J residue 602 LEU Chi-restraints excluded: chain J residue 604 ASP Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain J residue 642 GLN Chi-restraints excluded: chain J residue 661 ASP Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 669 LYS Chi-restraints excluded: chain J residue 674 VAL Chi-restraints excluded: chain J residue 685 GLU Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 219 HIS Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 450 THR Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 540 HIS Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 566 THR Chi-restraints excluded: chain K residue 578 LEU Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain K residue 596 GLN Chi-restraints excluded: chain K residue 620 VAL Chi-restraints excluded: chain K residue 631 LEU Chi-restraints excluded: chain K residue 642 GLN Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 219 HIS Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 271 LEU Chi-restraints excluded: chain L residue 285 VAL Chi-restraints excluded: chain L residue 345 VAL Chi-restraints excluded: chain L residue 365 PHE Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 460 THR Chi-restraints excluded: chain L residue 483 MET Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 562 VAL Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 589 ILE Chi-restraints excluded: chain L residue 594 LEU Chi-restraints excluded: chain L residue 596 GLN Chi-restraints excluded: chain L residue 599 LEU Chi-restraints excluded: chain L residue 604 ASP Chi-restraints excluded: chain L residue 617 THR Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 630 LEU Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 643 VAL Chi-restraints excluded: chain L residue 674 VAL Chi-restraints excluded: chain L residue 685 GLU Chi-restraints excluded: chain M residue 32 CYS Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 269 VAL Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 285 VAL Chi-restraints excluded: chain M residue 345 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 387 ARG Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain M residue 434 VAL Chi-restraints excluded: chain M residue 444 LEU Chi-restraints excluded: chain M residue 483 MET Chi-restraints excluded: chain M residue 521 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 562 VAL Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 589 ILE Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 599 LEU Chi-restraints excluded: chain M residue 604 ASP Chi-restraints excluded: chain M residue 617 THR Chi-restraints excluded: chain M residue 620 VAL Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 674 VAL Chi-restraints excluded: chain M residue 685 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 435 optimal weight: 5.9990 chunk 700 optimal weight: 6.9990 chunk 427 optimal weight: 5.9990 chunk 332 optimal weight: 1.9990 chunk 487 optimal weight: 5.9990 chunk 735 optimal weight: 0.0770 chunk 676 optimal weight: 4.9990 chunk 585 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 452 optimal weight: 10.0000 chunk 358 optimal weight: 3.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN A 413 HIS ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN C 283 ASN ** D 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.6819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 59010 Z= 0.278 Angle : 0.793 59.192 79776 Z= 0.425 Chirality : 0.048 0.480 8826 Planarity : 0.006 0.165 10464 Dihedral : 6.081 54.102 8292 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.13 % Favored : 89.85 % Rotamer: Outliers : 5.64 % Allowed : 20.82 % Favored : 73.55 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.86 (0.09), residues: 7440 helix: 0.08 (0.11), residues: 2250 sheet: 0.28 (0.15), residues: 1068 loop : -2.56 (0.09), residues: 4122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 251 HIS 0.252 0.002 HIS I 36 PHE 0.034 0.002 PHE F 332 TYR 0.036 0.002 TYR B 603 ARG 0.011 0.001 ARG H 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 345 poor density : 538 time to evaluate : 5.