Starting phenix.real_space_refine on Sun Dec 29 15:55:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f41_28849/12_2024/8f41_28849.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f41_28849/12_2024/8f41_28849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f41_28849/12_2024/8f41_28849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f41_28849/12_2024/8f41_28849.map" model { file = "/net/cci-nas-00/data/ceres_data/8f41_28849/12_2024/8f41_28849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f41_28849/12_2024/8f41_28849.cif" } resolution = 3.9 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: "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: "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: "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: "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: "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: "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: 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: "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: "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: "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: "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: "B" 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: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} 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: "C" 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} Time building chain proxies: 23.91, per 1000 atoms: 0.41 Number of scatterers: 57846 At special positions: 0 Unit cell: (160.6, 160.6, 243.1, 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: 11.72 Conformation dependent library (CDL) restraints added in 6.0 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: 5.36 Creating SS restraints... 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: 4.090A pdb=" N SER B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.585A pdb=" N ALA B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 395 removed outlier: 4.189A pdb=" N LEU B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 440 removed outlier: 3.576A pdb=" N ASN B 440 " --> pdb=" O ARG B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 451 removed outlier: 4.464A 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: 3.582A pdb=" N LEU B 637 " --> pdb=" O THR B 633 " (cutoff:3.500A) removed outlier: 3.652A 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: 3.900A pdb=" N GLU B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 696 removed outlier: 3.650A pdb=" N VAL B 688 " --> pdb=" O ASP B 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: 4.334A 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: 3.975A 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 '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: 3.584A 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: 4.465A 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: 3.846A 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: 3.596A 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: 3.730A 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: 3.902A 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 '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: 3.579A pdb=" N ARG I 33 " --> pdb=" O PHE I 29 " (cutoff:3.500A) removed outlier: 3.840A 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: 4.462A 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: 3.893A 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: 3.661A 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: 3.643A pdb=" N THR I 312 " --> pdb=" O GLU I 308 " (cutoff:3.500A) removed outlier: 3.730A 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: 3.914A 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: 3.613A pdb=" N LEU I 489 " --> pdb=" O ALA I 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: 3.581A 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: 4.462A 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: 3.660A 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: 3.642A 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: 3.527A 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: 3.924A 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 'M' and resid 22 through 35 removed outlier: 3.630A 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: 4.461A 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: 3.643A 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: 3.528A 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: 3.916A 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: 4.086A 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: 3.613A pdb=" N LEU M 489 " --> pdb=" O ALA M 485 " (cutoff:3.500A) 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: 4.333A 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: 4.190A pdb=" N LEU A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 440 removed outlier: 3.574A 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: 3.847A pdb=" N PHE A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 3.973A 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: 3.652A 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 '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: 3.734A 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: 3.930A 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: 3.585A pdb=" N ALA C 372 " --> pdb=" O ALA C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 395 removed outlier: 4.190A pdb=" N LEU C 395 " --> pdb=" O PRO C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 440 removed outlier: 3.576A 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: 3.848A 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: 3.730A 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: 3.902A 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 '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: 3.733A 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: 3.728A 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: 3.587A 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: 3.577A 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: 3.730A 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 '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: 3.586A pdb=" N CYS H 32 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 3.582A 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: 3.983A 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: 3.926A 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: 3.727A 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 '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: 3.526A 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: 3.915A pdb=" N THR J 450 " --> pdb=" O ARG J 446 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 456 removed outlier: 3.905A 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: 4.086A 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: 3.728A 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 '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: 4.460A 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: 3.893A 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: 3.642A pdb=" N THR L 312 " --> pdb=" O GLU L 308 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU L 314 " --> pdb=" O PRO L 310 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 335 removed outlier: 3.527A 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: 3.914A 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: 3.925A 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 sheet with id=AA1, 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: 3.575A pdb=" N ALA B 424 " --> pdb=" O ILE B 379 " (cutoff:3.500A) Processing sheet with id=AA2, 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: 6.141A 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: 6.483A pdb=" N THR B 591 " --> pdb=" O PHE B 616 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 266 through 273 removed outlier: 3.700A pdb=" N VAL D 380 " --> pdb=" O VAL D 359 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 424 " --> pdb=" O ILE D 379 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 498 through 499 removed outlier: 3.526A 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: 6.139A 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: 8.846A 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=AA5, 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=AA6, first strand: chain 'F' and resid 498 through 499 removed outlier: 3.525A 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: 7.207A 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=AA7, 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: 8.458A pdb=" N LEU I 42 " --> pdb=" O LEU I 16 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL I 18 " --> pdb=" O LEU I 42 " (cutoff:3.500A) removed outlier: 6.709A 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=AA8, first strand: chain 'I' and resid 218 through 226 removed outlier: 7.391A 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: 7.417A pdb=" N GLU I 286 " --> pdb=" O MET I 299 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET I 299 " --> pdb=" O GLU I 286 " (cutoff:3.500A) Processing sheet with id=AA9, 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: 7.482A pdb=" N GLU I 251 " --> pdb=" O CYS I 240 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL I 242 " --> pdb=" O VAL I 249 " (cutoff:3.500A) removed outlier: 3.622A 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=AB1, first strand: chain 'I' and resid 321 through 322 Processing sheet with id=AB2, 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=AB3, first strand: chain 'I' and resid 507 through 514 Processing sheet with id=AB4, first strand: chain 'I' and resid 532 through 537 removed outlier: 4.244A 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=AB5, first strand: chain 'I' and resid 664 through 666 Processing sheet with id=AB6, 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: 7.976A pdb=" N HIS K 90 " --> pdb=" O LYS K 15 " (cutoff:3.500A) removed outlier: 6.677A 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=AB7, 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=AB8, 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: 7.481A 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: 6.629A 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=AB9, first strand: chain 'K' and resid 321 through 322 Processing sheet with id=AC1, 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=AC2, first strand: chain 'K' and resid 507 through 514 Processing sheet with id=AC3, 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: 3.631A 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=AC4, first strand: chain 'K' and resid 664 through 666 Processing sheet with id=AC5, first strand: chain 'M' and resid 59 through 61 removed outlier: 6.871A 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: 7.977A 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=AC6, first strand: chain 'M' and resid 218 through 226 removed outlier: 7.389A 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=AC7, 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: 8.110A pdb=" N VAL M 242 " --> pdb=" O VAL M 249 " (cutoff:3.500A) removed outlier: 3.624A 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=AC8, first strand: chain 'M' and resid 321 through 322 Processing sheet with id=AC9, 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=AD1, first strand: chain 'M' and resid 507 through 514 Processing sheet with id=AD2, 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: 3.997A pdb=" N ILE M 589 " --> pdb=" O LEU M 578 " (cutoff:3.500A) removed outlier: 3.513A 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=AD3, first strand: chain 'M' and resid 664 through 666 Processing sheet with id=AD4, first strand: chain 'A' and resid 266 through 273 removed outlier: 3.700A 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=AD5, first strand: chain 'A' and resid 498 through 499 removed outlier: 3.527A 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: 6.576A pdb=" N LEU A 551 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL A 592 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE A 553 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 7.208A 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=AD6, first strand: chain 'C' and resid 266 through 273 removed outlier: 3.702A 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=AD7, 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: 3.537A 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: 8.845A 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=AD8, first strand: chain 'E' and resid 266 through 273 removed outlier: 3.701A 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=AD9, 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: 3.535A pdb=" N GLY E 511 " --> pdb=" O ILE E 522 " (cutoff:3.500A) removed outlier: 6.574A 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: 8.847A pdb=" N PHE E 616 " --> pdb=" O LYS E 589 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR E 591 " --> pdb=" O PHE E 616 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 59 through 61 removed outlier: 6.869A pdb=" N LEU H 16 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 8.457A 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: 6.709A 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: 6.678A pdb=" N LEU H 17 " --> pdb=" O HIS H 90 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE H 89 " --> pdb=" O GLU H 112 " (cutoff:3.500A) Processing sheet with id=AE2, 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=AE3, 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: 8.111A 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: 6.629A 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=AE4, first strand: chain 'H' and resid 321 through 322 Processing sheet with id=AE5, 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=AE6, first strand: chain 'H' and resid 507 through 514 Processing sheet with id=AE7, 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: 3.630A 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: 