Starting phenix.real_space_refine on Wed Nov 19 03:10:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6klx_0721/11_2025/6klx_0721.cif Found real_map, /net/cci-nas-00/data/ceres_data/6klx_0721/11_2025/6klx_0721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6klx_0721/11_2025/6klx_0721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6klx_0721/11_2025/6klx_0721.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6klx_0721/11_2025/6klx_0721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6klx_0721/11_2025/6klx_0721.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 35 5.16 5 C 12530 2.51 5 N 3304 2.21 5 O 4172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20055 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2863 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Chain: "B" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2863 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Chain: "C" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2863 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Chain: "D" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2863 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Chain: "E" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2863 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Chain: "F" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2863 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Chain: "G" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2863 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.99, per 1000 atoms: 0.25 Number of scatterers: 20055 At special positions: 0 Unit cell: (146.9, 145.77, 135.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 14 19.99 S 35 16.00 O 4172 8.00 N 3304 7.00 C 12530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 896.7 milliseconds 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4802 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 57 sheets defined 21.8% alpha, 38.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.538A pdb=" N PHE A 248 " --> pdb=" O ASN A 245 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU A 250 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.703A pdb=" N ASP A 290 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.933A pdb=" N ILE A 428 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 470 Processing helix chain 'A' and resid 501 through 504 removed outlier: 3.712A pdb=" N ASN A 504 " --> pdb=" O SER A 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 501 through 504' Processing helix chain 'A' and resid 505 through 512 removed outlier: 3.653A pdb=" N VAL A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 555 removed outlier: 3.519A pdb=" N PHE A 554 " --> pdb=" O ILE A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 593 removed outlier: 3.893A pdb=" N TYR A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.573A pdb=" N PHE B 248 " --> pdb=" O ASN B 245 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 249 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU B 250 " --> pdb=" O SER B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 250' Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 285 through 290 removed outlier: 3.586A pdb=" N ASP B 290 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 428 removed outlier: 3.841A pdb=" N ILE B 428 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 470 Processing helix chain 'B' and resid 502 through 512 removed outlier: 4.691A pdb=" N SER B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLN B 508 " --> pdb=" O ASN B 504 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 554 Processing helix chain 'B' and resid 580 through 593 removed outlier: 3.896A pdb=" N TYR B 593 " --> pdb=" O GLU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 602 Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 245 through 249 removed outlier: 3.579A pdb=" N PHE C 248 " --> pdb=" O ASN C 245 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C 249 " --> pdb=" O ASP C 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 245 through 249' Processing helix chain 'C' and resid 271 through 277 Processing helix chain 'C' and resid 285 through 290 removed outlier: 3.509A pdb=" N ASP C 290 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 428 removed outlier: 3.928A pdb=" N ILE C 428 " --> pdb=" O ASP C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 470 Processing helix chain 'C' and resid 501 through 504 removed outlier: 3.731A pdb=" N ASN C 504 " --> pdb=" O SER C 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 501 through 504' Processing helix chain 'C' and resid 505 through 512 removed outlier: 3.691A pdb=" N VAL C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 554 Processing helix chain 'C' and resid 580 through 593 removed outlier: 3.857A pdb=" N TYR C 593 " --> pdb=" O GLU C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 602 Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 245 through 250 removed outlier: 3.605A pdb=" N PHE D 248 " --> pdb=" O ASN D 245 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU D 250 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 285 through 290 removed outlier: 3.528A pdb=" N ASP D 290 " --> pdb=" O GLU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 428 removed outlier: 3.964A pdb=" N ILE D 428 " --> pdb=" O ASP D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 470 Processing helix chain 'D' and resid 501 through 504 removed outlier: 3.595A pdb=" N ASN D 504 " --> pdb=" O SER D 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 501 through 504' Processing helix chain 'D' and resid 505 through 512 removed outlier: 3.612A pdb=" N VAL D 512 " --> pdb=" O GLN D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 554 removed outlier: 3.566A pdb=" N PHE D 554 " --> pdb=" O ILE D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 575 removed outlier: 4.036A pdb=" N VAL D 575 " --> pdb=" O GLU D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 593 removed outlier: 3.756A pdb=" N TYR D 593 " --> pdb=" O GLU D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 602 Processing helix chain 'E' and resid 226 through 231 Processing helix chain 'E' and resid 245 through 250 removed outlier: 3.643A pdb=" N PHE E 248 " --> pdb=" O ASN E 245 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA E 249 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU E 250 " --> pdb=" O SER E 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 245 through 250' Processing helix chain 'E' and resid 271 through 277 Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 424 through 428 removed outlier: 3.872A pdb=" N ILE E 428 " --> pdb=" O ASP E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 470 Processing helix chain 'E' and resid 501 through 504 removed outlier: 3.718A pdb=" N ASN E 504 " --> pdb=" O SER E 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 501 through 504' Processing helix chain 'E' and resid 505 through 512 removed outlier: 3.534A pdb=" N VAL E 512 " --> pdb=" O GLN E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 554 removed outlier: 3.503A pdb=" N PHE E 554 " --> pdb=" O ILE E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 593 removed outlier: 3.814A pdb=" N TYR E 593 " --> pdb=" O GLU E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 602 Processing helix chain 'F' and resid 226 through 231 Processing helix chain 'F' and resid 245 through 250 removed outlier: 3.587A pdb=" N PHE F 248 " --> pdb=" O ASN F 245 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU F 250 " --> pdb=" O SER F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 277 Processing helix chain 'F' and resid 285 through 290 removed outlier: 3.513A pdb=" N ASP F 290 " --> pdb=" O GLU F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 470 Processing helix chain 'F' and resid 501 through 504 removed outlier: 3.668A pdb=" N ASN F 504 " --> pdb=" O SER F 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 501 through 