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5429 (pt0) REVERT: A 288 LYS cc_start: 0.1483 (mptt) cc_final: 0.0639 (mppt) REVERT: A 436 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.5666 (tpt170) REVERT: A 497 PHE cc_start: 0.5731 (OUTLIER) cc_final: 0.5200 (t80) REVERT: A 598 TYR cc_start: 0.6758 (OUTLIER) cc_final: 0.6511 (p90) REVERT: A 617 MET cc_start: 0.5920 (ttm) cc_final: 0.5710 (mtp) REVERT: B 153 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6879 (pp) REVERT: B 288 LYS cc_start: 0.2456 (mptt) cc_final: 0.1480 (mmtm) REVERT: B 395 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7325 (mt) REVERT: B 474 MET cc_start: 0.3693 (OUTLIER) cc_final: 0.2792 (mtp) REVERT: C 474 MET cc_start: 0.3364 (OUTLIER) cc_final: 0.2603 (mtp) REVERT: D 168 MET cc_start: 0.5816 (tpt) cc_final: 0.5549 (tpp) REVERT: D 272 LEU cc_start: 0.5843 (OUTLIER) cc_final: 0.5573 (tp) REVERT: D 288 LYS cc_start: 0.1876 (mptt) cc_final: 0.1211 (mppt) REVERT: D 436 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.5528 (tpt170) REVERT: D 474 MET cc_start: 0.3640 (OUTLIER) cc_final: 0.3163 (mtt) REVERT: E 183 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.6394 (mtm-85) REVERT: E 436 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6902 (mmm160) REVERT: E 474 MET cc_start: 0.3639 (ttt) cc_final: 0.2952 (tpp) REVERT: E 561 MET cc_start: 0.3302 (mmt) cc_final: 0.3032 (mmt) REVERT: E 598 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.6350 (p90) REVERT: E 674 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6302 (mp) REVERT: F 288 LYS cc_start: 0.2386 (mptt) cc_final: 0.1967 (mmtm) REVERT: F 436 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7035 (mmm160) REVERT: F 508 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7681 (tt) REVERT: F 598 TYR cc_start: 0.6722 (OUTLIER) cc_final: 0.6310 (p90) REVERT: F 674 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6316 (mp) REVERT: H 124 MET cc_start: 0.6287 (tpp) cc_final: 0.5653 (tpp) REVERT: H 209 ILE cc_start: 0.3138 (mm) cc_final: 0.2851 (mm) REVERT: H 220 ILE cc_start: 0.7819 (mt) cc_final: 0.7181 (tp) REVERT: H 251 GLU cc_start: 0.1650 (mp0) cc_final: 0.1300 (mp0) REVERT: H 260 MET cc_start: 0.6387 (mmp) cc_final: 0.6051 (mmm) REVERT: H 407 MET cc_start: 0.4348 (tpt) cc_final: 0.3586 (tpt) REVERT: H 642 GLN cc_start: 0.5153 (OUTLIER) cc_final: 0.4328 (tm-30) REVERT: H 685 GLU cc_start: 0.3601 (OUTLIER) cc_final: 0.2791 (tm-30) REVERT: I 36 HIS cc_start: 0.4860 (OUTLIER) cc_final: 0.4631 (p-80) REVERT: I 47 GLU cc_start: 0.5676 (mm-30) cc_final: 0.5447 (mm-30) REVERT: I 52 HIS cc_start: 0.5877 (OUTLIER) cc_final: 0.5456 (p90) REVERT: I 383 ARG cc_start: 0.2760 (OUTLIER) cc_final: 0.2493 (ptt90) REVERT: I 407 MET cc_start: 0.4834 (tpt) cc_final: 0.3752 (tpt) REVERT: I 483 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6317 (mtt) REVERT: I 642 GLN cc_start: 0.4509 (OUTLIER) cc_final: 0.4027 (tm-30) REVERT: I 665 SER cc_start: 0.3448 (OUTLIER) cc_final: 0.3206 (t) REVERT: I 685 GLU cc_start: 0.3191 (OUTLIER) cc_final: 0.2681 (tm-30) REVERT: J 52 HIS cc_start: 0.5767 (OUTLIER) cc_final: 0.5414 (p90) REVERT: J 179 MET cc_start: 0.2815 (mtp) cc_final: 0.1551 (tmm) REVERT: J 220 ILE cc_start: 0.7707 (mt) cc_final: 0.6982 (tp) REVERT: J 407 MET cc_start: 0.4943 (tpt) cc_final: 0.4019 (tpt) REVERT: J 483 MET cc_start: 0.6934 (mpp) cc_final: 0.6231 (mtt) REVERT: J 642 GLN cc_start: 0.5018 (OUTLIER) cc_final: 0.4319 (tm-30) REVERT: J 665 SER cc_start: 0.2991 (OUTLIER) cc_final: 0.2680 (t) REVERT: J 685 GLU cc_start: 0.3617 (OUTLIER) cc_final: 0.2588 (tm-30) REVERT: K 124 MET cc_start: 0.6425 (tpp) cc_final: 0.5829 (tpp) REVERT: K 132 ARG cc_start: 0.5875 (tmm160) cc_final: 0.5246 (ttp80) REVERT: K 179 MET cc_start: -0.0131 (tpt) cc_final: -0.0469 (tmm) REVERT: K 180 LYS cc_start: 0.3643 (mmtt) cc_final: 0.2958 (mttm) REVERT: K 407 MET cc_start: 0.4164 (tpt) cc_final: 0.3381 (tpt) REVERT: K 540 HIS cc_start: 0.5705 (OUTLIER) cc_final: 0.5306 (t-90) REVERT: K 642 GLN cc_start: 0.5514 (OUTLIER) cc_final: 0.4486 (tm-30) REVERT: L 179 MET cc_start: 0.2231 (mtm) cc_final: 0.1539 (tmm) REVERT: L 191 MET cc_start: 0.3755 (ppp) cc_final: 0.2911 (tmm) REVERT: L 301 MET