3.998A 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=AE8, first strand: chain 'H' and resid 664 through 666 Processing sheet with id=AE9, 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: 8.206A 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: 6.678A pdb=" N LEU J 17 " --> pdb=" O HIS J 90 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE J 89 " --> pdb=" O GLU J 112 " (cutoff:3.500A) Processing sheet with id=AF1, 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: 5.127A 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=AF2, 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: 7.479A 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=AF3, first strand: chain 'J' and resid 321 through 322 Processing sheet with id=AF4, first strand: chain 'J' and resid 374 through 375 removed outlier: 3.752A pdb=" N PHE J 374 " --> pdb=" O ALA J 435 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 507 through 514 Processing sheet with id=AF6, first strand: chain 'J' and resid 532 through 537 removed outlier: 4.244A pdb=" N ILE J 561 " --> pdb=" O ALA J 581 " (cutoff:3.500A) removed outlier: 3.631A 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: 3.997A pdb=" N ILE J 589 " --> pdb=" O LEU J 578 " (cutoff:3.500A) removed outlier: 3.514A 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=AF7, first strand: chain 'J' and resid 664 through 666 Processing sheet with id=AF8, 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: 8.457A 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: 6.710A 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: 3.655A pdb=" N ILE L 89 " --> pdb=" O GLU L 112 " (cutoff:3.500A) Processing sheet with id=AF9, 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=AG1, 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=AG2, first strand: chain 'L' and resid 321 through 322 Processing sheet with id=AG3, 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=AG4, first strand: chain 'L' and resid 507 through 514 Processing sheet with id=AG5, 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: 3.546A 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: 3.515A 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=AG6, first strand: chain 'L' 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: 25.37 Time building geometry restraints manager: 13.80 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: 18882 1.34 - 1.46: 9112 1.46 - 1.58: 30530 1.58 - 1.70: 0 1.70 - 1.82: 486 Bond restraints: 59010 Sorted by residual: bond pdb=" CA LEU F 178 " pdb=" C LEU F 178 " ideal model delta sigma weight residual 1.524 1.479 0.046 1.24e-02 6.50e+03 1.36e+01 bond pdb=" CA LEU B 178 " pdb=" C LEU B 178 " ideal model delta sigma weight residual 1.524 1.479 0.046 1.24e-02 6.50e+03 1.35e+01 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 1.34e+01 bond pdb=" CA GLU A 143 " pdb=" C GLU A 143 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.34e-02 5.57e+03 1.32e+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 1.30e+01 ... (remaining 59005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 78073 2.77 - 5.54: 1481 5.54 - 8.31: 171 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 97.88 13.83 1.15e+00 7.56e-01 1.45e+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 97.93 13.78 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 97.94 13.77 1.15e+00 7.56e-01 1.43e+02 angle pdb=" N ARG A 144 " pdb=" CA ARG A 144 " pdb=" C ARG A 144 " ideal model delta sigma weight residual 111.71 97.95 13.76 1.15e+00 7.56e-01 1.43e+02 ... (remaining 79771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 31919 16.06 - 32.11: 2896 32.11 - 48.17: 604 48.17 - 64.23: 143 64.23 - 80.28: 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 180.00 156.23 23.77 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 180.00 156.27 23.73 0 5.00e+00 4.00e-02 2.25e+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: 6484 0.048 - 0.096: 1708 0.096 - 0.145: 555 0.145 - 0.193: 60 0.193 - 0.241: 19 Chirality restraints: 8826 Sorted by residual: 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 1.45e+00 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 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 1.43e+00 ... (remaining 8823 not shown) Planarity restraints: 10464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTI D 801 " -0.014 2.00e-02 2.50e+03 3.66e-02 2.01e+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 F 801 " 0.014 2.00e-02 2.50e+03 3.61e-02 1.95e+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 " 0.053 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 delta sigma weight rms_deltas residual plane pdb=" C3 BTI B 801 " 0.015 2.00e-02 2.50e+03 3.58e-02 1.92e+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 ... (remaining 10461 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 39 2.13 - 2.82: 18329 2.82 - 3.51: 82251 3.51 - 4.21: 130451 4.21 - 4.90: 223047 Nonbonded interactions: 454117 Sorted by model distance: nonbonded pdb=" ND1 HIS M 257 " pdb=" OE1 GLU L 261 " model vdw 1.432 3.120 nonbonded pdb=" OE1 GLU I 261 " pdb=" ND1 HIS H 257 " model vdw 1.446 3.120 nonbonded pdb=" OE1 GLU K 261 " pdb=" ND1 HIS J 257 " model vdw 1.618 3.120 nonbonded pdb=" ND1 HIS I 257 " pdb=" OE1 GLU H 261 " model vdw 1.664 3.120 nonbonded pdb=" ND1 HIS K 257 " pdb=" OE1 GLU J 261 " model vdw 1.682 3.120 ... (remaining 454112 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.690 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: 0.080 Extract box with map and model: 1.860 Check model and map are aligned: 0.340 Set scattering table: 0.440 Process input model: 104.430 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.410 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: 0.030 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5495 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= 0.350 Angle : 0.930 13.850 79776 Z= 0.587 Chirality : 0.049 0.241 8826 Planarity : 0.005 0.091 10464 Dihedral : 13.028 80.285 21990 Min Nonbonded Distance : 1.432 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.39 % Allowed : 2.63 % Favored : 96.98 % 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 0.008 0.001 TRP J 488 HIS 0.012 0.002 HIS A 311 PHE 0.022 0.002 PHE C 500 TYR 0.037 0.002 TYR A 504 ARG 0.006 0.001 ARG E 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 1798 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 1774 time to evaluate : 5.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 MET cc_start: 0.5980 (tpp) cc_final: 0.5510 (tpp) REVERT: D 135 TYR cc_start: 0.4758 (m-80) cc_final: 0.4171 (t80) REVERT: D 488 ILE cc_start: 0.8332 (pt) cc_final: 0.7953 (mt) REVERT: D 549 VAL cc_start: 0.8054 (t) cc_final: 0.7846 (t) REVERT: F 425 THR cc_start: 0.6098 (p) cc_final: 0.5745 (t) REVERT: F 438 VAL cc_start: 0.6184 (t) cc_final: 0.5858 (t) REVERT: I 34 GLU cc_start: 0.7664 (mm-30) cc_final: 0.6921 (mt-10) REVERT: I 260 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6017 (mmt) REVERT: I 295 GLU cc_start: 0.6582 (pt0) cc_final: 0.6322 (tp30) REVERT: I 327 LYS cc_start: 0.7984 (tttt) cc_final: 0.7774 (ttmt) REVERT: I 342 GLN cc_start: 0.5012 (tm-30) cc_final: 0.4741 (tm-30) REVERT: I 377 GLU cc_start: 0.6955 (tp30) cc_final: 0.6701 (tp30) REVERT: I 506 THR cc_start: 0.6298 (m) cc_final: 0.5407 (p) REVERT: I 652 MET cc_start: 0.6751 (tpt) cc_final: 0.6536 (mmt) REVERT: K 34 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6983 (mt-10) REVERT: K 233 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8512 (t) REVERT: K 244 ARG cc_start: 0.6590 (ttp80) cc_final: 0.6004 (tmm-80) REVERT: K 260 MET cc_start: 0.6504 (OUTLIER) cc_final: 0.6275 (mmt) REVERT: K 506 THR cc_start: 0.6411 (m) cc_final: 0.5920 (m) REVERT: K 604 ASP cc_start: 0.4480 (p0) cc_final: 0.3989 (p0) REVERT: M 215 LYS cc_start: 0.6721 (tttm) cc_final: 0.6481 (tptt) REVERT: M 231 ARG cc_start: 0.6999 (tpt170) cc_final: 0.6675 (mmp-170) REVERT: M 295 GLU cc_start: 0.7155 (pt0) cc_final: 0.6885 (tp30) REVERT: M 296 PHE cc_start: 0.7470 (p90) cc_final: 0.7083 (p90) REVERT: M 342 GLN cc_start: 0.6313 (tm-30) cc_final: 0.6051 (tp40) REVERT: M 352 ILE cc_start: 0.7679 (mt) cc_final: 0.7346 (mt) REVERT: A 216 HIS cc_start: 0.3440 (t-90) cc_final: 0.3019 (t-90) REVERT: A 425 THR cc_start: 0.6393 (p) cc_final: 0.5907 (t) REVERT: A 544 CYS cc_start: 0.7496 (m) cc_final: 0.7039 (m) REVERT: A 626 MET cc_start: 0.2796 (ttp) cc_final: 0.2527 (tpt) REVERT: C 135 TYR cc_start: 0.4637 (m-80) cc_final: 0.4329 (t80) REVERT: C 179 ARG cc_start: 0.6448 (mtp-110) cc_final: 0.5797 (mmm160) REVERT: C 425 THR cc_start: 0.6226 (p) cc_final: 0.5629 (t) REVERT: E 178 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6530 (tt) REVERT: H 34 GLU cc_start: 0.7521 (mm-30) cc_final: 0.6777 (mt-10) REVERT: H 226 PHE cc_start: 0.6520 (m-80) cc_final: 0.6089 (m-80) REVERT: H 231 ARG cc_start: 0.6854 (tpt170) cc_final: 0.6435 (tpp-160) REVERT: H 342 GLN cc_start: 0.4993 (tm-30) cc_final: 0.4729 (tm-30) REVERT: H 377 GLU cc_start: 0.6820 (tp30) cc_final: 0.6619 (tp30) REVERT: H 506 THR cc_start: 0.6059 (m) cc_final: 0.5198 (p) REVERT: J 17 LEU cc_start: 0.7699 (tp) cc_final: 0.7446 (tt) REVERT: J 215 LYS cc_start: 0.6910 (tttm) cc_final: 0.6527 (tptt) REVERT: J 311 VAL cc_start: 0.8023 (t) cc_final: 0.7754 (t) REVERT: J 316 CYS cc_start: 0.6225 (p) cc_final: 0.5950 (p) REVERT: J 506 THR cc_start: 0.6325 (m) cc_final: 0.5893 (p) REVERT: L 20 ASN cc_start: 0.6806 (m-40) cc_final: 0.6574 (t0) REVERT: L 34 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7414 (mt-10) REVERT: L 231 ARG cc_start: 0.6953 (tpt170) cc_final: 0.6182 (tpp-160) REVERT: L 244 ARG cc_start: 0.6658 (ttp80) cc_final: 0.6260 (tmm-80) REVERT: L 260 MET cc_start: 0.6610 (OUTLIER) cc_final: 0.6319 (mmt) REVERT: L 326 VAL cc_start: 0.8124 (t) cc_final: 0.7839 (p) REVERT: L 327 LYS cc_start: 0.7580 (tttt) cc_final: 0.7326 (tttp) REVERT: L 496 TRP cc_start: 0.4302 (m100) cc_final: 0.4038 (m100) REVERT: L 604 ASP cc_start: 0.4724 (p0) cc_final: 0.4287 (p0) outliers start: 24 outliers final: 1 residues processed: 1787 average time/residue: 0.6299 time to fit residues: 1789.4303 Evaluate side-chains 755 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 749 time to evaluate : 5.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 260 MET Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain K residue 260 MET Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain J residue 260 MET Chi-restraints excluded: chain L residue 260 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 623 optimal weight: 6.9990 chunk 559 optimal weight: 7.9990 chunk 310 optimal weight: 4.9990 chunk 191 optimal weight: 0.7980 chunk 377 optimal weight: 2.9990 chunk 298 optimal weight: 0.4980 chunk 578 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 351 optimal weight: 7.9990 chunk 430 optimal weight: 9.9990 chunk 670 optimal weight: 9.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 HIS B 186 GLN B 216 HIS B 446 HIS B 506 ASN B 526 GLN ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 HIS D 151 ASN D 186 GLN D 309 GLN D 447 ASN D 546 GLN F 186 GLN ** F 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 GLN I 20 ASN I 36 HIS I 219 HIS ** I 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 540 HIS K 36 HIS ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 247 GLN K 495 ASN K 540 HIS M 36 HIS M 219 HIS M 329 GLN M 403 HIS ** M 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 540 HIS A 138 HIS A 151 ASN A 186 GLN A 300 HIS A 526 GLN C 138 HIS C 186 GLN E 138 HIS E 151 ASN E 186 GLN E 447 ASN E 546 GLN H 36 HIS H 219 HIS ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 540 HIS ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 HIS J 219 HIS ** J 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 329 GLN J 403 HIS ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 540 HIS L 36 HIS ** L 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 GLN ** L 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 495 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 59010 Z= 0.278 Angle : 0.733 14.884 79776 Z= 0.377 Chirality : 0.048 0.222 8826 Planarity : 0.006 0.073 10464 Dihedral : 5.232 40.908 8307 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.73 % Allowed : 12.06 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (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: -1.05 (0.10), residues: 7440 helix: 0.47 (0.11), residues: 2256 sheet: 1.16 (0.15), residues: 1008 loop : -1.95 (0.09), residues: 4176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 488 HIS 0.010 0.002 HIS L 654 PHE 0.025 0.002 PHE I 296 TYR 0.028 0.002 TYR F 142 ARG 0.016 0.001 ARG A 213 *********************** 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 937 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 770 time to evaluate : 5.