504' Processing helix chain 'F' and resid 505 through 512 removed outlier: 3.710A pdb=" N VAL F 512 " --> pdb=" O GLN F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 554 Processing helix chain 'F' and resid 580 through 593 removed outlier: 3.886A pdb=" N TYR F 593 " --> pdb=" O GLU F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 602 Processing helix chain 'G' and resid 226 through 231 Processing helix chain 'G' and resid 245 through 250 removed outlier: 3.618A pdb=" N PHE G 248 " --> pdb=" O ASN G 245 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA G 249 " --> pdb=" O ASP G 246 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU G 250 " --> pdb=" O SER G 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 245 through 250' Processing helix chain 'G' and resid 271 through 277 Processing helix chain 'G' and resid 285 through 290 Processing helix chain 'G' and resid 424 through 428 removed outlier: 3.869A pdb=" N ILE G 428 " --> pdb=" O ASP G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 470 Processing helix chain 'G' and resid 502 through 504 No H-bonds generated for 'chain 'G' and resid 502 through 504' Processing helix chain 'G' and resid 505 through 512 removed outlier: 3.573A pdb=" N VAL G 512 " --> pdb=" O GLN G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 554 removed outlier: 3.532A pdb=" N PHE G 554 " --> pdb=" O ILE G 550 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 575 removed outlier: 3.973A pdb=" N VAL G 575 " --> pdb=" O GLU G 572 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 593 removed outlier: 3.875A pdb=" N TYR G 593 " --> pdb=" O GLU G 589 " (cutoff:3.500A) Processing helix chain 'G' and resid 598 through 602 Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 237 Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 310 removed outlier: 6.805A pdb=" N ASN A 391 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU A 306 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASN A 389 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE A 308 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR A 387 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 310 removed outlier: 6.805A pdb=" N ASN A 391 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU A 306 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASN A 389 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE A 308 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR A 387 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE A 459 " --> pdb=" O ILE A 388 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 324 removed outlier: 3.961A pdb=" N ARG G 324 " --> pdb=" O ASN A 370 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL G 322 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR A 376 " --> pdb=" O GLN G 318 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG F 324 " --> pdb=" O ASN G 370 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL F 322 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP G 374 " --> pdb=" O LYS F 320 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR G 376 " --> pdb=" O GLN F 318 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG E 324 " --> pdb=" O ASN F 370 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP F 374 " --> pdb=" O LYS E 320 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG D 324 " --> pdb=" O ASN E 370 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL D 322 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP E 374 " --> pdb=" O LYS D 320 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG C 324 " --> pdb=" O ASN D 370 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR D 376 " --> pdb=" O GLN C 318 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG B 324 " --> pdb=" O ASN C 370 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL B 322 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR C 376 " --> pdb=" O GLN B 318 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG A 324 " --> pdb=" O ASN B 370 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 322 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP B 374 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 376 " --> pdb=" O GLN A 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 416 through 422 removed outlier: 3.505A pdb=" N GLU A 416 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 411 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR A 420 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR A 409 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYS A 422 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR A 403 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN A 431 " --> pdb=" O TYR A 403 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 416 through 422 removed outlier: 3.505A pdb=" N GLU A 416 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 411 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR A 420 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR A 409 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYS A 422 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LYS A 404 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASN A 485 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 481 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN A 410 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N THR A 479 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A 412 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU A 477 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA8, first strand: chain 'A' and resid 524 through 530 removed outlier: 9.167A pdb=" N ILE A 610 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER A 515 " --> pdb=" O ILE A 610 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE A 612 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 517 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 557 through 559 Processing sheet with id=AB1, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AB2, first strand: chain 'B' and resid 299 through 310 removed outlier: 6.829A pdb=" N ASN B 391 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU B 306 " --> pdb=" O ASN B 389 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN B 389 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE B 308 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR B 387 " --> pdb=" O ILE B 308 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 299 through 310 removed outlier: 6.829A pdb=" N ASN B 391 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU B 306 " --> pdb=" O ASN B 389 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN B 389 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE B 308 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR B 387 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE B 459 " --> pdb=" O ILE B 388 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 416 through 422 removed outlier: 3.617A pdb=" N GLU B 416 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 411 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR B 420 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR B 409 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS B 422 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR B 403 " --> pdb=" O ASN B 431 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN B 431 " --> pdb=" O TYR B 403 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 416 through 422 removed outlier: 3.617A pdb=" N GLU B 416 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 411 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR B 420 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR B 409 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS B 422 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL B 405 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER B 483 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLN B 481 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR B 409 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR B 479 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU B 411 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU B 477 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 488 through 489 Processing sheet with id=AB7, first strand: chain 'B' and resid 524 through 530 removed outlier: 9.163A pdb=" N ILE B 610 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER B 515 " --> pdb=" O ILE B 610 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE B 612 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE B 517 " --> pdb=" O ILE B 612 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 557 through 559 Processing sheet with id=AB9, first strand: chain 'C' and resid 234 through 237 Processing sheet with id=AC1, first strand: chain 'C' and resid 299 through 310 removed outlier: 6.750A pdb=" N ASN C 391 " --> pdb=" O GLU C 304 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU C 306 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN C 389 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE C 308 " --> pdb=" O TYR C 387 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR C 387 " --> pdb=" O ILE C 308 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 437 through 438 removed outlier: 4.568A pdb=" N ILE C 459 " --> pdb=" O ILE C 388 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 416 through 422 removed outlier: 3.679A pdb=" N GLU C 416 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU C 411 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR C 420 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR C 409 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS C 422 " --> pdb=" O PRO C 407 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASN C 430 " --> pdb=" O LYS C 404 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 416 through 422 removed outlier: 3.679A pdb=" N GLU C 416 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU C 411 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR C 420 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR C 409 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS C 422 " --> pdb=" O PRO C 407 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL C 405 " --> pdb=" O SER C 483 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER C 483 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLN C 481 " --> pdb=" O PRO C 407 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR C 409 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR C 479 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C 411 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU C 477 " --> pdb=" O LEU C 411 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AC6, first strand: chain 'C' and resid 524 through 530 removed outlier: 9.184A pdb=" N ILE C 610 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N SER C 515 " --> pdb=" O ILE C 610 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE C 612 " --> pdb=" O SER C 515 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE C 517 " --> pdb=" O ILE C 612 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 557 through 559 Processing sheet with id=AC8, first strand: chain 'D' and resid 234 through 237 Processing sheet with id=AC9, first strand: chain 'D' and resid 299 through 310 removed outlier: 6.785A pdb=" N ASN D 391 " --> pdb=" O GLU D 304 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU D 306 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASN D 389 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE D 308 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR D 387 " --> pdb=" O ILE D 308 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 437 through 438 removed outlier: 4.548A pdb=" N ILE D 459 " --> pdb=" O ILE D 388 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 416 through 422 removed outlier: 3.616A pdb=" N GLU D 416 " --> pdb=" O LEU D 413 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU D 411 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR D 420 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR D 409 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LYS D 422 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR D 403 " --> pdb=" O ASN D 431 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN D 431 " --> pdb=" O TYR D 403 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 416 through 422 removed outlier: 3.616A pdb=" N GLU D 416 " --> pdb=" O LEU D 413 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU D 411 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR D 420 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR D 409 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LYS D 422 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL D 405 " --> pdb=" O SER D 483 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER D 483 " --> pdb=" O VAL D 405 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLN D 481 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR D 409 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR D 479 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU D 411 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU D 477 " --> pdb=" O LEU D 411 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 488 through 489 Processing sheet with id=AD5, first strand: chain 'D' and resid 524 through 530 removed outlier: 9.208A pdb=" N ILE D 610 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER D 515 " --> pdb=" O ILE D 610 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE D 612 " --> pdb=" O SER D 515 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE D 517 " --> pdb=" O ILE D 612 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 557 through 559 Processing sheet with id=AD7, first strand: chain 'E' and resid 234 through 237 Processing sheet with id=AD8, first strand: chain 'E' and resid 299 through 310 removed outlier: 6.759A pdb=" N ASN E 391 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU E 306 " --> pdb=" O ASN E 389 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN E 389 " --> pdb=" O LEU E 306 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE E 308 " --> pdb=" O TYR E 387 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR E 387 " --> pdb=" O ILE E 308 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 299 through 310 removed outlier: 6.759A pdb=" N ASN E 391 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU E 306 " --> pdb=" O ASN E 389 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN E 389 " --> pdb=" O LEU E 306 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE E 308 " --> pdb=" O TYR E 387 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR E 387 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE E 459 " --> pdb=" O ILE E 388 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 416 through 422 removed outlier: 3.540A pdb=" N GLU E 416 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU E 411 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR E 420 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR E 409 " --> pdb=" O THR E 420 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS E 422 " --> pdb=" O PRO E 407 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR E 403 " --> pdb=" O ASN E 431 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN E 431 " --> pdb=" O TYR E 403 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 416 through 422 removed outlier: 3.540A pdb=" N GLU E 416 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU E 411 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR E 420 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR E 409 " --> pdb=" O THR E 420 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS E 422 " --> pdb=" O PRO E 407 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL E 405 " --> pdb=" O SER E 483 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER E 483 " --> pdb=" O VAL E 405 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLN E 481 " --> pdb=" O PRO E 407 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR E 409 " --> pdb=" O THR E 479 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR E 479 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU E 411 " --> pdb=" O LEU E 477 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU E 477 " --> pdb=" O LEU E 411 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 488 through 489 Processing sheet with id=AE4, first strand: chain 'E' and resid 524 through 530 removed outlier: 9.179A pdb=" N ILE E 610 " --> pdb=" O SER E 513 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N SER E 515 " --> pdb=" O ILE E 610 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE E 612 " --> pdb=" O SER E 515 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE E 517 " --> pdb=" O ILE E 612 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 557 through 559 Processing sheet with id=AE6, first strand: chain 'F' and resid 234 through 237 Processing sheet with id=AE7, first strand: chain 'F' and resid 299 through 310 removed outlier: 6.746A pdb=" N ASN F 391 " --> pdb=" O GLU F 304 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU F 306 " --> pdb=" O ASN F 389 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASN F 389 " --> pdb=" O LEU F 306 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE F 308 " --> pdb=" O TYR F 387 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TYR F 387 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 437 through 438 removed outlier: 4.599A pdb=" N ILE F 459 " --> pdb=" O ILE F 388 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 416 through 422 removed outlier: 3.535A pdb=" N GLU F 416 " --> pdb=" O LEU F 413 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU F 411 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR F 420 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N THR F 409 " --> pdb=" O THR F 420 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS F 422 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR F 403 " --> pdb=" O ASN F 431 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN F 431 " --> pdb=" O TYR F 403 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 416 through 422 removed outlier: 3.535A pdb=" N GLU F 416 " --> pdb=" O LEU F 413 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU F 411 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR F 420 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N THR F 409 " --> pdb=" O THR F 420 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS F 422 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL F 405 " --> pdb=" O SER F 483 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER F 483 " --> pdb=" O VAL F 405 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLN F 481 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR F 409 " --> pdb=" O THR F 479 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR F 479 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU F 411 " --> pdb=" O LEU F 477 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU F 477 " --> pdb=" O LEU F 411 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 488 through 489 Processing sheet with id=AF3, first strand: chain 'F' and resid 524 through 530 removed outlier: 9.200A pdb=" N ILE F 610 " --> pdb=" O SER F 513 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER F 515 " --> pdb=" O ILE F 610 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE F 612 " --> pdb=" O SER F 515 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE F 517 " --> pdb=" O ILE F 612 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 557 through 559 Processing sheet with id=AF5, first strand: chain 'G' and resid 234 through 237 Processing sheet with id=AF6, first strand: chain 'G' and resid 299 through 310 removed outlier: 6.869A pdb=" N ASN G 391 " --> pdb=" O GLU G 304 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU G 306 " --> pdb=" O ASN G 389 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN G 389 " --> pdb=" O LEU G 306 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE G 308 " --> pdb=" O TYR G 387 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N TYR G 387 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA G 390 " --> pdb=" O LEU G 448 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 437 through 438 removed outlier: 4.596A pdb=" N ILE G 459 " --> pdb=" O ILE G 388 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 416 through 422 removed outlier: 3.674A pdb=" N GLU G 416 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU G 411 " --> pdb=" O LEU G 418 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR G 420 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR G 409 " --> pdb=" O THR G 420 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS G 422 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TYR G 403 " --> pdb=" O ASN G 431 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN G 431 " --> pdb=" O TYR G 403 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 416 through 422 removed outlier: 3.674A pdb=" N GLU G 416 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU G 411 " --> pdb=" O LEU G 418 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR G 420 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR G 409 " --> pdb=" O THR G 420 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS G 422 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL G 405 " --> pdb=" O SER G 483 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER G 483 " --> pdb=" O VAL G 405 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN G 481 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR G 409 " --> pdb=" O THR G 479 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR G 479 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU G 411 " --> pdb=" O LEU G 477 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU G 477 " --> pdb=" O LEU G 411 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 488 through 489 Processing sheet with id=AG2, first strand: chain 'G' and resid 524 through 530 removed outlier: 9.219A pdb=" N ILE G 610 " --> pdb=" O SER G 513 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER G 515 " --> pdb=" O ILE G 610 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE G 612 " --> pdb=" O SER G 515 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE G 517 " --> pdb=" O ILE G 612 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 557 through 559 683 hydrogen bonds defined for protein. 1743 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: 4.03 Time building geometry restraints manager: 2.35 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: 6621 1.34 - 1.45: 2995 1.45 - 1.57: 10691 1.57 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 20370 Sorted by residual: bond pdb=" CG PRO E 439 " pdb=" CD PRO E 439 " ideal model delta sigma weight residual 1.512 1.457 0.055 2.70e-02 1.37e+03 4.08e+00 bond pdb=" CG PRO G 439 " pdb=" CD PRO G 439 " ideal model delta sigma weight residual 1.512 1.458 0.054 2.70e-02 1.37e+03 4.02e+00 bond pdb=" CG PRO F 439 " pdb=" CD PRO F 439 " ideal model delta sigma weight residual 1.512 1.460 0.052 2.70e-02 1.37e+03 3.68e+00 bond pdb=" CG PRO A 439 " pdb=" CD PRO A 439 " ideal model delta sigma weight residual 1.512 1.462 0.050 2.70e-02 1.37e+03 3.50e+00 bond pdb=" CG PRO D 439 " pdb=" CD PRO D 439 " ideal model delta sigma weight residual 1.512 1.462 0.050 2.70e-02 1.37e+03 3.49e+00 ... (remaining 20365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 25956 1.36 - 2.72: 1436 2.72 - 4.07: 197 4.07 - 5.43: 21 5.43 - 6.79: 5 Bond angle restraints: 27615 Sorted by residual: angle pdb=" CA TYR F 438 " pdb=" CB TYR F 438 " pdb=" CG TYR F 438 " ideal model delta sigma weight residual 113.90 109.05 4.85 1.80e+00 3.09e-01 7.26e+00 angle pdb=" C ALA A 288 " pdb=" N ARG A 289 " pdb=" CA ARG A 289 " ideal model delta sigma weight residual 122.54 118.28 4.26 1.65e+00 3.67e-01 6.67e+00 angle pdb=" C SER G 385 " pdb=" N ALA G 386 " pdb=" CA ALA G 386 " ideal model delta sigma weight