cc_start: 0.4648 (ttt) cc_final: 0.4387 (ttt) REVERT: L 407 MET cc_start: 0.4702 (tpt) cc_final: 0.3731 (tpt) REVERT: L 559 LYS cc_start: 0.5929 (tttm) cc_final: 0.4664 (tmmt) REVERT: L 685 GLU cc_start: 0.3396 (tp30) cc_final: 0.2483 (tm-30) REVERT: M 52 HIS cc_start: 0.5780 (p-80) cc_final: 0.5367 (p90) REVERT: M 124 MET cc_start: 0.6413 (mmm) cc_final: 0.6046 (tpp) REVERT: M 483 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6455 (mpp) REVERT: M 685 GLU cc_start: 0.4458 (OUTLIER) cc_final: 0.2905 (tm-30) outliers start: 345 outliers final: 295 residues processed: 820 average time/residue: 0.5435 time to fit residues: 762.9373 Evaluate side-chains 866 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 331 poor density : 535 time to evaluate : 5.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 436 ARG Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 314 CYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 436 ARG Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 591 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 617 MET Chi-restraints excluded: chain D residue 655 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 183 ARG Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 436 ARG Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 591 THR Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 598 TYR Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 314 CYS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 436 ARG Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 478 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 591 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 598 TYR Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 629 THR Chi-restraints excluded: chain F residue 655 ASP Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain H residue 345 VAL Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 450 THR Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 562 VAL Chi-restraints excluded: chain H residue 566 THR Chi-restraints excluded: chain H residue 578 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 594 LEU Chi-restraints excluded: chain H residue 596 GLN Chi-restraints excluded: chain H residue 602 LEU Chi-restraints excluded: chain H residue 604 ASP Chi-restraints excluded: chain H residue 617 THR Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain H residue 642 GLN Chi-restraints excluded: chain H residue 650 MET Chi-restraints excluded: chain H residue 661 ASP Chi-restraints excluded: chain H residue 685 GLU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 52 HIS Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 154 PHE Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 314 GLU Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain I residue 383 ARG Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 483 MET Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 519 VAL Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 562 VAL Chi-restraints excluded: chain I residue 578 LEU Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 589 ILE Chi-restraints excluded: chain I residue 596 GLN Chi-restraints excluded: chain I residue 604 ASP Chi-restraints excluded: chain I residue 642 GLN Chi-restraints excluded: chain I residue 665 SER Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain I residue 668 VAL Chi-restraints excluded: chain I residue 669 LYS Chi-restraints excluded: chain I residue 685 GLU Chi-restraints excluded: chain J residue 52 HIS Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 444 LEU Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 519 VAL Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 562 VAL Chi-restraints excluded: chain J residue 578 LEU Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 589 ILE Chi-restraints excluded: chain J residue 596 GLN Chi-restraints excluded: chain J residue 602 LEU Chi-restraints excluded: chain J residue 604 ASP Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain J residue 642 GLN Chi-restraints excluded: chain J residue 661 ASP Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 668 VAL Chi-restraints excluded: chain J residue 669 