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 143 GLU cc_start: 0.6015 (OUTLIER) cc_final: 0.4692 (tt0) REVERT: D 168 MET cc_start: 0.7134 (tmm) cc_final: 0.6615 (ttp) REVERT: D 179 ARG cc_start: 0.6264 (mtp-110) cc_final: 0.6031 (ttt180) REVERT: F 168 MET cc_start: 0.7586 (tmm) cc_final: 0.7110 (ttp) REVERT: F 179 ARG cc_start: 0.6122 (mtp-110) cc_final: 0.5780 (mtp180) REVERT: F 518 MET cc_start: 0.6885 (mtm) cc_final: 0.6304 (mtm) REVERT: F 673 ARG cc_start: 0.5221 (mtt180) cc_final: 0.4461 (mtm180) REVERT: I 34 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7123 (mm-30) REVERT: I 268 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6751 (tp30) REVERT: I 272 GLN cc_start: 0.7561 (mt0) cc_final: 0.6302 (tp-100) REVERT: I 301 MET cc_start: 0.5792 (ppp) cc_final: 0.5551 (ppp) REVERT: I 377 GLU cc_start: 0.7050 (tp30) cc_final: 0.6796 (tp30) REVERT: K 215 LYS cc_start: 0.7021 (tttm) cc_final: 0.6788 (tptt) REVERT: K 268 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6956 (mm-30) REVERT: K 272 GLN cc_start: 0.7653 (mt0) cc_final: 0.7022 (mm110) REVERT: K 308 GLU cc_start: 0.6589 (mm-30) cc_final: 0.6363 (mm-30) REVERT: K 374 PHE cc_start: 0.7034 (t80) cc_final: 0.6808 (t80) REVERT: K 652 MET cc_start: 0.4857 (mmt) cc_final: 0.4589 (mmm) REVERT: M 34 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6907 (mt-10) REVERT: M 231 ARG cc_start: 0.6999 (tpt170) cc_final: 0.6753 (mmp-170) REVERT: M 237 GLU cc_start: 0.7495 (mp0) cc_final: 0.7100 (mp0) REVERT: M 308 GLU cc_start: 0.6601 (mm-30) cc_final: 0.6101 (mm-30) REVERT: M 353 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7583 (tm-30) REVERT: A 338 PHE cc_start: 0.5923 (t80) cc_final: 0.5672 (m-80) REVERT: A 348 MET cc_start: 0.6618 (mmt) cc_final: 0.6417 (mmt) REVERT: A 673 ARG cc_start: 0.5465 (mtt180) cc_final: 0.4800 (mtm180) REVERT: C 179 ARG cc_start: 0.6029 (mtp-110) cc_final: 0.5502 (mtp180) REVERT: C 522 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.6440 (mp) REVERT: E 179 ARG cc_start: 0.6010 (mtp-110) cc_final: 0.5700 (mtp180) REVERT: E 190 VAL cc_start: 0.6048 (t) cc_final: 0.5787 (t) REVERT: E 250 TYR cc_start: 0.4593 (m-80) cc_final: 0.4179 (m-80) REVERT: E 251 TRP cc_start: 0.4377 (t60) cc_final: 0.4156 (t60) REVERT: E 554 LEU cc_start: 0.7760 (mt) cc_final: 0.7497 (mt) REVERT: H 34 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7252 (mt-10) REVERT: H 231 ARG cc_start: 0.6998 (tpt170) cc_final: 0.6665 (tpp-160) REVERT: H 268 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6453 (tp30) REVERT: H 272 GLN cc_start: 0.7228 (mt0) cc_final: 0.6153 (tp-100) REVERT: H 483 MET cc_start: 0.7085 (mpp) cc_final: 0.6849 (mmt) REVERT: J 215 LYS cc_start: 0.6973 (tttm) cc_final: 0.6634 (tptt) REVERT: J 301 MET cc_start: 0.5841 (ptm) cc_final: 0.5472 (ptm) REVERT: J 342 GLN cc_start: 0.6805 (tm-30) cc_final: 0.6590 (tp40) REVERT: J 563 ASN cc_start: 0.6815 (OUTLIER) cc_final: 0.6391 (m110) REVERT: L 215 LYS cc_start: 0.7067 (tttm) cc_final: 0.6768 (tptt) REVERT: L 231 ARG cc_start: 0.6891 (tpt170) cc_final: 0.6101 (tpp-160) REVERT: L 260 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.5610 (mmt) REVERT: L 268 GLU cc_start: 0.7291 (mm-30) cc_final: 0.5930 (tp30) REVERT: L 272 GLN cc_start: 0.7697 (mt0) cc_final: 0.6876 (mm110) REVERT: L 483 MET cc_start: 0.7154 (mpp) cc_final: 0.6921 (mmm) outliers start: 167 outliers final: 101 residues processed: 895 average time/residue: 0.5728 time to fit residues: 852.4103 Evaluate side-chains 633 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 528 time to evaluate : 5.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 501 LYS Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 506 ASN Chi-restraints excluded: chain F residue 510 CYS Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 636 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 563 ASN Chi-restraints excluded: chain I residue 577 VAL Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 217 SER Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 412 ILE Chi-restraints excluded: chain K residue 447 CYS Chi-restraints excluded: chain K residue 506 THR Chi-restraints excluded: chain K residue 577 VAL Chi-restraints excluded: chain M residue 412 ILE Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 563 ASN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 605 MET Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 369 TYR Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 396 GLU Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 506 THR Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 217 SER Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 412 ILE Chi-restraints excluded: chain J residue 447 CYS Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 563 ASN Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 217 SER Chi-restraints excluded: chain L residue 260 MET Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 577 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 372 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 557 optimal weight: 9.9990 chunk 456 optimal weight: 9.9990 chunk 184 optimal weight: 20.0000 chunk 671 optimal weight: 1.9990 chunk 725 optimal weight: 10.0000 chunk 597 optimal weight: 7.9990 chunk 665 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 538 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN B 186 GLN B 309 GLN B 442 ASN ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 HIS D 151 ASN D 355 GLN D 442 ASN F 304 GLN F 442 ASN F 447 ASN I 20 ASN I 247 GLN I 306 GLN I 380 GLN I 495 ASN I 503 ASN K 85 ASN K 219 HIS ** K 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS M 302 ASN ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 HIS A 442 ASN C 138 HIS C 309 GLN ** C 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN E 186 GLN E 309 GLN E 355 GLN E 442 ASN H 20 ASN H 380 GLN ** H 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 ASN J 302 ASN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 540 HIS L 20 ASN ** L 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 ASN L 219 HIS ** L 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.6228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 59010 Z= 0.385 Angle : 0.815 12.899 79776 Z= 0.424 Chirality : 0.051 0.252 8826 Planarity : 0.007 0.095 10464 Dihedral : 5.879 54.466 8295 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.95 % Allowed : 16.19 % Favored : 79.85 % 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: -1.40 (0.09), residues: 7440 helix: 0.19 (0.11), residues: 2262 sheet: 0.89 (0.16), residues: 1008 loop : -2.16 (0.09), residues: 4170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP H 538 HIS 0.023 0.002 HIS F 539 PHE 0.031 0.003 PHE B 540 TYR 0.031 0.003 TYR L 432 ARG 0.013 0.001 ARG C 686 *********************** 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 820 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 578 time to evaluate : 5.148 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: B 143 GLU cc_start: 0.5193 (OUTLIER) cc_final: 0.4809 (mt-10) REVERT: B 488 ILE cc_start: 0.8180 (pt) cc_final: 0.7811 (mm) REVERT: D 143 GLU cc_start: 0.5134 (OUTLIER) cc_final: 0.3861 (tt0) REVERT: D 179 ARG cc_start: 0.6803 (mtp-110) cc_final: 0.6564 (mtp180) REVERT: D 477 ASP cc_start: 0.4381 (p0) cc_final: 0.3938 (p0) REVERT: D 626 MET cc_start: 0.2502 (tpt) cc_final: 0.2152 (tpt) REVERT: D 668 TYR cc_start: 0.3760 (m-80) cc_final: 0.3169 (m-80) REVERT: F 179 ARG cc_start: 0.6406 (mtp-110) cc_final: 0.6130 (mtm180) REVERT: F 360 MET cc_start: 0.5106 (OUTLIER) cc_final: 0.4150 (mtt) REVERT: F 488 ILE cc_start: 0.8388 (pt) cc_final: 0.7969 (mm) REVERT: F 673 ARG cc_start: 0.5484 (mtt180) cc_final: 0.4995 (mtt90) REVERT: I 453 PHE cc_start: 0.6699 (OUTLIER) cc_final: 0.6259 (p90) REVERT: I 513 TYR cc_start: 0.5493 (t80) cc_final: 0.5281 (t80) REVERT: I 563 ASN cc_start: 0.7349 (OUTLIER) cc_final: 0.6701 (m110) REVERT: K 308 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6488 (mm-30) REVERT: K 353 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7872 (tm-30) REVERT: K 404 TYR cc_start: 0.4485 (OUTLIER) cc_final: 0.2986 (m-80) REVERT: K 453 PHE cc_start: 0.6725 (OUTLIER) cc_final: 0.6084 (p90) REVERT: K 652 MET cc_start: 0.4530 (mmt) cc_final: 0.4326 (mmm) REVERT: M 34 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6497 (mm-30) REVERT: M 179 MET cc_start: 0.2095 (mmm) cc_final: 0.1048 (ppp) REVERT: M 231 ARG cc_start: 0.7146 (tpt170) cc_final: 0.6651 (mmp-170) REVERT: M 251 GLU cc_start: 0.6363 (mp0) cc_final: 0.5972 (mp0) REVERT: M 299 MET cc_start: 0.6857 (tpt) cc_final: 0.6581 (tpt) REVERT: M 353 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7683 (tm-30) REVERT: M 404 TYR cc_start: 0.5379 (OUTLIER) cc_final: 0.4200 (m-80) REVERT: M 453 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.6215 (p90) REVERT: M 563 ASN cc_start: 0.7032 (OUTLIER) cc_final: 0.6305 (m110) REVERT: M 599 LEU cc_start: 0.8173 (tp) cc_final: 0.7801 (tp) REVERT: A 143 GLU cc_start: 0.4966 (OUTLIER) cc_final: 0.3799 (mt-10) REVERT: A 369 TYR cc_start: 0.4145 (m-80) cc_final: 0.3390 (m-10) REVERT: A 488 ILE cc_start: 0.8269 (pt) cc_final: 0.7777 (mm) REVERT: A 673 ARG cc_start: 0.5734 (mtt180) cc_final: 0.5169 (mtm180) REVERT: C 144 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6659 (mmm160) REVERT: C 168 MET cc_start: 0.7620 (tmm) cc_final: 0.7321 (ttp) REVERT: C 179 ARG cc_start: 0.6406 (mtp-110) cc_final: 0.6151 (mtm180) REVERT: C 292 TYR cc_start: 0.3654 (p90) cc_final: 0.3356 (p90) REVERT: C 488 ILE cc_start: 0.8262 (pt) cc_final: 0.7874 (mm) REVERT: E 143 GLU cc_start: 0.5156 (OUTLIER) cc_final: 0.3930 (tt0) REVERT: E 179 ARG cc_start: 0.6591 (mtp-110) cc_final: 0.6247 (mtp85) REVERT: E 477 ASP cc_start: 0.4160 (p0) cc_final: 0.3691 (p0) REVERT: E 500 PHE cc_start: 0.4581 (m-10) cc_final: 0.4254 (m-10) REVERT: E 626 MET cc_start: 0.2843 (tpt) cc_final: 0.2619 (tpt) REVERT: H 231 ARG cc_start: 0.7175 (tpt170) cc_final: 0.6877 (mmp-170) REVERT: H 404 TYR cc_start: 0.5050 (OUTLIER) cc_final: 0.3807 (m-80) REVERT: H 453 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.6317 (p90) REVERT: H 483 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6819 (mmt) REVERT: J 179 MET cc_start: 0.2264 (mmm) cc_final: 0.1381 (ppp) REVERT: J 215 LYS cc_start: 0.7205 (tttm) cc_final: 0.6901 (tptt) REVERT: J 237 GLU cc_start: 0.7423 (mp0) cc_final: 0.7113 (mp0) REVERT: J 251 GLU cc_start: 0.6070 (mp0) cc_final: 0.5780 (mp0) REVERT: J 299 MET cc_start: 0.7406 (ttp) cc_final: 0.6981 (tpt) REVERT: J 300 GLU cc_start: 0.7317 (tt0) cc_final: 0.7004 (tt0) REVERT: J 308 GLU cc_start: 0.6692 (mm-30) cc_final: 0.6437 (mm-30) REVERT: J 317 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6258 (mmt-90) REVERT: J 404 TYR cc_start: 0.5200 (OUTLIER) cc_final: 0.3610 (m-80) REVERT: J 453 PHE cc_start: 0.6930 (OUTLIER) cc_final: 0.6404 (p90) REVERT: J 563 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.6968 (m110) REVERT: J 602 LEU cc_start: 0.3714 (OUTLIER) cc_final: 0.3357 (tp) REVERT: L 21 ARG cc_start: 0.7503 (ttp-170) cc_final: 0.5621 (ttp-170) REVERT: L 34 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6833 (mm-30) REVERT: L 231 ARG cc_start: 0.7077 (tpt170) cc_final: 0.6744 (mmp-170) REVERT: L 260 MET cc_start: 0.6721 (mpt) cc_final: 0.5774 (mmt) REVERT: L 404 TYR cc_start: 0.4470 (OUTLIER) cc_final: 0.2821 (m-80) REVERT: L 453 PHE cc_start: 0.6764 (OUTLIER) cc_final: 0.6167 (p90) REVERT: L 483 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6649 (mmt) outliers start: 242 outliers final: 141 residues processed: 781 average time/residue: 0.5343 time to fit residues: 711.7288 Evaluate side-chains 604 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 439 time to evaluate : 5.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 422 HIS Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 422 HIS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 510 CYS Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 555 GLN Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 594 ILE Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 260 MET Chi-restraints excluded: chain I residue 314 GLU Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 392 THR Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 563 ASN Chi-restraints excluded: chain I residue 577 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 217 SER Chi-restraints excluded: chain K residue 260 MET Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 404 TYR Chi-restraints excluded: chain K residue 447 CYS Chi-restraints excluded: chain K residue 453 PHE Chi-restraints excluded: chain K residue 506 THR Chi-restraints excluded: chain K residue 577 VAL Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 266 ILE Chi-restraints excluded: chain M residue 404 TYR Chi-restraints excluded: chain M residue 434 VAL Chi-restraints excluded: chain M residue 453 PHE Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 491 ASN Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 563 ASN Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 605 MET Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 422 HIS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 636 THR Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 396 GLU Chi-restraints excluded: chain H residue 404 TYR Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 483 MET Chi-restraints excluded: chain H residue 506 THR Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain H residue 577 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 264 GLN Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 317 ARG Chi-restraints excluded: chain J residue 404 TYR Chi-restraints excluded: chain J residue 412 ILE Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain J residue 447 CYS Chi-restraints excluded: chain J residue 453 PHE Chi-restraints excluded: chain J residue 476 VAL Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 519 VAL Chi-restraints excluded: chain J residue 540 HIS Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 563 ASN Chi-restraints excluded: chain J residue 602 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 217 SER Chi-restraints excluded: chain L residue 284 THR Chi-restraints excluded: chain L residue 318 ILE Chi-restraints excluded: chain L residue 404 TYR Chi-restraints excluded: chain L residue 453 PHE Chi-restraints excluded: chain L residue 483 MET Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 577 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 663 optimal weight: 9.9990 chunk 504 optimal weight: 9.9990 chunk 348 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 320 optimal weight: 9.9990 chunk 450 optimal weight: 20.0000 chunk 673 optimal weight: 4.9990 chunk 713 optimal weight: 9.9990 chunk 352 optimal weight: 6.9990 chunk 638 optimal weight: 0.0040 chunk 192 optimal weight: 6.9990 overall best weight: 5.