residual 121.87 117.71 4.16 1.64e+00 3.72e-01 6.44e+00 angle pdb=" C ALA F 288 " pdb=" N ARG F 289 " pdb=" CA ARG F 289 " ideal model delta sigma weight residual 122.65 118.59 4.06 1.60e+00 3.91e-01 6.43e+00 angle pdb=" C ALA C 288 " pdb=" N ARG C 289 " pdb=" CA ARG C 289 " ideal model delta sigma weight residual 122.65 118.83 3.82 1.60e+00 3.91e-01 5.70e+00 ... (remaining 27610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 11158 17.00 - 34.01: 965 34.01 - 51.01: 235 51.01 - 68.02: 27 68.02 - 85.02: 12 Dihedral angle restraints: 12397 sinusoidal: 4893 harmonic: 7504 Sorted by residual: dihedral pdb=" CA GLU E 605 " pdb=" C GLU E 605 " pdb=" N ARG E 606 " pdb=" CA ARG E 606 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLU B 605 " pdb=" C GLU B 605 " pdb=" N ARG B 606 " pdb=" CA ARG B 606 " ideal model delta harmonic sigma weight residual 180.00 154.83 25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA VAL E 602 " pdb=" C VAL E 602 " pdb=" N LYS E 603 " pdb=" CA LYS E 603 " ideal model delta harmonic sigma weight residual -180.00 -154.98 -25.02 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 12394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1705 0.038 - 0.076: 968 0.076 - 0.114: 353 0.114 - 0.152: 80 0.152 - 0.190: 9 Chirality restraints: 3115 Sorted by residual: chirality pdb=" CA PHE B 248 " pdb=" N PHE B 248 " pdb=" C PHE B 248 " pdb=" CB PHE B 248 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA ASN G 224 " pdb=" N ASN G 224 " pdb=" C ASN G 224 " pdb=" CB ASN G 224 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.98e-01 chirality pdb=" CA PHE F 248 " pdb=" N PHE F 248 " pdb=" C PHE F 248 " pdb=" CB PHE F 248 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.84e-01 ... (remaining 3112 not shown) Planarity restraints: 3619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 406 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.75e+00 pdb=" N PRO E 407 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO E 407 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 407 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 406 " 0.039 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO C 407 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 407 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 407 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 406 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO D 407 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 407 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 407 " 0.031 5.00e-02 4.00e+02 ... (remaining 3616 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1398 2.72 - 3.27: 19012 3.27 - 3.81: 31779 3.81 - 4.36: 42065 4.36 - 4.90: 73159 Nonbonded interactions: 167413 Sorted by model distance: nonbonded pdb=" OE1 GLU B 230 " pdb="CA CA B1001 " model vdw 2.177 2.510 nonbonded pdb=" OE1 GLU G 230 " pdb="CA CA G1001 " model vdw 2.182 2.510 nonbonded pdb=" O GLU B 262 " pdb="CA CA B1001 " model vdw 2.193 2.510 nonbonded pdb=" O GLU F 262 " pdb="CA CA F1001 " model vdw 2.205 2.510 nonbonded pdb=" OE1 GLU F 230 " pdb="CA CA F1001 " model vdw 2.207 2.510 ... (remaining 167408 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.250 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:7.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 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 : 0.008 0.059 20370 Z= 0.325 Angle : 0.695 6.790 27615 Z= 0.393 Chirality : 0.052 0.190 3115 Planarity : 0.006 0.060 3619 Dihedral : 13.797 85.022 7595 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.13 % Allowed : 4.43 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.13), residues: 2548 helix: -3.02 (0.17), residues: 441 sheet: -1.78 (0.18), residues: 644 loop : -2.51 (0.13), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 527 TYR 0.023 0.002 TYR F 438 PHE 0.020 0.003 PHE F 248 TRP 0.007 0.002 TRP E 374 HIS 0.002 0.001 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00781 (20370) covalent geometry : angle 0.69531 (27615) hydrogen bonds : bond 0.18520 ( 654) hydrogen bonds : angle 8.00746 ( 1743) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 233 time to evaluate : 0.830 Fit side-chains REVERT: A 218 LEU cc_start: 0.8861 (tp) cc_final: 0.8616 (tt) REVERT: A 367 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7027 (tm-30) REVERT: A 589 GLU cc_start: 0.7992 (pp20) cc_final: 0.7446 (pp20) REVERT: B 608 MET cc_start: 0.8557 (mtt) cc_final: 0.8315 (mmm) REVERT: C 564 TYR cc_start: 0.7826 (m-80) cc_final: 0.7501 (m-80) REVERT: D 441 LYS cc_start: 0.8115 (ttpp) cc_final: 0.7836 (ttpt) REVERT: E 240 ILE cc_start: 0.8237 (mt) cc_final: 0.8033 (tp) REVERT: E 318 GLN cc_start: 0.7709 (mt0) cc_final: 0.7475 (mt0) REVERT: E 367 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: E 597 LYS cc_start: 0.7704 (mttt) cc_final: 0.7495 (mmtt) REVERT: F 367 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: F 576 GLU cc_start: 0.7347 (tt0) cc_final: 0.6981 (mt-10) REVERT: G 303 MET cc_start: 0.9025 (ttp) cc_final: 0.8612 (ttp) outliers start: 3 outliers final: 0 residues processed: 236 average time/residue: 0.7014 time to fit residues: 185.7856 Evaluate side-chains 169 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain E residue 367 GLN Chi-restraints excluded: chain F residue 367 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 370 ASN A 449 ASN A 485 ASN B 224 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN C 620 ASN D 224 ASN ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 ASN F 485 ASN G 485 ASN G 582 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.116939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.096189 restraints weight = 26724.358| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.68 r_work: 0.2968 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20370 Z= 0.168 Angle : 0.560 5.872 27615 Z= 0.314 Chirality : 0.047 0.131 3115 Planarity : 0.005 0.054 3619 Dihedral : 6.024 43.296 2760 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.30 % Allowed : 9.90 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.14), residues: 2548 helix: -1.70 (0.22), residues: 448 sheet: -1.02 (0.18), residues: 637 loop : -1.93 (0.14), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 324 TYR 0.017 0.001 TYR F 438 PHE 0.022 0.002 PHE F 248 TRP 0.011 0.001 TRP A 374 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00396 (20370) covalent geometry : angle 0.56014 (27615) hydrogen bonds : bond 0.03963 ( 654) hydrogen bonds : angle 5.35991 ( 1743) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 262 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8197 (tp30) REVERT: B 451 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8720 (ptm) REVERT: C 543 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7473 (mm-30) REVERT: D 279 SER cc_start: 0.8739 (m) cc_final: 0.8465 (p) REVERT: D 318 GLN cc_start: 0.7706 (mt0) cc_final: 0.7493 (mt0) REVERT: D 441 LYS cc_start: 0.8273 (ttpp) cc_final: 0.7967 (ttpt) REVERT: E 318 GLN cc_start: 0.7744 (mt0) cc_final: 0.7496 (mt0) REVERT: E 543 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7401 (mm-30) REVERT: F 317 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7585 (m-30) REVERT: F 576 GLU cc_start: 0.7847 (tt0) cc_final: 0.7278 (mt-10) REVERT: G 303 MET cc_start: 0.9236 (ttp) cc_final: 0.8845 (ttp) REVERT: G 317 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7470 (m-30) outliers start: 29 outliers final: 9 residues processed: 199 average time/residue: 0.6051 time to fit residues: 137.5807 Evaluate side-chains 166 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 317 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 100 optimal weight: 2.9990 chunk 214 optimal weight: 0.5980 chunk 249 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 449 ASN B 224 ASN B 370 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN D 224 ASN ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN G 370 ASN G 582 