LYS Chi-restraints excluded: chain J residue 674 VAL Chi-restraints excluded: chain J residue 685 GLU Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 219 HIS Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 450 THR Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 540 HIS Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 566 THR Chi-restraints excluded: chain K residue 578 LEU Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain K residue 596 GLN Chi-restraints excluded: chain K residue 604 ASP Chi-restraints excluded: chain K residue 617 THR Chi-restraints excluded: chain K residue 620 VAL Chi-restraints excluded: chain K residue 631 LEU Chi-restraints excluded: chain K residue 642 GLN Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 219 HIS Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 271 LEU Chi-restraints excluded: chain L residue 285 VAL Chi-restraints excluded: chain L residue 345 VAL Chi-restraints excluded: chain L residue 365 PHE Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 460 THR Chi-restraints excluded: chain L residue 483 MET Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 562 VAL Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 589 ILE Chi-restraints excluded: chain L residue 594 LEU Chi-restraints excluded: chain L residue 596 GLN Chi-restraints excluded: chain L residue 599 LEU Chi-restraints excluded: chain L residue 604 ASP Chi-restraints excluded: chain L residue 617 THR Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 630 LEU Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 643 VAL Chi-restraints excluded: chain L residue 674 VAL Chi-restraints excluded: chain M residue 32 CYS Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 219 HIS Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 269 VAL Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 285 VAL Chi-restraints excluded: chain M residue 345 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 387 ARG Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain M residue 434 VAL Chi-restraints excluded: chain M residue 444 LEU Chi-restraints excluded: chain M residue 483 MET Chi-restraints excluded: chain M residue 521 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 562 VAL Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 589 ILE Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 599 LEU Chi-restraints excluded: chain M residue 604 ASP Chi-restraints excluded: chain M residue 617 THR Chi-restraints excluded: chain M residue 620 VAL Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 674 VAL Chi-restraints excluded: chain M residue 685 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 465 optimal weight: 0.8980 chunk 623 optimal weight: 0.6980 chunk 179 optimal weight: 0.8980 chunk 539 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 586 optimal weight: 4.9990 chunk 245 optimal weight: 0.9990 chunk 602 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN A 413 HIS ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN C 165 GLN C 283 ASN ** D 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.147666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.119536 restraints weight = 123931.663| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.52 r_work: 0.3500 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.6820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 59010 Z= 0.278 Angle : 0.793 59.192 79776 Z= 0.425 Chirality : 0.048 0.480 8826 Planarity : 0.006 0.165 10464 Dihedral : 6.081 54.102 8292 Min Nonbonded Distance : 1.203 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.13 % Favored : 89.85 % Rotamer: Outliers : 5.42 % Allowed : 20.98 % Favored : 73.59 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.86 (0.09), residues: 7440 helix: 0.08 (0.11), residues: 2250 sheet: 0.28 (0.15), residues: 1068 loop : -2.56 (0.09), residues: 4122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 251 HIS 0.252 0.002 HIS I 36 PHE 0.034 0.002 PHE F 332 TYR 0.036 0.002 TYR B 603 ARG 0.011 0.001 ARG H 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13870.13 seconds wall clock time: 243 minutes 4.40 seconds (14584.40 seconds total)