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN D 186 GLN ** I 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN ** M 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 306 GLN H 495 ASN J 495 ASN J 540 HIS ** L 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.7036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 59010 Z= 0.376 Angle : 0.753 13.577 79776 Z= 0.393 Chirality : 0.049 0.324 8826 Planarity : 0.007 0.079 10464 Dihedral : 5.866 56.018 8292 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 4.48 % Allowed : 18.61 % Favored : 76.91 % 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: -1.45 (0.09), residues: 7440 helix: 0.15 (0.10), residues: 2310 sheet: 0.80 (0.16), residues: 1074 loop : -2.24 (0.09), residues: 4056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 488 HIS 0.031 0.002 HIS J 540 PHE 0.024 0.002 PHE I 374 TYR 0.020 0.002 TYR J 432 ARG 0.007 0.001 ARG E 230 *********************** 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 782 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 274 poor density : 508 time to evaluate : 5.113 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: B 488 ILE cc_start: 0.8040 (pt) cc_final: 0.7573 (mm) REVERT: D 143 GLU cc_start: 0.4439 (OUTLIER) cc_final: 0.3429 (tt0) REVERT: D 626 MET cc_start: 0.2065 (tpt) cc_final: 0.1838 (tpt) REVERT: D 685 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8055 (t) REVERT: F 179 ARG cc_start: 0.6362 (mtp-110) cc_final: 0.6103 (mtm180) REVERT: F 477 ASP cc_start: 0.3589 (p0) cc_final: 0.3097 (p0) REVERT: F 488 ILE cc_start: 0.8231 (pt) cc_final: 0.7733 (mm) REVERT: F 500 PHE cc_start: 0.4592 (OUTLIER) cc_final: 0.4057 (m-10) REVERT: F 673 ARG cc_start: 0.5299 (mtt180) cc_final: 0.5012 (mtt90) REVERT: I 133 ILE cc_start: 0.6765 (mm) cc_final: 0.6563 (tp) REVERT: I 295 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7142 (tm-30) REVERT: I 404 TYR cc_start: 0.5106 (OUTLIER) cc_final: 0.4135 (m-80) REVERT: I 441 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7781 (mt) REVERT: I 453 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.6258 (p90) REVERT: K 34 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6593 (tp30) REVERT: K 404 TYR cc_start: 0.4827 (OUTLIER) cc_final: 0.3220 (m-80) REVERT: K 441 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7783 (mt) REVERT: K 453 PHE cc_start: 0.6578 (OUTLIER) cc_final: 0.5999 (p90) REVERT: K 652 MET cc_start: 0.4761 (mmt) cc_final: 0.4541 (mmm) REVERT: K 672 GLU cc_start: 0.5763 (mp0) cc_final: 0.4481 (pp20) REVERT: M 108 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.7156 (ttm110) REVERT: M 126 SER cc_start: 0.7248 (t) cc_final: 0.6937 (m) REVERT: M 179 MET cc_start: 0.2303 (mmm) cc_final: 0.1496 (ppp) REVERT: M 231 ARG cc_start: 0.7095 (tpt170) cc_final: 0.6700 (mmp-170) REVERT: M 251 GLU cc_start: 0.6087 (mp0) cc_final: 0.5787 (mp0) REVERT: M 295 GLU cc_start: 0.7723 (tp30) cc_final: 0.7484 (tp30) REVERT: M 299 MET cc_start: 0.6845 (tpt) cc_final: 0.6617 (tpt) REVERT: M 301 MET cc_start: 0.6609 (ptm) cc_final: 0.6326 (ttp) REVERT: M 353 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8100 (tm-30) REVERT: M 404 TYR cc_start: 0.5539 (OUTLIER) cc_final: 0.4807 (m-80) REVERT: M 407 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7567 (tpt) REVERT: M 453 PHE cc_start: 0.6831 (OUTLIER) cc_final: 0.6266 (p90) REVERT: M 465 GLU cc_start: 0.6895 (pm20) cc_final: 0.6680 (tp30) REVERT: M 488 TRP cc_start: 0.7686 (t60) cc_final: 0.7399 (t60) REVERT: M 563 ASN cc_start: 0.7202 (OUTLIER) cc_final: 0.6923 (m110) REVERT: A 222 MET cc_start: 0.4469 (OUTLIER) cc_final: 0.4204 (mtp) REVERT: C 143 GLU cc_start: 0.4949 (OUTLIER) cc_final: 0.3368 (mt-10) REVERT: C 144 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6919 (mmm160) REVERT: C 179 ARG cc_start: 0.6445 (mtp-110) cc_final: 0.6236 (mtm180) REVERT: C 477 ASP cc_start: 0.3908 (p0) cc_final: 0.3557 (p0) REVERT: C 488 ILE cc_start: 0.8272 (pt) cc_final: 0.7821 (mm) REVERT: E 143 GLU cc_start: 0.4601 (OUTLIER) cc_final: 0.3030 (mt-10) REVERT: E 288 LYS cc_start: 0.4178 (mptt) cc_final: 0.3951 (mtpt) REVERT: E 477 ASP cc_start: 0.4360 (p0) cc_final: 0.3806 (p0) REVERT: H 231 ARG cc_start: 0.7052 (tpt170) cc_final: 0.6835 (mmp-170) REVERT: H 265 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7192 (ttp80) REVERT: H 295 GLU cc_start: 0.7395 (tp30) cc_final: 0.7081 (tp30) REVERT: H 404 TYR cc_start: 0.4916 (OUTLIER) cc_final: 0.4022 (m-80) REVERT: H 453 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.6174 (p90) REVERT: H 483 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6811 (mmt) REVERT: J 251 GLU cc_start: 0.6187 (mp0) cc_final: 0.5840 (mp0) REVERT: J 299 MET cc_start: 0.7412 (ttp) cc_final: 0.7063 (tpt) REVERT: J 353 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7782 (tm-30) REVERT: J 404 TYR cc_start: 0.5285 (OUTLIER) cc_final: 0.4245 (m-80) REVERT: J 407 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7585 (tpt) REVERT: J 453 PHE cc_start: 0.6952 (OUTLIER) cc_final: 0.6448 (p90) REVERT: J 563 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.7041 (m110) REVERT: L 21 ARG cc_start: 0.7564 (ttp-170) cc_final: 0.6308 (ttp-170) REVERT: L 34 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6770 (mm-30) REVERT: L 231 ARG cc_start: 0.6775 (tpt170) cc_final: 0.6569 (mmp-170) REVERT: L 260 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.5610 (mmt) REVERT: L 317 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6995 (mmt90) REVERT: L 404 TYR cc_start: 0.4781 (OUTLIER) cc_final: 0.3228 (m-80) REVERT: L 441 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7774 (mt) REVERT: L 453 PHE cc_start: 0.6730 (OUTLIER) cc_final: 0.6097 (p90) REVERT: L 483 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6519 (mmt) REVERT: L 490 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7011 (mm) outliers start: 274 outliers final: 151 residues processed: 740 average time/residue: 0.5563 time to fit residues: 708.9187 Evaluate side-chains 610 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 424 time to evaluate : 5.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 422 HIS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 555 GLN Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 500 PHE Chi-restraints excluded: chain F residue 510 CYS Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 555 GLN Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 594 ILE Chi-restraints excluded: chain F residue 636 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 679 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 260 MET Chi-restraints excluded: chain I residue 295 GLU Chi-restraints excluded: chain I residue 314 GLU Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 404 TYR Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 441 ILE Chi-restraints excluded: chain I residue 447 CYS Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 577 VAL Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 217 SER Chi-restraints excluded: chain K residue 228 LYS Chi-restraints excluded: chain K residue 260 MET Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 346 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 404 TYR Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 412 ILE Chi-restraints excluded: chain K residue 441 ILE Chi-restraints excluded: chain K residue 447 CYS Chi-restraints excluded: chain K residue 453 PHE Chi-restraints excluded: chain K residue 506 THR Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 577 VAL Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 108 ARG Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 266 ILE Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain M residue 346 THR Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain M residue 404 TYR Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 453 PHE Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 491 ASN Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 563 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 605 MET Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 375 ASP Chi-restraints excluded: chain E residue 422 HIS Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 154 PHE Chi-restraints excluded: chain H residue 265 ARG Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 396 GLU Chi-restraints excluded: chain H residue 404 TYR Chi-restraints excluded: chain H residue 411 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 483 MET Chi-restraints excluded: chain H residue 506 THR Chi-restraints excluded: chain H residue 568 LEU Chi-restraints excluded: chain H residue 577 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 264 GLN Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 318 ILE Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 404 TYR Chi-restraints excluded: chain J residue 407 MET Chi-restraints excluded: chain J residue 412 ILE Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain J residue 447 CYS Chi-restraints excluded: chain J residue 453 PHE Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 563 ASN Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 217 SER Chi-restraints excluded: chain L residue 228 LYS Chi-restraints excluded: chain L residue 260 MET Chi-restraints excluded: chain L residue 284 THR Chi-restraints excluded: chain L residue 317 ARG Chi-restraints excluded: chain L residue 318 ILE Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 404 TYR Chi-restraints excluded: chain L residue 412 ILE Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 447 CYS Chi-restraints excluded: chain L residue 453 PHE Chi-restraints excluded: chain L residue 483 MET Chi-restraints excluded: chain L residue 490 LEU Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 547 CYS Chi-restraints excluded: chain L residue 577 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 594 optimal weight: 9.9990 chunk 404 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 531 optimal weight: 20.0000 chunk 294 optimal weight: 0.0000 chunk 608 optimal weight: 3.9990 chunk 493 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 364 optimal weight: 3.9990 chunk 640 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 GLN B 447 ASN D 138 HIS D 186 GLN D 442 ASN F 442 ASN I 20 ASN K 20 ASN K 99 ASN K 529 ASN ** M 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 660 GLN A 151 ASN A 304 GLN A 442 ASN A 447 ASN C 309 GLN E 442 ASN H 529 ASN J 20 ASN J 302 ASN L 563 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.7268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 59010 Z= 0.235 Angle : 0.648 12.158 79776 Z= 0.334 Chirality : 0.046 0.205 8826 Planarity : 0.005 0.057 10464 Dihedral : 5.449 54.967 8292 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 4.26 % Allowed : 19.61 % Favored : 76.13 % 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: -1.18 (0.09), residues: 7440 helix: 0.51 (0.11), residues: 2352 sheet: 0.89 (0.15), residues: 1092 loop : -2.20 (0.09), residues: 3996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 488 HIS 0.009 0.001 HIS M 654 PHE 0.024 0.002 PHE H 298 TYR 0.017 0.002 TYR A 262 ARG 0.006 0.001 ARG M 389 *********************** 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 754 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 261 poor density : 493 time to evaluate : 5.204 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: B 168 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.6569 (tmm) REVERT: D 143 GLU cc_start: 0.4327 (OUTLIER) cc_final: 0.3436 (tt0) REVERT: D 360 MET cc_start: 0.4923 (mtt) cc_final: 0.4683 (mtt) REVERT: D 554 LEU cc_start: 0.7753 (mp) cc_final: 0.7337 (mt) REVERT: D 626 MET cc_start: 0.2240 (tpt) cc_final: 0.1954 (tpt) REVERT: F 421 ASP cc_start: 0.5986 (OUTLIER) cc_final: 0.5736 (m-30) REVERT: F 500 PHE cc_start: 0.4491 (OUTLIER) cc_final: 0.3903 (m-10) REVERT: I 272 GLN cc_start: 0.7810 (mt0) cc_final: 0.7212 (mm110) REVERT: I 404 TYR cc_start: 0.4928 (OUTLIER) cc_final: 0.4117 (m-80) REVERT: I 563 ASN cc_start: 0.7218 (OUTLIER) cc_final: 0.6803 (m110) REVERT: I 631 LEU cc_start: 0.5737 (OUTLIER) cc_final: 0.4763 (mt) REVERT: K 34 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6676 (tp30) REVERT: K 404 TYR cc_start: 0.4836 (OUTLIER) cc_final: 0.3332 (m-80) REVERT: K 407 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7619 (tpt) REVERT: K 441 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7789 (mt) REVERT: K 453 PHE cc_start: 0.6591 (OUTLIER) cc_final: 0.5989 (p90) REVERT: K 602 LEU cc_start: 0.3979 (OUTLIER) cc_final: 0.3601 (tt) REVERT: K 672 GLU cc_start: 0.5821 (mp0) cc_final: 0.5589 (mm-30) REVERT: M 108 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.7082 (ttm110) REVERT: M 126 SER cc_start: 0.7283 (t) cc_final: 0.6937 (m) REVERT: M 179 MET cc_start: 0.2095 (mmm) cc_final: 0.1696 (ppp) REVERT: M 231 ARG cc_start: 0.7093 (tpt170) cc_final: 0.6697 (mmp-170) REVERT: M 299 MET cc_start: 0.6579 (tpt) cc_final: 0.6344 (tpt) REVERT: M 353 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8190 (tm-30) REVERT: M 404 TYR cc_start: 0.5528 (OUTLIER) cc_final: 0.4769 (m-80) REVERT: M 407 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7420 (tpt) REVERT: M 441 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7607 (mt) REVERT: M 453 PHE cc_start: 0.6602 (OUTLIER) cc_final: 0.6105 (p90) REVERT: M 465 GLU cc_start: 0.6858 (pm20) cc_final: 0.6597 (tp30) REVERT: M 650 MET cc_start: 0.4830 (tmm) cc_final: 0.3969 (ttm) REVERT: A 222 MET cc_start: 0.4316 (OUTLIER) cc_final: 0.3956 (mtp) REVERT: A 474 MET cc_start: 0.2782 (mmm) cc_final: 0.2518 (mmm) REVERT: A 634 VAL cc_start: 0.6941 (t) cc_final: 0.6713 (p) REVERT: A 694 ARG cc_start: 0.7233 (mtt90) cc_final: 0.6985 (mtp85) REVERT: C 144 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6098 (mmm160) REVERT: C 179 ARG cc_start: 0.6200 (mtp-110) cc_final: 0.5996 (mtm180) REVERT: C 477 ASP cc_start: 0.4107 (p0) cc_final: 0.3690 (p0) REVERT: C 668 TYR cc_start: 0.3700 (m-80) cc_final: 0.3348 (m-80) REVERT: E 143 GLU cc_start: 0.4139 (OUTLIER) cc_final: 0.3212 (tt0) REVERT: E 477 ASP cc_start: 0.4271 (p0) cc_final: 0.3818 (p0) REVERT: H 21 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6891 (ttp-170) REVERT: H 231 ARG cc_start: 0.7005 (tpt170) cc_final: 0.6736 (mmp-170) REVERT: H 295 GLU cc_start: 0.7615 (tp30) cc_final: 0.7217 (tp30) REVERT: H 453 PHE cc_start: 0.6622 (OUTLIER) cc_final: 0.6271 (p90) REVERT: H 483 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6162 (mpp) REVERT: H 500 PHE cc_start: 0.7174 (t80) cc_final: 0.6948 (t80) REVERT: H 563 ASN cc_start: 0.7245 (OUTLIER) cc_final: 0.6804 (m110) REVERT: J 299 MET cc_start: 0.7448 (ttp) cc_final: 0.7089 (tpt) REVERT: J 317 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6550 (mmt-90) REVERT: J 404 TYR cc_start: 0.5416 (OUTLIER) cc_final: 0.4725 (m-80) REVERT: J 407 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7489 (tpt) REVERT: J 441 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7687 (mt) REVERT: J 453 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.6345 (p90) REVERT: J 490 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6959 (mm) REVERT: L 21 ARG cc_start: 0.7525 (ttp-170) cc_final: 0.6646 (ttp-170) REVERT: L 34 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6792 (mm-30) REVERT: L 231 ARG cc_start: 0.6886 (tpt170) cc_final: 0.6454 (mmp-170) REVERT: L 246 TYR cc_start: 0.6454 (m-80) cc_final: 0.6093 (m-80) REVERT: L 404 TYR cc_start: 0.4826 (OUTLIER) cc_final: 0.3641 (m-80) REVERT: L 407 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7496 (tpt) REVERT: L 441 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7812 (mt) REVERT: L 453 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.6156 (p90) REVERT: L 483 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6461 (mmt) outliers start: 261 outliers final: 140 residues processed: 711 average time/residue: 0.5634 time to fit residues: 693.9641 Evaluate side-chains 604 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 429 time to evaluate : 5.