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.114704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.093803 restraints weight = 26950.320| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.67 r_work: 0.2949 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 20370 Z= 0.235 Angle : 0.595 6.581 27615 Z= 0.331 Chirality : 0.048 0.146 3115 Planarity : 0.006 0.058 3619 Dihedral : 5.990 43.443 2757 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.15 % Allowed : 11.91 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.15), residues: 2548 helix: -1.24 (0.23), residues: 448 sheet: -0.69 (0.19), residues: 637 loop : -1.79 (0.14), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 324 TYR 0.020 0.002 TYR F 438 PHE 0.027 0.002 PHE F 248 TRP 0.007 0.002 TRP E 374 HIS 0.002 0.001 HIS F 313 Details of bonding type rmsd covalent geometry : bond 0.00570 (20370) covalent geometry : angle 0.59525 (27615) hydrogen bonds : bond 0.04049 ( 654) hydrogen bonds : angle 5.23870 ( 1743) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 262 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8276 (tp30) REVERT: B 441 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8020 (ttpm) REVERT: B 608 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.7289 (mmm) REVERT: C 543 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7490 (mm-30) REVERT: D 251 GLN cc_start: 0.8225 (mp10) cc_final: 0.8003 (mp10) REVERT: D 320 LYS cc_start: 0.7932 (mttm) cc_final: 0.7691 (tppt) REVERT: E 318 GLN cc_start: 0.7924 (mt0) cc_final: 0.7722 (mt0) REVERT: E 543 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7433 (mm-30) REVERT: F 304 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7343 (mm-30) REVERT: F 317 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: F 576 GLU cc_start: 0.7869 (tt0) cc_final: 0.7302 (mt-10) REVERT: G 303 MET cc_start: 0.9254 (ttp) cc_final: 0.8868 (ttp) REVERT: G 317 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7477 (m-30) outliers start: 48 outliers final: 25 residues processed: 194 average time/residue: 0.6370 time to fit residues: 140.2723 Evaluate side-chains 183 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain C residue 588 LYS Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 310 THR Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain F residue 304 GLU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain G residue 451 MET Chi-restraints excluded: chain G residue 491 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 217 optimal weight: 0.5980 chunk 228 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 173 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 449 ASN B 224 ASN B 485 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN D 224 ASN D 318 GLN D 367 GLN ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 485 ASN G 224 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.118550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.097711 restraints weight = 26714.256| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.70 r_work: 0.2993 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20370 Z= 0.124 Angle : 0.498 4.681 27615 Z= 0.279 Chirality : 0.045 0.125 3115 Planarity : 0.005 0.053 3619 Dihedral : 5.487 42.944 2757 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.15 % Allowed : 13.70 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.15), residues: 2548 helix: -0.80 (0.24), residues: 448 sheet: -0.23 (0.19), residues: 644 loop : -1.68 (0.14), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 324 TYR 0.014 0.001 TYR B 438 PHE 0.016 0.001 PHE B 248 TRP 0.008 0.001 TRP E 374 HIS 0.001 0.000 HIS G 313 Details of bonding type rmsd covalent geometry : bond 0.00289 (20370) covalent geometry : angle 0.49765 (27615) hydrogen bonds : bond 0.03168 ( 654) hydrogen bonds : angle 4.77257 ( 1743) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 172 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: B 262 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8301 (tp30) REVERT: B 451 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8708 (ptm) REVERT: C 576 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6621 (pt0) REVERT: D 251 GLN cc_start: 0.8112 (mp10) cc_final: 0.7903 (mp10) REVERT: E 318 GLN cc_start: 0.7835 (mt0) cc_final: 0.7607 (mt0) REVERT: E 543 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7464 (mm-30) REVERT: E 588 LYS cc_start: 0.7654 (ttpt) cc_final: 0.7046 (ttmm) REVERT: F 304 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7008 (mm-30) REVERT: F 317 ASP cc_start: 0.7937 (t70) cc_final: 0.7532 (m-30) REVERT: F 491 SER cc_start: 0.7073 (OUTLIER) cc_final: 0.6539 (p) REVERT: F 576 GLU cc_start: 0.7841 (tt0) cc_final: 0.7284 (mt-10) REVERT: G 303 MET cc_start: 0.9218 (ttp) cc_final: 0.8808 (ttp) REVERT: G 317 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: G 491 SER cc_start: 0.7388 (OUTLIER) cc_final: 0.6978 (p) outliers start: 48 outliers final: 18 residues processed: 199 average time/residue: 0.6434 time to fit residues: 145.6311 Evaluate side-chains 176 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 588 LYS Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 310 THR Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 568 ILE Chi-restraints excluded: chain F residue 304 GLU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain G residue 491 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 159 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 189 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 247 optimal weight: 4.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 370 ASN A 449 ASN B 224 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN D 224 ASN D 318 GLN ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 449 ASN G 224 ASN G 582 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.095407 restraints weight = 26644.247| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.68 r_work: 0.2976 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20370 Z= 0.170 Angle : 0.527 5.476 27615 Z= 0.294 Chirality : 0.046 0.139 3115 Planarity : 0.005 0.054 3619 Dihedral : 5.557 42.673 2757 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.51 % Allowed : 14.60 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.15), residues: 2548 helix: -0.70 (0.24), residues: 448 sheet: -0.17 (0.19), residues: 651 loop : -1.62 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 324 TYR 0.018 0.001 TYR F 438 PHE 0.021 0.002 PHE F 248 TRP 0.006 0.001 TRP C 374 HIS 0.001 0.000 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00409 (20370) covalent geometry : angle 0.52730 (27615) hydrogen bonds : bond 0.03379 ( 654) hydrogen bonds : angle 4.81539 ( 1743) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 166 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: A 543 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: B 262 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8321 (tp30) REVERT: B 441 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8057 (ttpm) REVERT: B 451 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8760 (ptm) REVERT: C 576 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6581 (pt0) REVERT: D 251 GLN cc_start: 0.8143 (mp10) cc_final: 0.7899 (mp10) REVERT: E 318 GLN cc_start: 0.7851 (mt0) cc_final: 0.7619 (mt0) REVERT: E 543 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7474 (mm-30) REVERT: F 304 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7220 (mm-30) REVERT: F 379 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8326 (p) REVERT: F 576 GLU cc_start: 0.7838 (tt0) cc_final: 0.7270 (mt-10) REVERT: G 303 MET cc_start: 0.9222 (ttp) cc_final: 0.8823 (ttp) REVERT: G 317 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7481 (m-30) outliers start: 56 outliers final: 32 residues processed: 197 average time/residue: 0.6402 time to fit residues: 143.0346 Evaluate side-chains 194 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 588 LYS Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain E residue 310 