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 555 GLN Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 421 ASP Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 500 PHE Chi-restraints excluded: chain F residue 510 CYS Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 555 GLN Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 594 ILE Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 392 THR Chi-restraints excluded: chain I residue 404 TYR Chi-restraints excluded: chain I residue 412 ILE Chi-restraints excluded: chain I residue 447 CYS Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 545 GLU Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 563 ASN Chi-restraints excluded: chain I residue 631 LEU Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 217 SER Chi-restraints excluded: chain K residue 228 LYS Chi-restraints excluded: chain K residue 260 MET Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 404 TYR Chi-restraints excluded: chain K residue 407 MET Chi-restraints excluded: chain K residue 412 ILE Chi-restraints excluded: chain K residue 441 ILE Chi-restraints excluded: chain K residue 447 CYS Chi-restraints excluded: chain K residue 453 PHE Chi-restraints excluded: chain K residue 506 THR Chi-restraints excluded: chain K residue 602 LEU Chi-restraints excluded: chain K residue 664 VAL Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 108 ARG Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 264 GLN Chi-restraints excluded: chain M residue 266 ILE Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain M residue 404 TYR Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 434 VAL Chi-restraints excluded: chain M residue 437 ILE Chi-restraints excluded: chain M residue 441 ILE Chi-restraints excluded: chain M residue 453 PHE Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 545 GLU Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 605 MET Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 375 ASP Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 555 GLN Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain H residue 21 ARG Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 154 PHE Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 396 GLU Chi-restraints excluded: chain H residue 412 ILE Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 483 MET Chi-restraints excluded: chain H residue 506 THR Chi-restraints excluded: chain H residue 545 GLU Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain H residue 577 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 264 GLN Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 317 ARG Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 404 TYR Chi-restraints excluded: chain J residue 407 MET Chi-restraints excluded: chain J residue 411 VAL Chi-restraints excluded: chain J residue 412 ILE Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 447 CYS Chi-restraints excluded: chain J residue 453 PHE Chi-restraints excluded: chain J residue 476 VAL Chi-restraints excluded: chain J residue 490 LEU Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 545 GLU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 217 SER Chi-restraints excluded: chain L residue 284 THR Chi-restraints excluded: chain L residue 293 THR Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 404 TYR Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 447 CYS Chi-restraints excluded: chain L residue 453 PHE Chi-restraints excluded: chain L residue 483 MET Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 547 CYS Chi-restraints excluded: chain L residue 563 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 240 optimal weight: 10.0000 chunk 642 optimal weight: 7.9990 chunk 141 optimal weight: 0.9980 chunk 418 optimal weight: 20.0000 chunk 176 optimal weight: 3.9990 chunk 714 optimal weight: 1.9990 chunk 592 optimal weight: 5.9990 chunk 330 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 374 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 151 ASN D 442 ASN F 442 ASN I 529 ASN K 99 ASN ** K 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 563 ASN M 302 ASN ** M 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 660 GLN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN E 442 ASN J 503 ASN ** J 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 563 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.7598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 59010 Z= 0.284 Angle : 0.683 14.254 79776 Z= 0.353 Chirality : 0.046 0.252 8826 Planarity : 0.005 0.091 10464 Dihedral : 5.521 58.378 8292 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 4.87 % Allowed : 19.62 % Favored : 75.51 % 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 (0.09), residues: 7440 helix: 0.41 (0.11), residues: 2394 sheet: 0.82 (0.15), residues: 1092 loop : -2.29 (0.09), residues: 3954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 488 HIS 0.024 0.001 HIS D 138 PHE 0.035 0.002 PHE H 298 TYR 0.016 0.002 TYR E 566 ARG 0.010 0.001 ARG B 694 *********************** 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 754 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 298 poor density : 456 time to evaluate : 5.202 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: B 168 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6593 (tmm) REVERT: B 222 MET cc_start: 0.6262 (pmm) cc_final: 0.4998 (ptp) REVERT: D 143 GLU cc_start: 0.4021 (OUTLIER) cc_final: 0.2988 (tt0) REVERT: D 288 LYS cc_start: 0.3835 (mptt) cc_final: 0.3630 (mtpt) REVERT: D 626 MET cc_start: 0.2101 (tpt) cc_final: 0.1867 (tpt) REVERT: F 421 ASP cc_start: 0.5882 (OUTLIER) cc_final: 0.5571 (m-30) REVERT: F 474 MET cc_start: 0.3043 (mmm) cc_final: 0.2812 (mmm) REVERT: F 488 ILE cc_start: 0.7935 (pt) cc_final: 0.7452 (mm) REVERT: F 500 PHE cc_start: 0.4775 (OUTLIER) cc_final: 0.4128 (m-10) REVERT: I 295 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7121 (tm-30) REVERT: I 404 TYR cc_start: 0.5012 (OUTLIER) cc_final: 0.4119 (m-80) REVERT: I 407 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7076 (tpt) REVERT: I 631 LEU cc_start: 0.5851 (OUTLIER) cc_final: 0.4816 (mt) REVERT: K 34 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6612 (tp30) REVERT: K 404 TYR cc_start: 0.4920 (OUTLIER) cc_final: 0.3598 (m-80) REVERT: K 407 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7652 (tpt) REVERT: K 441 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7781 (mt) REVERT: K 453 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.6074 (p90) REVERT: K 672 GLU cc_start: 0.5943 (mp0) cc_final: 0.4716 (pp20) REVERT: M 108 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.7041 (ttm110) REVERT: M 179 MET cc_start: 0.2231 (mmm) cc_final: 0.1798 (ppp) REVERT: M 231 ARG cc_start: 0.7083 (tpt170) cc_final: 0.6781 (mmp-170) REVERT: M 299 MET cc_start: 0.6601 (tpt) cc_final: 0.6338 (tpt) REVERT: M 404 TYR cc_start: 0.5637 (OUTLIER) cc_final: 0.4766 (m-80) REVERT: M 407 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7534 (tpt) REVERT: M 441 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7633 (mt) REVERT: M 453 PHE cc_start: 0.6777 (OUTLIER) cc_final: 0.6299 (p90) REVERT: M 465 GLU cc_start: 0.6888 (pm20) cc_final: 0.6504 (tp30) REVERT: A 222 MET cc_start: 0.4307 (OUTLIER) cc_final: 0.3973 (mtp) REVERT: C 477 ASP cc_start: 0.4324 (p0) cc_final: 0.3803 (p0) REVERT: C 488 ILE cc_start: 0.8001 (pt) cc_final: 0.7693 (mm) REVERT: E 143 GLU cc_start: 0.3908 (OUTLIER) cc_final: 0.3049 (tt0) REVERT: E 474 MET cc_start: 0.3276 (mmm) cc_final: 0.2839 (tpt) REVERT: E 477 ASP cc_start: 0.4123 (p0) cc_final: 0.3771 (p0) REVERT: H 21 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6884 (ttp-170) REVERT: H 295 GLU cc_start: 0.7620 (tp30) cc_final: 0.7219 (tp30) REVERT: H 404 TYR cc_start: 0.5039 (OUTLIER) cc_final: 0.4153 (m-80) REVERT: H 407 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7064 (tpt) REVERT: H 453 PHE cc_start: 0.6509 (OUTLIER) cc_final: 0.6125 (p90) REVERT: H 483 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6176 (mpp) REVERT: H 500 PHE cc_start: 0.7235 (t80) cc_final: 0.6972 (t80) REVERT: H 563 ASN cc_start: 0.7374 (OUTLIER) cc_final: 0.6986 (m110) REVERT: H 631 LEU cc_start: 0.5505 (OUTLIER) cc_final: 0.4547 (mt) REVERT: H 650 MET cc_start: 0.4219 (tmm) cc_final: 0.2961 (ttm) REVERT: J 179 MET cc_start: 0.2021 (mmm) cc_final: 0.1129 (ppp) REVERT: J 299 MET cc_start: 0.7478 (ttp) cc_final: 0.7005 (tpt) REVERT: J 317 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6575 (mmt-90) REVERT: J 404 TYR cc_start: 0.5568 (OUTLIER) cc_final: 0.4862 (m-80) REVERT: J 407 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7484 (tpt) REVERT: J 441 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7728 (mt) REVERT: J 453 PHE cc_start: 0.6857 (OUTLIER) cc_final: 0.6408 (p90) REVERT: J 652 MET cc_start: 0.5032 (mmt) cc_final: 0.4706 (mmt) REVERT: L 21 ARG cc_start: 0.7540 (ttp-170) cc_final: 0.6610 (ttp-170) REVERT: L 231 ARG cc_start: 0.6924 (tpt170) cc_final: 0.6518 (mmp-170) REVERT: L 317 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.7056 (mmt90) REVERT: L 404 TYR cc_start: 0.4961 (OUTLIER) cc_final: 0.3733 (m-80) REVERT: L 407 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7537 (tpt) REVERT: L 441 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7787 (mt) REVERT: L 453 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.6315 (p90) REVERT: L 483 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6470 (mmt) REVERT: L 490 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7136 (mm) outliers start: 298 outliers final: 194 residues processed: 713 average time/residue: 0.5379 time to fit residues: 661.0654 Evaluate side-chains 640 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 408 time to evaluate : 5.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 555 GLN Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 421 ASP Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 500 PHE Chi-restraints excluded: chain F residue 510 CYS Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 555 GLN Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 679 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 260 MET Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 295 GLU Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 392 THR Chi-restraints excluded: chain I residue 396 GLU Chi-restraints excluded: chain I residue 404 TYR Chi-restraints excluded: chain I residue 407 MET Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 412 ILE Chi-restraints excluded: chain I residue 447 CYS Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 545 GLU Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 577 VAL Chi-restraints excluded: chain I residue 631 LEU Chi-restraints excluded: chain I residue 664 VAL Chi-restraints excluded: chain K residue 32 CYS Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 217 SER Chi-restraints excluded: chain K residue 228 LYS Chi-restraints excluded: chain K residue 260 MET Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 312 THR Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 346 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 404 TYR Chi-restraints excluded: chain K residue 407 MET Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain K residue 441 ILE Chi-restraints excluded: chain K residue 447 CYS Chi-restraints excluded: chain K residue 453 PHE Chi-restraints excluded: chain K residue 506 THR Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 563 ASN Chi-restraints excluded: chain K residue 577 VAL Chi-restraints excluded: chain K residue 664 VAL Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 108 ARG Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 264 GLN Chi-restraints excluded: chain M residue 266 ILE Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain M residue 404 TYR Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 434 VAL Chi-restraints excluded: chain M residue 437 ILE Chi-restraints excluded: chain M residue 441 ILE Chi-restraints excluded: chain M residue 453 PHE Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 545 GLU Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 555 GLN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 375 ASP Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 555 GLN Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 669 TYR Chi-restraints excluded: chain H residue 21 ARG Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 154 PHE Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 396 GLU Chi-restraints excluded: chain H residue 404 TYR Chi-restraints excluded: chain H residue 407 MET Chi-restraints excluded: chain H residue 411 VAL Chi-restraints excluded: chain H residue 412 ILE Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 483 MET Chi-restraints excluded: chain H residue 506 THR Chi-restraints excluded: chain H residue 545 GLU Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 562 VAL Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain H residue 577 VAL Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 664 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 317 ARG Chi-restraints excluded: chain J residue 346 