THR Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 451 MET Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 568 ILE Chi-restraints excluded: chain F residue 304 GLU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain G residue 399 THR Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 523 GLN Chi-restraints excluded: chain G residue 568 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 234 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 chunk 243 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 449 ASN B 224 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 620 ASN D 224 ASN D 318 GLN D 367 GLN ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.115894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.095164 restraints weight = 26529.057| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.67 r_work: 0.2964 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20370 Z= 0.190 Angle : 0.543 5.460 27615 Z= 0.302 Chirality : 0.046 0.135 3115 Planarity : 0.005 0.054 3619 Dihedral : 5.658 42.831 2757 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.60 % Allowed : 15.05 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.15), residues: 2548 helix: -0.66 (0.24), residues: 448 sheet: -0.12 (0.19), residues: 651 loop : -1.58 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 324 TYR 0.019 0.002 TYR F 438 PHE 0.023 0.002 PHE F 248 TRP 0.006 0.001 TRP E 374 HIS 0.001 0.000 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00458 (20370) covalent geometry : angle 0.54327 (27615) hydrogen bonds : bond 0.03476 ( 654) hydrogen bonds : angle 4.86363 ( 1743) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 164 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: B 262 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8287 (tp30) REVERT: C 576 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6406 (pt0) REVERT: D 251 GLN cc_start: 0.8150 (mp10) cc_final: 0.7872 (mp10) REVERT: D 289 ARG cc_start: 0.8731 (mtm-85) cc_final: 0.8505 (mtm-85) REVERT: E 304 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.7884 (mm-30) REVERT: E 318 GLN cc_start: 0.7853 (mt0) cc_final: 0.7623 (mt0) REVERT: E 543 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7448 (mm-30) REVERT: E 588 LYS cc_start: 0.7638 (ttpt) cc_final: 0.7064 (ttmm) REVERT: F 286 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8470 (tp) REVERT: F 304 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7280 (mm-30) REVERT: F 576 GLU cc_start: 0.7850 (tt0) cc_final: 0.7273 (mt-10) REVERT: G 303 MET cc_start: 0.9236 (ttp) cc_final: 0.8846 (ttp) outliers start: 58 outliers final: 40 residues processed: 198 average time/residue: 0.6567 time to fit residues: 147.1692 Evaluate side-chains 203 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 588 LYS Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 310 THR Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 451 MET Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 568 ILE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 304 GLU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 399 THR Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 523 GLN Chi-restraints excluded: chain G residue 568 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 218 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 241 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 449 ASN B 224 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 620 ASN D 224 ASN D 318 GLN D 582 ASN ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.118383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.097579 restraints weight = 26671.404| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.69 r_work: 0.2986 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20370 Z= 0.139 Angle : 0.503 4.954 27615 Z= 0.281 Chirality : 0.045 0.165 3115 Planarity : 0.005 0.052 3619 Dihedral : 5.408 42.346 2757 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.42 % Allowed : 15.85 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.15), residues: 2548 helix: -0.52 (0.24), residues: 448 sheet: 0.11 (0.19), residues: 644 loop : -1.54 (0.14), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 324 TYR 0.015 0.001 TYR F 438 PHE 0.017 0.001 PHE F 248 TRP 0.007 0.001 TRP A 374 HIS 0.001 0.000 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00329 (20370) covalent geometry : angle 0.50328 (27615) hydrogen bonds : bond 0.03111 ( 654) hydrogen bonds : angle 4.65706 ( 1743) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 165 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7411 (mt-10) REVERT: B 262 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8308 (tp30) REVERT: B 451 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8766 (ptm) REVERT: C 576 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6407 (pt0) REVERT: D 251 GLN cc_start: 0.8115 (mp10) cc_final: 0.7822 (mp10) REVERT: E 304 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.7842 (mm-30) REVERT: E 318 GLN cc_start: 0.7816 (mt0) cc_final: 0.7594 (mt0) REVERT: E 543 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: E 588 LYS cc_start: 0.7645 (ttpt) cc_final: 0.7037 (ttmm) REVERT: F 304 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7152 (mm-30) REVERT: F 317 ASP cc_start: 0.7930 (t0) cc_final: 0.7448 (m-30) REVERT: F 379 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8369 (p) REVERT: F 576 GLU cc_start: 0.7842 (tt0) cc_final: 0.7276 (mt-10) REVERT: G 303 MET cc_start: 0.9209 (ttp) cc_final: 0.8804 (ttp) outliers start: 54 outliers final: 34 residues processed: 199 average time/residue: 0.6422 time to fit residues: 144.7747 Evaluate side-chains 196 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 588 LYS Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 310 THR Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 451 MET Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 568 ILE Chi-restraints excluded: chain F residue 304 GLU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 399 THR Chi-restraints excluded: chain G residue 523 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 158 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 178 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 236 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 370 ASN A 449 ASN B 224 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 620 ASN D 224 ASN D 318 GLN ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN G 582 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.096268 restraints weight = 26528.796| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.68 r_work: 0.2987 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20370 Z= 0.143 Angle : 0.505 5.044 27615 Z= 0.281 Chirality : 0.045 0.137 3115 Planarity : 0.005 0.053 3619 Dihedral : 5.370 42.054 2757 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.15 % Allowed : 16.35 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.15), residues: 2548 helix: -0.41 (0.24), residues: 448 sheet: 0.15 (0.20), residues: 651 loop : -1.48 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 289 TYR 0.017 0.001 TYR F 438 PHE 0.019 0.002 PHE F 248 TRP 0.006 0.001 TRP E 374 HIS 0.001 0.000 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00341 (20370) covalent geometry : angle 0.50470 (27615) hydrogen bonds : bond 0.03126 ( 654) hydrogen bonds : angle 4.62807 ( 1743) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7410 (mt-10) REVERT: B 262 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8306 (tp30) REVERT: B 451 MET cc_start: 0.9220 (ptp) cc_final: 0.8775 (ptm) REVERT: C 576 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6241 (pt0) REVERT: D 251 GLN cc_start: 0.8099 (mp10) cc_final: 0.7799 (mp10) REVERT: E 304 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.7864 (mm-30) REVERT: E 318 GLN cc_start: 0.7806 (mt0) cc_final: 0.7570 (mt0) REVERT: E 543 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7510 (mm-30) REVERT: E 588 LYS cc_start: 0.7634 (ttpt) cc_final: 0.7040 (ttmm) REVERT: F 286 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8535 (tp) REVERT: F 304 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: F 379 SER cc_start: 0.8545 (OUTLIER) cc_final: 0.8345 (p) REVERT: F 576 GLU cc_start: 0.7853 (tt0) cc_final: 0.7303 (mt-10) REVERT: G 303 MET cc_start: 0.9207 (ttp) cc_final: 0.8802 (ttp) outliers start: 48 outliers final: 35 residues processed: 189 average time/residue: 0.6489 time to fit residues: 138.8545 Evaluate side-chains 194 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 310 THR Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 451 MET Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 568 ILE Chi-restraints excluded: chain E residue 579 PHE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 304 GLU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 568 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 54 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 162 optimal weight: 0.3980 chunk 244 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 449 ASN B 224 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 620 ASN D 224 ASN D 318 GLN ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.118388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.097650 restraints weight = 26493.589| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.67 r_work: 0.2985 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20370 Z= 0.156 Angle : 0.513 5.283 27615 Z= 0.285 Chirality : 0.045 0.129 3115 Planarity : 0.005 0.056 3619 Dihedral : 5.404 41.761 2757 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.24 % Allowed : 16.35 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.15), residues: 2548 helix: -0.36 (0.24), residues: 448 sheet: 0.18 (0.20), residues: 651 loop : -1.48 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 289 TYR 0.017 0.001 TYR F 438 PHE 0.019 0.002 PHE F 248 TRP 0.007 0.001 TRP A 374 HIS 0.001 0.000 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00373 (20370) covalent geometry : angle 0.51291 (27615) hydrogen bonds : bond 0.03185 ( 654) hydrogen bonds : angle 4.65343 ( 1743) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 155 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7427 (mt-10) REVERT: B 262 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8299 (tp30) REVERT: B 451 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8796 (ptm) REVERT: C 576 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.6247 (pt0) REVERT: D 251 GLN cc_start: 0.8104 (mp10) cc_final: 0.7798 (mp10) REVERT: E 304 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.7886 (mm-30) REVERT: E 318 GLN cc_start: 0.7821 (mt0) cc_final: 0.7586 (mt0) REVERT: E 543 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7495 (mm-30) REVERT: E 588 LYS cc_start: 0.7632 (ttpt) cc_final: 0.7035 (ttmm) REVERT: F 286 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8526 (tp) REVERT: F 304 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7179 (mm-30) REVERT: F 379 SER cc_start: 0.8589 (OUTLIER) cc_final: 0.8369 (p) REVERT: F 576 GLU cc_start: 0.7852 (tt0) cc_final: 0.7302 (mt-10) REVERT: G 303 MET cc_start: 0.9207 (ttp) cc_final: 0.8800 (ttp) outliers start: 50 outliers final: 37 residues processed: 186 average time/residue: 0.6622 time to fit residues: 139.5793 Evaluate side-chains 196 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 310 THR Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 568 ILE Chi-restraints excluded: chain E residue 579 PHE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 304 GLU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 399 THR Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 568 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 229 optimal weight: 1.9990 chunk 186 optimal weight: 0.5980 chunk 218 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 208 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 175 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 449 ASN B 224 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN D 224 ASN D 318 GLN ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.097917 restraints weight = 26651.549| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.69 r_work: 0.2994 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20370 Z= 0.131 Angle : 0.493 4.881 27615 Z= 0.275 Chirality : 0.044 0.125 3115 Planarity : 0.005 0.055 3619 Dihedral : 5.264 41.195 2757 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.93 % Allowed : 16.66 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.15), residues: 2548 helix: -0.27 (0.25), residues: 448 sheet: 0.36 (0.20), residues: 644 loop : -1.45 (0.14), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 289 TYR 0.015 0.001 TYR F 438 PHE 0.017 0.001 PHE E 579 TRP 0.007 0.001 TRP A 374 HIS 0.001 0.000 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00311 (20370) covalent geometry : angle 0.49251 (27615) hydrogen bonds : bond 0.03011 ( 654) hydrogen bonds : angle 4.54176 ( 1743) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: B 262 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8323 (tp30) REVERT: B 451 MET cc_start: 0.9232 (ptp) cc_final: 0.8810 (ptm) REVERT: B 588 LYS cc_start: 0.7951 (ptmt) cc_final: 0.7569 (pptt) REVERT: C 576 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6234 (pt0) REVERT: D 251 GLN cc_start: 0.8081 (mp10) cc_final: 0.7792 (mp10) REVERT: E 304 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.7823 (mm-30) REVERT: E 318 GLN cc_start: 0.7810 (mt0) cc_final: 0.7579 (mt0) REVERT: E 543 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7380 (mm-30) REVERT: E 588 LYS cc_start: 0.7619 (ttpt) cc_final: 0.7026 (ttmm) REVERT: F 286 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8541 (tp) REVERT: F 304 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7012 (mm-30) REVERT: F 379 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8345 (p) REVERT: F 576 GLU cc_start: 0.7834 (tt0) cc_final: 0.7285 (mt-10) REVERT: G 303 MET cc_start: 0.9199 (ttp) cc_final: 0.8791 (ttp) outliers start: 43 outliers final: 33 residues processed: 189 average time/residue: 0.6511 time to fit residues: 139.4693 Evaluate side-chains 192 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 310 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 568 ILE Chi-restraints excluded: chain E residue 579 PHE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 304 GLU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 399 THR Chi-restraints excluded: chain G residue 568 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 54 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 238 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 212 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 449 ASN B 224 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN D 224 ASN D 318 GLN ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN G 582 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.119788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.099127 restraints weight = 26366.163| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.67 r_work: 0.3008 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20370 Z= 0.117 Angle : 0.480 4.674 27615 Z= 0.268 Chirality : 0.044 0.126 3115 Planarity : 0.004 0.054 3619 Dihedral : 5.134 40.387 2757 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.93 % Allowed : 16.79 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.15), residues: 2548 helix: -0.17 (0.25), residues: 448 sheet: 0.44 (0.20), residues: 644 loop : -1.42 (0.14), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 289 TYR 0.014 0.001 TYR C 438 PHE 0.016 0.001 PHE E 579 TRP 0.007 0.001 TRP A 374 HIS 0.001 0.000 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00276 (20370) covalent geometry : angle 0.48037 (27615) hydrogen bonds : bond 0.02892 ( 654) hydrogen bonds : angle 4.43694 ( 1743) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6155.60 seconds wall clock time: 106 minutes 1.89 seconds (6361.89 seconds total)