THR Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 404 TYR Chi-restraints excluded: chain J residue 407 MET Chi-restraints excluded: chain J residue 411 VAL Chi-restraints excluded: chain J residue 412 ILE Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 447 CYS Chi-restraints excluded: chain J residue 453 PHE Chi-restraints excluded: chain J residue 476 VAL Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 545 GLU Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 217 SER Chi-restraints excluded: chain L residue 228 LYS Chi-restraints excluded: chain L residue 260 MET Chi-restraints excluded: chain L residue 284 THR Chi-restraints excluded: chain L residue 293 THR Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 317 ARG Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 404 TYR Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 412 ILE Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 447 CYS Chi-restraints excluded: chain L residue 453 PHE Chi-restraints excluded: chain L residue 483 MET Chi-restraints excluded: chain L residue 490 LEU Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 545 GLU Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 547 CYS Chi-restraints excluded: chain L residue 577 VAL Chi-restraints excluded: chain L residue 664 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 688 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 406 optimal weight: 5.9990 chunk 521 optimal weight: 6.9990 chunk 404 optimal weight: 0.9980 chunk 601 optimal weight: 7.9990 chunk 398 optimal weight: 10.0000 chunk 711 optimal weight: 2.9990 chunk 445 optimal weight: 6.9990 chunk 433 optimal weight: 6.9990 chunk 328 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 442 ASN D 137 HIS D 138 HIS D 442 ASN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 HIS F 442 ASN K 99 ASN K 491 ASN K 503 ASN K 563 ASN M 380 GLN ** M 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN E 309 GLN H 503 ASN J 529 ASN J 563 ASN L 99 ASN ** L 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.7865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 59010 Z= 0.261 Angle : 0.665 14.166 79776 Z= 0.344 Chirality : 0.046 0.210 8826 Planarity : 0.005 0.057 10464 Dihedral : 5.473 56.768 8292 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.59 % Allowed : 20.15 % Favored : 75.26 % 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: -1.20 (0.09), residues: 7440 helix: 0.58 (0.11), residues: 2358 sheet: 0.81 (0.15), residues: 1080 loop : -2.24 (0.09), residues: 4002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 488 HIS 0.008 0.001 HIS M 654 PHE 0.021 0.002 PHE I 298 TYR 0.015 0.002 TYR E 566 ARG 0.010 0.001 ARG K 212 *********************** 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 734 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 281 poor density : 453 time to evaluate : 5.161 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: B 168 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6583 (tmm) REVERT: B 227 ARG cc_start: 0.7167 (mtt180) cc_final: 0.6901 (ptp-110) REVERT: D 143 GLU cc_start: 0.3845 (OUTLIER) cc_final: 0.3186 (mt-10) REVERT: D 288 LYS cc_start: 0.3980 (mptt) cc_final: 0.3729 (mtpt) REVERT: F 421 ASP cc_start: 0.5807 (OUTLIER) cc_final: 0.5490 (m-30) REVERT: F 488 ILE cc_start: 0.7942 (pt) cc_final: 0.7397 (mm) REVERT: F 500 PHE cc_start: 0.5067 (OUTLIER) cc_final: 0.3914 (m-10) REVERT: I 112 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7832 (mt-10) REVERT: I 264 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6617 (tp40) REVERT: I 272 GLN cc_start: 0.7874 (mt0) cc_final: 0.7274 (mm110) REVERT: I 295 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7149 (tm-30) REVERT: I 404 TYR cc_start: 0.5153 (OUTLIER) cc_final: 0.4294 (m-80) REVERT: I 407 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7097 (tpt) REVERT: I 631 LEU cc_start: 0.5686 (OUTLIER) cc_final: 0.4665 (mt) REVERT: K 34 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6583 (tp30) REVERT: K 179 MET cc_start: 0.1829 (mmm) cc_final: 0.0720 (ppp) REVERT: K 404 TYR cc_start: 0.5008 (OUTLIER) cc_final: 0.3738 (m-80) REVERT: K 407 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7651 (tpt) REVERT: K 441 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7806 (mt) REVERT: K 453 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.6297 (p90) REVERT: K 602 LEU cc_start: 0.4250 (OUTLIER) cc_final: 0.3997 (tt) REVERT: K 672 GLU cc_start: 0.6193 (mp0) cc_final: 0.4896 (pp20) REVERT: M 21 ARG cc_start: 0.7364 (ttp-170) cc_final: 0.6664 (ttp-170) REVERT: M 108 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.7045 (ttm110) REVERT: M 179 MET cc_start: 0.2313 (mmm) cc_final: 0.1954 (ppp) REVERT: M 231 ARG cc_start: 0.7034 (tpt170) cc_final: 0.6749 (mmp-170) REVERT: M 299 MET cc_start: 0.6543 (tpt) cc_final: 0.6314 (tpt) REVERT: M 317 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6611 (mmt-90) REVERT: M 404 TYR cc_start: 0.5358 (OUTLIER) cc_final: 0.4328 (m-80) REVERT: M 407 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7526 (tpt) REVERT: M 441 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7639 (mt) REVERT: M 453 PHE cc_start: 0.6757 (OUTLIER) cc_final: 0.6233 (p90) REVERT: M 465 GLU cc_start: 0.6734 (pm20) cc_final: 0.6466 (tp30) REVERT: M 650 MET cc_start: 0.4752 (tmm) cc_final: 0.4361 (ttm) REVERT: A 222 MET cc_start: 0.4459 (OUTLIER) cc_final: 0.4147 (mtp) REVERT: A 447 ASN cc_start: 0.7293 (OUTLIER) cc_final: 0.7037 (t0) REVERT: A 669 TYR cc_start: 0.5891 (OUTLIER) cc_final: 0.5502 (m-80) REVERT: C 477 ASP cc_start: 0.4392 (p0) cc_final: 0.3848 (p0) REVERT: C 488 ILE cc_start: 0.8057 (pt) cc_final: 0.7562 (mm) REVERT: C 500 PHE cc_start: 0.4741 (OUTLIER) cc_final: 0.4134 (m-10) REVERT: E 143 GLU cc_start: 0.3885 (OUTLIER) cc_final: 0.3211 (mt-10) REVERT: E 222 MET cc_start: 0.4471 (OUTLIER) cc_final: 0.4260 (mtp) REVERT: E 474 MET cc_start: 0.3512 (mmm) cc_final: 0.2910 (tpt) REVERT: E 626 MET cc_start: 0.2819 (tpt) cc_final: 0.2592 (tpt) REVERT: H 295 GLU cc_start: 0.7618 (tp30) cc_final: 0.7244 (tp30) REVERT: H 404 TYR cc_start: 0.5172 (OUTLIER) cc_final: 0.4272 (m-80) REVERT: H 407 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7070 (tpt) REVERT: H 453 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.6222 (p90) REVERT: H 483 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6256 (mpp) REVERT: H 631 LEU cc_start: 0.5482 (OUTLIER) cc_final: 0.4510 (mt) REVERT: H 650 MET cc_start: 0.4289 (tmm) cc_final: 0.3411 (ttt) REVERT: J 179 MET cc_start: 0.2077 (mmm) cc_final: 0.1141 (ppp) REVERT: J 299 MET cc_start: 0.7520 (ttp) cc_final: 0.7160 (tpt) REVERT: J 317 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6598 (mmt-90) REVERT: J 404 TYR cc_start: 0.5606 (OUTLIER) cc_final: 0.4837 (m-80) REVERT: J 407 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7499 (tpt) REVERT: J 453 PHE cc_start: 0.6827 (OUTLIER) cc_final: 0.6357 (p90) REVERT: L 21 ARG cc_start: 0.7468 (ttp-170) cc_final: 0.6798 (ttp-170) REVERT: L 34 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6640 (tp30) REVERT: L 231 ARG cc_start: 0.6938 (tpt170) cc_final: 0.6652 (mmp-170) REVERT: L 404 TYR cc_start: 0.5044 (OUTLIER) cc_final: 0.3985 (m-80) REVERT: L 407 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7531 (tpt) REVERT: L 453 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.6287 (p90) REVERT: L 483 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6503 (mmt) REVERT: L 490 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7128 (mm) REVERT: L 650 MET cc_start: 0.4558 (tmm) cc_final: 0.3663 (ttm) outliers start: 281 outliers final: 197 residues processed: 693 average time/residue: 0.5082 time to fit residues: 609.3632 Evaluate side-chains 643 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 406 time to evaluate : 5.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 300 HIS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 555 GLN Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 222 MET Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 421 ASP Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 500 PHE Chi-restraints excluded: chain F residue 510 CYS Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 679 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 260 MET Chi-restraints excluded: chain I residue 264 GLN Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 295 GLU Chi-restraints excluded: chain I residue 312 THR Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 392 THR Chi-restraints excluded: chain I residue 396 GLU Chi-restraints excluded: chain I residue 404 TYR Chi-restraints excluded: chain I residue 407 MET Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 412 ILE Chi-restraints excluded: chain I residue 447 CYS Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 545 GLU Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 577 VAL Chi-restraints excluded: chain I residue 631 LEU Chi-restraints excluded: chain I residue 664 VAL Chi-restraints excluded: chain K residue 32 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 217 SER Chi-restraints excluded: chain K residue 228 LYS Chi-restraints excluded: chain K residue 260 MET Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 312 THR Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 346 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 404 TYR Chi-restraints excluded: chain K residue 407 MET Chi-restraints excluded: chain K residue 441 ILE Chi-restraints excluded: chain K residue 447 CYS Chi-restraints excluded: chain K residue 453 PHE Chi-restraints excluded: chain K residue 506 THR Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 602 LEU Chi-restraints excluded: chain K residue 664 VAL Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 108 ARG Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 264 GLN Chi-restraints excluded: chain M residue 266 ILE Chi-restraints excluded: chain M residue 317 ARG Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain M residue 346 THR Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain M residue 404 TYR Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 434 VAL Chi-restraints excluded: chain M residue 437 ILE Chi-restraints excluded: chain M residue 441 ILE Chi-restraints excluded: chain M residue 453 PHE Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 545 GLU Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 664 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 669 TYR Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 300 HIS Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 500 PHE Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 555 GLN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 375 ASP Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 555 GLN Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 154 PHE Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 404 TYR Chi-restraints excluded: chain H residue 407 MET Chi-restraints excluded: chain H residue 411 VAL Chi-restraints excluded: chain H residue 412 ILE Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 483 MET Chi-restraints excluded: chain H residue 506 THR Chi-restraints excluded: chain H residue 545 GLU Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 562 VAL Chi-restraints excluded: chain H residue 568 LEU Chi-restraints excluded: chain H residue 577 VAL Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 664 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 264 GLN Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 317 ARG Chi-restraints excluded: chain J residue 318 ILE Chi-restraints excluded: chain J residue 346 THR Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 404 TYR Chi-restraints excluded: chain J residue 407 MET Chi-restraints excluded: chain J residue 411 VAL Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain J residue 447 CYS Chi-restraints excluded: chain J residue 453 PHE Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 476 VAL Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 545 GLU Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 217 SER Chi-restraints excluded: chain L residue 228 LYS Chi-restraints excluded: chain L residue 260 MET Chi-restraints excluded: chain L residue 284 THR Chi-restraints excluded: chain L residue 293 THR Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 404 TYR Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 412 ILE Chi-restraints excluded: chain L residue 447 CYS Chi-restraints excluded: chain L residue 453 PHE Chi-restraints excluded: chain L residue 483 MET Chi-restraints excluded: chain L residue 490 LEU Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 545 GLU Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 547 CYS Chi-restraints excluded: chain L residue 577 VAL Chi-restraints excluded: chain L residue 664 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 440 optimal weight: 0.8980 chunk 284 optimal weight: 9.9990 chunk 424 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 137 optimal weight: 0.6980 chunk 452 optimal weight: 10.0000 chunk 484 optimal weight: 5.9990 chunk 351 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 559 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 HIS ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN I 595 HIS K 491 ASN K 563 ASN ** M 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN C 309 GLN C 442 ASN C 539 HIS E 309 GLN E 442 ASN J 99 ASN ** L 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.7927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 59010 Z= 0.181 Angle : 0.615 14.240 79776 Z= 0.316 Chirality : 0.045 0.204 8826 Planarity : 0.005 0.057 10464 Dihedral : 5.103 57.814 8292 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.42 % Allowed : 21.47 % Favored : 75.11 % 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: -0.93 (0.10), residues: 7440 helix: 0.92 (0.11), residues: 2358 sheet: 0.97 (0.15), residues: 1056 loop : -2.14 (0.09), residues: 4026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 251 HIS 0.018 0.001 HIS D 138 PHE 0.015 0.001 PHE I 298 TYR 0.024 0.001 TYR D 135 ARG 0.009 0.000 ARG B 227 *********************** 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 691 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 482 time to evaluate : 5.066 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: B 227 ARG cc_start: 0.6838 (mtt180) cc_final: 0.6626 (ptp-110) REVERT: B 262 TYR cc_start: 0.3887 (OUTLIER) cc_final: 0.3442 (m-80) REVERT: B 474 MET cc_start: 0.3218 (OUTLIER) cc_final: 0.2527 (mmt) REVERT: D 143 GLU cc_start: 0.3793 (OUTLIER) cc_final: 0.2945 (tt0) REVERT: D 288 LYS cc_start: 0.4162 (mptt) cc_final: 0.3886 (mtpt) REVERT: D 634 VAL cc_start: 0.6484 (t) cc_final: 0.6235 (p) REVERT: F 421 ASP cc_start: 0.5761 (OUTLIER) cc_final: 0.5533 (m-30) REVERT: F 500 PHE cc_start: 0.4849 (OUTLIER) cc_final: 0.3997 (m-10) REVERT: I 112 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7584 (mt-10) REVERT: I 179 MET cc_start: 0.2958 (mmm) cc_final: 0.2462 (ppp) REVERT: I 404 TYR cc_start: 0.4975 (OUTLIER) cc_final: 0.4096 (m-80) REVERT: I 407 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7165 (tpt) REVERT: I 631 LEU cc_start: 0.5827 (OUTLIER) cc_final: 0.4788 (mt) REVERT: K 34 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6521 (tp30) REVERT: K 407 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7570 (tpt) REVERT: K 441 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7838 (mt) REVERT: K 453 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.6172 (p90) REVERT: K 602 LEU cc_start: 0.4273 (OUTLIER) cc_final: 0.4005 (tt) REVERT: K 672 GLU cc_start: 0.6100 (mp0) cc_final: 0.4935 (pp20) REVERT: M 21 ARG cc_start: 0.7348 (ttp-170) cc_final: 0.6864 (ttp-170) REVERT: M 108 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.7106 (ttm110) REVERT: M 126 SER cc_start: 0.6832 (t) cc_final: 0.6585 (m) REVERT: M 179 MET cc_start: 0.2917 (mmm) cc_final: 0.2449 (ppp) REVERT: M 231 ARG cc_start: 0.6982 (tpt170) cc_final: 0.6706 (mmp-170) REVERT: M 272 GLN cc_start: 0.7802 (mt0) cc_final: 0.7257 (tt0) REVERT: M 317 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6597 (mmt-90) REVERT: M 404 TYR cc_start: 0.5300 (OUTLIER) cc_final: 0.4404 (m-80) REVERT: M 407 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7413 (tpt) REVERT: M 439 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7911 (m) REVERT: M 453 PHE cc_start: 0.6553 (OUTLIER) cc_final: 0.6141 (p90) REVERT: M 545 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7229 (pt0) REVERT: M 650 MET cc_start: 0.4789 (tmm) cc_final: 0.4521 (ttm) REVERT: A 447 ASN cc_start: 0.7248 (OUTLIER) cc_final: 0.6995 (t0) REVERT: C 477 ASP cc_start: 0.4606 (p0) cc_final: 0.4365 (p0) REVERT: E 393 LEU cc_start: 0.7281 (tt) cc_final: 0.7016 (tp) REVERT: E 474 MET cc_start: 0.3644 (mmm) cc_final: 0.2994 (tpt) REVERT: E 477 ASP cc_start: 0.4675 (p0) cc_final: 0.4305 (p0) REVERT: E 626 MET cc_start: 0.2839 (tpt) cc_final: 0.2623 (tpt) REVERT: H 272 GLN cc_start: 0.7803 (mt0) cc_final: 0.7222 (mm110) REVERT: H 295 GLU cc_start: 0.7705 (tp30) cc_final: 0.7390 (tp30) REVERT: H 404 TYR cc_start: 0.4936 (OUTLIER) cc_final: 0.4058 (m-80) REVERT: H 483 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6255 (mpp) REVERT: H 631 LEU cc_start: 0.5456 (OUTLIER) cc_final: 0.4490 (mt) REVERT: J 264 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7175 (mt0) REVERT: J 272 GLN cc_start: 0.7721 (mt0) cc_final: 0.7258 (mm110) REVERT: J 299 MET cc_start: 0.7313 (ttp) cc_final: 0.6841 (tpt) REVERT: J 314 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6867 (mt-10) REVERT: J 317 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6561 (mmt-90) REVERT: J 404 TYR cc_start: 0.5383 (OUTLIER) cc_final: 0.4539 (m-80) REVERT: J 407 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7498 (tpt) REVERT: J 453 PHE cc_start: 0.6649 (OUTLIER) cc_final: 0.6317 (p90) REVERT: J 545 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7220 (pt0) REVERT: L 21 ARG cc_start: 0.7438 (ttp-170) cc_final: 0.6854 (ttp-170) REVERT: L 34 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6511 (tp30) REVERT: L 404 TYR cc_start: 0.4998 (OUTLIER) cc_final: 0.3993 (m-80) REVERT: L 453 PHE cc_start: 0.6662 (OUTLIER) cc_final: 0.6228 (p90) REVERT: L 483 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6434 (mpp) REVERT: L 490 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7114 (mm) REVERT: L 650 MET cc_start: 0.4504 (tmm) cc_final: 0.3926 (ttm) outliers start: 209 outliers final: 130 residues processed: 650 average time/residue: 0.5090 time to fit residues: 573.1566 Evaluate side-chains 602 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 438 time to evaluate : 5.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 300 HIS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 555 GLN Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 421 ASP Chi-restraints excluded: chain F residue 500 PHE Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 555 GLN Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 260 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 392 THR Chi-restraints excluded: chain I residue 404 TYR Chi-restraints excluded: chain I residue 407 MET Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 412 ILE Chi-restraints excluded: chain I residue 447 CYS Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 545 GLU Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 577 VAL Chi-restraints excluded: chain I residue 631 LEU Chi-restraints excluded: chain K residue 32 CYS Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 217 SER Chi-restraints excluded: chain K residue 260 MET Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 407 MET Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain K residue 441 ILE Chi-restraints excluded: chain K residue 453 PHE Chi-restraints excluded: chain K residue 506 THR Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 563 ASN Chi-restraints excluded: chain K residue 602 LEU Chi-restraints excluded: chain K residue 664 VAL Chi-restraints excluded: chain M residue 108 ARG Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 317 ARG Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain M residue 404 TYR Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 437 ILE Chi-restraints excluded: chain M residue 439 THR Chi-restraints excluded: chain M residue 453 PHE Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 545 GLU Chi-restraints excluded: chain M residue 664 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 300 HIS Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 555 GLN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 375 ASP Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 555 GLN Chi-restraints excluded: chain E residue 594 ILE Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 154 PHE Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 404 TYR Chi-restraints excluded: chain H residue 411 VAL Chi-restraints excluded: chain H residue 412 ILE Chi-restraints excluded: chain H residue 483 MET Chi-restraints excluded: chain H residue 506 THR Chi-restraints excluded: chain H residue 545 GLU Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 577 VAL Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 664 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 264 GLN Chi-restraints excluded: chain J residue 317 ARG Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 404 TYR Chi-restraints excluded: chain J residue 407 MET Chi-restraints excluded: chain J residue 411 VAL Chi-restraints excluded: chain J residue 447 CYS Chi-restraints excluded: chain J residue 453 PHE Chi-restraints excluded: chain J residue 476 VAL Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 545 GLU Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 664 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 217 SER Chi-restraints excluded: chain L residue 260 MET Chi-restraints excluded: chain L residue 293 THR Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 404 TYR Chi-restraints excluded: chain L residue 412 ILE Chi-restraints excluded: chain L residue 453 PHE Chi-restraints excluded: chain L residue 483 MET Chi-restraints excluded: chain L residue 490 LEU Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 545 GLU Chi-restraints excluded: chain L residue 547 CYS Chi-restraints excluded: chain L residue 664 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 647 optimal weight: 9.9990 chunk 681 optimal weight: 0.7980 chunk 621 optimal weight: 5.9990 chunk 662 optimal weight: 4.9990 chunk 398 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 chunk 520 optimal weight: 20.0000 chunk 203 optimal weight: 0.0670 chunk 598 optimal weight: 20.0000 chunk 626 optimal weight: 8.9990 chunk 660 optimal weight: 0.7980 overall best weight: 2.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 243 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 539 HIS I 99 ASN K 563 ASN M 466 HIS ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN E 309 GLN ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN L 99 ASN L 503 ASN ** L 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.8068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 59010 Z= 0.218 Angle : 0.644 15.635 79776 Z= 0.328 Chirality : 0.045 0.229 8826 Planarity : 0.005 0.056 10464 Dihedral : 5.105 59.938 8292 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.46 % Allowed : 21.75 % Favored : 74.79 % 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: -0.93 (0.10), residues: 7440 helix: 0.90 (0.11), residues: 2382 sheet: 0.92 (0.15), residues: 1074 loop : -2.14 (0.09), residues: 3984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 488 HIS 0.006 0.001 HIS B 539 PHE 0.031 0.002 PHE B 560 TYR 0.016 0.001 TYR E 669 ARG 0.010 0.000 ARG E 154 *********************** 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 661 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 449 time to evaluate : 5.177 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: B 262 TYR cc_start: 0.3871 (OUTLIER) cc_final: 0.3432 (m-80) REVERT: B 474 MET cc_start: 0.3269 (OUTLIER) cc_final: 0.2614 (mmt) REVERT: D 143 GLU cc_start: 0.3553 (OUTLIER) cc_final: 0.2675 (mt-10) REVERT: D 288 LYS cc_start: 0.4138 (mptt) cc_final: 0.3862 (mtpt) REVERT: D 634 VAL cc_start: 0.6590 (t) cc_final: 0.6388 (p) REVERT: F 421 ASP cc_start: 0.5581 (OUTLIER) cc_final: 0.5330 (m-30) REVERT: F 500 PHE cc_start: 0.4889 (OUTLIER) cc_final: 0.4010 (m-10) REVERT: I 179 MET cc_start: 0.3122 (mmm) cc_final: 0.2562 (ppp) REVERT: I 295 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: I 404 TYR cc_start: 0.5140 (OUTLIER) cc_final: 0.4284 (m-80) REVERT: I 407 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7112 (tpt) REVERT: I 631 LEU cc_start: 0.5841 (OUTLIER) cc_final: 0.4800 (mt) REVERT: K 34 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6531 (tp30) REVERT: K 179 MET cc_start: 0.1530 (mmm) cc_final: 0.0519 (ppp) REVERT: K 268 GLU cc_start: 0.6568 (mm-30) cc_final: 0.6295 (mp0) REVERT: K 404 TYR cc_start: 0.4987 (OUTLIER) cc_final: 0.3823 (m-80) REVERT: K 407 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7562 (tpt) REVERT: K 441 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7814 (mt) REVERT: K 453 PHE cc_start: 0.6752 (OUTLIER) cc_final: 0.6172 (p90) REVERT: K 660 GLN cc_start: 0.3307 (OUTLIER) cc_final: 0.3078 (mm-40) REVERT: K 672 GLU cc_start: 0.6299 (mp0) cc_final: 0.5090 (pp20) REVERT: M 21 ARG cc_start: 0.7370 (ttp-170) cc_final: 0.6906 (ttp-170) REVERT: M 108 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.7073 (ttm110) REVERT: M 179 MET cc_start: 0.3137 (mmm) cc_final: 0.2597 (ppp) REVERT: M 231 ARG cc_start: 0.7028 (tpt170) cc_final: 0.6758 (mmp-170) REVERT: M 272 GLN cc_start: 0.7827 (mt0) cc_final: 0.7273 (tt0) REVERT: M 317 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6578 (mmt-90) REVERT: M 404 TYR cc_start: 0.5322 (OUTLIER) cc_final: 0.4419 (m-80) REVERT: M 407 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7501 (tpt) REVERT: M 439 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7922 (m) REVERT: M 441 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7488 (mt) REVERT: M 453 PHE cc_start: 0.6686 (OUTLIER) cc_final: 0.6257 (p90) REVERT: M 465 GLU cc_start: 0.6228 (tp30) cc_final: 0.5844 (tp30) REVERT: M 545 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7276 (pt0) REVERT: A 447 ASN cc_start: 0.7262 (OUTLIER) cc_final: 0.7003 (t0) REVERT: C 477 ASP cc_start: 0.4751 (p0) cc_final: 0.4290 (p0) REVERT: C 500 PHE cc_start: 0.4837 (OUTLIER) cc_final: 0.4177 (m-10) REVERT: E 617 MET cc_start: 0.6590 (mtp) cc_final: 0.6366 (mtm) REVERT: E 626 MET cc_start: 0.2441 (tpt) cc_final: 0.2231 (tpt) REVERT: H 295 GLU cc_start: 0.7678 (tp30) cc_final: 0.7353 (tp30) REVERT: H 404 TYR cc_start: 0.4965 (OUTLIER) cc_final: 0.4147 (m-80) REVERT: H 407 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7139 (tpt) REVERT: H 483 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6232 (mpp) REVERT: H 631 LEU cc_start: 0.5383 (OUTLIER) cc_final: 0.4438 (mt) REVERT: J 179 MET cc_start: 0.1609 (mmm) cc_final: 0.0678 (ppp) REVERT: J 264 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7126 (mt0) REVERT: J 299 MET cc_start: 0.7324 (ttp) cc_final: 0.6865 (tpt) REVERT: J 314 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7009 (mt-10) REVERT: J 317 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6618 (mmt-90) REVERT: J 404 TYR cc_start: 0.5501 (OUTLIER) cc_final: 0.4617 (m-80) REVERT: J 407 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7501 (tpt) REVERT: J 453 PHE cc_start: 0.6706 (OUTLIER) cc_final: 0.6350 (p90) REVERT: J 545 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7262 (pt0) REVERT: L 21 ARG cc_start: 0.7413 (ttp-170) cc_final: 0.6834 (ttp-170) REVERT: L 34 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6595 (tp30) REVERT: L 317 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6989 (mmt90) REVERT: L 404 TYR cc_start: 0.5023 (OUTLIER) cc_final: 0.3972 (m-80) REVERT: L 453 PHE cc_start: 0.6744 (OUTLIER) cc_final: 0.6169 (p90) REVERT: L 483 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6433 (mpp) REVERT: L 490 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7125 (mm) outliers start: 212 outliers final: 155 residues processed: 627 average time/residue: 0.5009 time to fit residues: 546.6735 Evaluate side-chains 614 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 420 time to evaluate : 5.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 300 HIS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 555 GLN Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 421 ASP Chi-restraints excluded: chain F residue 500 PHE Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 260 MET Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 295 GLU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 392 THR Chi-restraints excluded: chain I residue 404 TYR Chi-restraints excluded: chain I residue 407 MET Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 412 ILE Chi-restraints excluded: chain I residue 447 CYS Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 545 GLU Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 577 VAL Chi-restraints excluded: chain I residue 631 LEU Chi-restraints excluded: chain I residue 664 VAL Chi-restraints excluded: chain K residue 32 CYS Chi-restraints excluded: chain K residue 217 SER Chi-restraints excluded: chain K residue 260 MET Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 404 TYR Chi-restraints excluded: chain K residue 407 MET Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain K residue 441 ILE Chi-restraints excluded: chain K residue 453 PHE Chi-restraints excluded: chain K residue 506 THR Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 563 ASN Chi-restraints excluded: chain K residue 660 GLN Chi-restraints excluded: chain K residue 664 VAL Chi-restraints excluded: chain M residue 108 ARG Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 266 ILE Chi-restraints excluded: chain M residue 317 ARG Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain M residue 404 TYR Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 437 ILE Chi-restraints excluded: chain M residue 439 THR Chi-restraints excluded: chain M residue 441 ILE Chi-restraints excluded: chain M residue 453 PHE Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 545 GLU Chi-restraints excluded: chain M residue 664 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 669 TYR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 300 HIS Chi-restraints excluded: chain C residue 500 PHE Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 555 GLN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 375 ASP Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 555 GLN Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 154 PHE Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 404 TYR Chi-restraints excluded: chain H residue 407 MET Chi-restraints excluded: chain H residue 411 VAL Chi-restraints excluded: chain H residue 412 ILE Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 483 MET Chi-restraints excluded: chain H residue 506 THR Chi-restraints excluded: chain H residue 545 GLU Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 568 LEU Chi-restraints excluded: chain H residue 577 VAL Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 664 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 264 GLN Chi-restraints excluded: chain J residue 317 ARG Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 404 TYR Chi-restraints excluded: chain J residue 407 MET Chi-restraints excluded: chain J residue 411 VAL Chi-restraints excluded: chain J residue 447 CYS Chi-restraints excluded: chain J residue 453 PHE Chi-restraints excluded: chain J residue 476 VAL Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 545 GLU Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 664 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain L residue 217 SER Chi-restraints excluded: chain L residue 228 LYS Chi-restraints excluded: chain L residue 260 MET Chi-restraints excluded: chain L residue 293 THR Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 317 ARG Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 404 TYR Chi-restraints excluded: chain L residue 412 ILE Chi-restraints excluded: chain L residue 453 PHE Chi-restraints excluded: chain L residue 483 MET Chi-restraints excluded: chain L residue 490 LEU Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 545 GLU Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 547 CYS Chi-restraints excluded: chain L residue 577 VAL Chi-restraints excluded: chain L residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 435 optimal weight: 9.9990 chunk 700 optimal weight: 10.0000 chunk 427 optimal weight: 2.9990 chunk 332 optimal weight: 0.6980 chunk 487 optimal weight: 6.9990 chunk 735 optimal weight: 0.7980 chunk 676 optimal weight: 6.9990 chunk 585 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 452 optimal weight: 0.9990 chunk 358 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 539 HIS K 563 ASN M 99 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN E 309 GLN H 99 ASN J 99 ASN L 99 ASN ** L 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.8095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 59010 Z= 0.170 Angle : 0.622 17.423 79776 Z= 0.315 Chirality : 0.044 0.197 8826 Planarity : 0.005 0.102 10464 Dihedral : 4.854 47.300 8292 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.53 % Allowed : 22.84 % Favored : 74.62 % 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: -0.73 (0.10), residues: 7440 helix: 1.05 (0.11), residues: 2388 sheet: 0.86 (0.15), residues: 1134 loop : -2.00 (0.09), residues: 3918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 251 HIS 0.006 0.001 HIS B 539 PHE 0.035 0.001 PHE B 560 TYR 0.013 0.001 TYR B 423 ARG 0.013 0.000 ARG I 11 ********************** 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 642 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 487 time to evaluate : 5.084 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: B 138 HIS cc_start: 0.5020 (m-70) cc_final: 0.4811 (m170) REVERT: B 144 ARG cc_start: 0.6384 (mmm160) cc_final: 0.6117 (mmm160) REVERT: B 393 LEU cc_start: 0.7512 (tt) cc_final: 0.7190 (tp) REVERT: B 474 MET cc_start: 0.3202 (OUTLIER) cc_final: 0.2616 (mmt) REVERT: D 143 GLU cc_start: 0.3276 (OUTLIER) cc_final: 0.2548 (tt0) REVERT: D 288 LYS cc_start: 0.4201 (mptt) cc_final: 0.3988 (mtpt) REVERT: F 500 PHE cc_start: 0.4908 (OUTLIER) cc_final: 0.4017 (m-10) REVERT: I 179 MET cc_start: 0.2557 (mmm) cc_final: 0.1901 (ppp) REVERT: I 272 GLN cc_start: 0.7600 (mt0) cc_final: 0.7102 (mm110) REVERT: I 295 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: I 404 TYR cc_start: 0.4851 (OUTLIER) cc_final: 0.3989 (m-80) REVERT: I 407 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7179 (tpt) REVERT: I 631 LEU cc_start: 0.5773 (OUTLIER) cc_final: 0.4769 (mt) REVERT: K 34 GLU cc_start: 0.6897 (mm-30) cc_final: 0.6536 (tp30) REVERT: K 179 MET cc_start: 0.1651 (mmm) cc_final: 0.0606 (ppp) REVERT: K 268 GLU cc_start: 0.6609 (mm-30) cc_final: 0.6341 (mp0) REVERT: K 407 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7627 (tpt) REVERT: K 672 GLU cc_start: 0.6180 (mp0) cc_final: 0.5010 (pp20) REVERT: M 179 MET cc_start: 0.3011 (mmm) cc_final: 0.2577 (ppp) REVERT: M 231 ARG cc_start: 0.6959 (tpt170) cc_final: 0.6729 (mmp-170) REVERT: M 295 GLU cc_start: 0.7376 (tp30) cc_final: 0.7154 (tp30) REVERT: M 317 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6720 (mmt-90) REVERT: M 407 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7415 (tpt) REVERT: M 439 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7922 (m) REVERT: M 441 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7450 (mt) REVERT: M 545 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7252 (pt0) REVERT: M 650 MET cc_start: 0.4828 (tmm) cc_final: 0.4256 (ttm) REVERT: A 447 ASN cc_start: 0.7213 (OUTLIER) cc_final: 0.6954 (t0) REVERT: A 663 LYS cc_start: 0.3855 (tptt) cc_final: 0.3173 (mttm) REVERT: C 477 ASP cc_start: 0.5235 (p0) cc_final: 0.4737 (p0) REVERT: C 500 PHE cc_start: 0.4901 (OUTLIER) cc_final: 0.4329 (m-10) REVERT: E 393 LEU cc_start: 0.7488 (tt) cc_final: 0.7120 (tp) REVERT: E 474 MET cc_start: 0.3142 (mmm) cc_final: 0.2893 (tpt) REVERT: E 626 MET cc_start: 0.2765 (tpt) cc_final: 0.2527 (tpt) REVERT: H 272 GLN cc_start: 0.7662 (mt0) cc_final: 0.7143 (mm110) REVERT: H 295 GLU cc_start: 0.7756 (tp30) cc_final: 0.7447 (tp30) REVERT: H 404 TYR cc_start: 0.4823 (OUTLIER) cc_final: 0.4011 (m-80) REVERT: H 407 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7132 (tpt) REVERT: H 483 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6114 (mpp) REVERT: H 631 LEU cc_start: 0.5479 (OUTLIER) cc_final: 0.4493 (mt) REVERT: H 650 MET cc_start: 0.5386 (tmm) cc_final: 0.4820 (ptm) REVERT: J 179 MET cc_start: 0.1801 (mmm) cc_final: 0.0768 (ppp) REVERT: J 264 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.7222 (mt0) REVERT: J 295 GLU cc_start: 0.7373 (tp30) cc_final: 0.7130 (tp30) REVERT: J 299 MET cc_start: 0.7184 (ttp) cc_final: 0.6699 (tpt) REVERT: J 545 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7176 (pt0) REVERT: L 34 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6571 (tp30) REVERT: L 246 TYR cc_start: 0.6458 (m-80) cc_final: 0.6160 (m-80) REVERT: L 268 GLU cc_start: 0.6745 (mm-30) cc_final: 0.6508 (mp0) REVERT: L 272 GLN cc_start: 0.7841 (mt0) cc_final: 0.7516 (tt0) REVERT: L 295 GLU cc_start: 0.7325 (tp30) cc_final: 0.7108 (tp30) REVERT: L 407 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7497 (tpt) REVERT: L 483 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6282 (mpp) REVERT: L 490 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7103 (mm) REVERT: L 650 MET cc_start: 0.4950 (tmm) cc_final: 0.3636 (ttm) outliers start: 155 outliers final: 118 residues processed: 616 average time/residue: 0.5115 time to fit residues: 547.2536 Evaluate side-chains 580 residues out of total 6120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 438 time to evaluate : 5.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 300 HIS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 555 GLN Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 500 PHE Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 260 MET Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 295 GLU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 392 THR Chi-restraints excluded: chain I residue 404 TYR Chi-restraints excluded: chain I residue 407 MET Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 412 ILE Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 545 GLU Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 577 VAL Chi-restraints excluded: chain I residue 631 LEU Chi-restraints excluded: chain I residue 664 VAL Chi-restraints excluded: chain K residue 32 CYS Chi-restraints excluded: chain K residue 260 MET Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 407 MET Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain K residue 506 THR Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 563 ASN Chi-restraints excluded: chain K residue 664 VAL Chi-restraints excluded: chain M residue 317 ARG Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 437 ILE Chi-restraints excluded: chain M residue 439 THR Chi-restraints excluded: chain M residue 441 ILE Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 545 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 300 HIS Chi-restraints excluded: chain C residue 500 PHE Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 555 GLN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 375 ASP Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 555 GLN Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 154 PHE Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 404 TYR Chi-restraints excluded: chain H residue 407 MET Chi-restraints excluded: chain H residue 411 VAL Chi-restraints excluded: chain H residue 412 ILE Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 483 MET Chi-restraints excluded: chain H residue 506 THR Chi-restraints excluded: chain H residue 545 GLU Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 577 VAL Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 664 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 264 GLN Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 476 VAL Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 545 GLU Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 664 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain L residue 293 THR Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 412 ILE Chi-restraints excluded: chain L residue 483 MET Chi-restraints excluded: chain L residue 490 LEU Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 545 GLU Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 547 CYS Chi-restraints excluded: chain L residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 465 optimal weight: 8.9990 chunk 623 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 539 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 586 optimal weight: 0.6980 chunk 245 optimal weight: 9.9990 chunk 602 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 539 HIS I 99 ASN ** K 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 563 ASN M 99 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN C 355 GLN E 309 GLN E 442 ASN E 526 GLN ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 ASN J 99 ASN ** L 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.123315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.100411 restraints weight = 149474.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.099058 restraints weight = 121546.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.099313 restraints weight = 109623.075| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.8273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 59010 Z= 0.252 Angle : 0.674 16.422 79776 Z= 0.344 Chirality : 0.045 0.242 8826 Planarity : 0.005 0.055 10464 Dihedral : 5.122 47.524 8292 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.09 % Allowed : 22.60 % Favored : 74.31 % 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: -0.89 (0.10), residues: 7440 helix: 0.88 (0.11), residues: 2382 sheet: 0.94 (0.15), residues: 1098 loop : -2.09 (0.09), residues: 3960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP M 488 HIS 0.008 0.001 HIS M 52 PHE 0.039 0.002 PHE B 560 TYR 0.021 0.002 TYR E 566 ARG 0.010 0.001 ARG B 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11981.88 seconds wall clock time: 211 minutes 55.87 seconds (12715.87 seconds total)