Starting phenix.real_space_refine on Sun Sep 13 02:19:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6klx_0721/09_2026/6klx_0721.cif Found real_map, /net/cci-nas-00/data/ceres_data/6klx_0721/09_2026/6klx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6klx_0721/09_2026/6klx_0721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6klx_0721/09_2026/6klx_0721.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6klx_0721/09_2026/6klx_0721.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6klx_0721/09_2026/6klx_0721.cif" model { file = "/net/cci-nas-00/data/ceres_data/6klx_0721/09_2026/6klx_0721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6klx_0721/09_2026/6klx_0721.cif" } 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-2.2.1-6174/lib/python3.11/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: 4.98, 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: 1.59 Conformation dependent library (CDL) restraints added in 873.6 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: 0.84 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: 3.84 Time building geometry restraints manager: 2.19 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.690 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 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/Z covalent geometry : bond 0.00781 / 0.32 (20370) covalent geometry : angle 0.69531 / 0.39 (27615) hydrogen bonds : bond 0.18520 / 11.51 ( 654) hydrogen bonds : angle 8.00746 / 5.49 ( 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 : 0.799 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: 0.8556 (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: 0.6569 time to fit residues: 175.0072 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 : 0.806 ------------------------------------------------------------------------------- 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... 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.116900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.096156 restraints weight = 26725.649| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.68 r_work: 0.2967 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: 0.8689 moved from start: 0.1019 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= 0.167 Angle : 0.561 5.837 27615 Z= 0.314 Chirality : 0.046 0.129 3115 Planarity : 0.005 0.053 3619 Dihedral : 6.035 43.284 2760 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.25 % Allowed : 9.90 % Favored : 88.85 % 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: -2.47 (0.14), residues: 2548 helix: -1.71 (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 0.013 0.000 ARG B 324 TYR 0.017 0.001 TYR F 438 PHE 0.023 0.002 PHE B 248 TRP 0.011 0.001 TRP E 374 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (20370) covalent geometry : angle 0.56138 / 0.31 (27615) hydrogen bonds : bond 0.04011 / 2.58 ( 654) hydrogen bonds : angle 5.37787 / 3.69 ( 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 209 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 262 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8193 (tp30) REVERT: B 451 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8721 (ptm) REVERT: C 543 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7469 (mm-30) REVERT: D 279 SER cc_start: 0.8739 (m) cc_final: 0.8463 (p) REVERT: D 318 GLN cc_start: 0.7720 (mt0) cc_final: 0.7519 (mt0) REVERT: D 441 LYS cc_start: 0.8274 (ttpp) cc_final: 0.7967 (ttpt) REVERT: E 318 GLN cc_start: 0.7781 (mt0) cc_final: 0.7537 (mt0) REVERT: E 543 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7397 (mm-30) REVERT: F 317 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: F 576 GLU cc_start: 0.7844 (tt0) cc_final: 0.7275 (mt-10) REVERT: G 303 MET cc_start: 0.9238 (ttp) cc_final: 0.8848 (ttp) REVERT: G 317 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7470 (m-30) outliers start: 28 outliers final: 9 residues processed: 197 average time/residue: 0.5602 time to fit residues: 126.8169 Evaluate side-chains 168 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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: 0.6980 chunk 214 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 203 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 E 224 ASN ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 485 ASN G 224 ASN G 370 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 = 0.3363 r_free = 0.3363 target = 0.116710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.095866 restraints weight = 26728.398| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.68 r_work: 0.2957 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1144 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= 0.208 Angle : 0.574 6.161 27615 Z= 0.319 Chirality : 0.047 0.139 3115 Planarity : 0.005 0.057 3619 Dihedral : 5.899 43.425 2757 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.10 % Allowed : 11.87 % Favored : 86.03 % 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: -2.06 (0.15), residues: 2548 helix: -1.20 (0.23), residues: 448 sheet: -0.65 (0.19), residues: 637 loop : -1.78 (0.14), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 324 TYR 0.019 0.002 TYR F 438 PHE 0.025 0.002 PHE F 248 TRP 0.007 0.001 TRP E 374 HIS 0.002 0.001 HIS F 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (20370) covalent geometry : angle 0.57375 / 0.32 (27615) hydrogen bonds : bond 0.03903 / 2.50 ( 654) hydrogen bonds : angle 5.17378 / 3.55 ( 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 213 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: B 262 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8273 (tp30) REVERT: B 451 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8726 (ptm) REVERT: B 608 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7335 (mmm) REVERT: C 543 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7490 (mm-30) REVERT: D 279 SER cc_start: 0.8778 (m) cc_final: 0.8491 (p) REVERT: D 320 LYS cc_start: 0.7907 (mttm) cc_final: 0.7661 (tppt) REVERT: D 441 LYS cc_start: 0.8265 (ttpp) cc_final: 0.7956 (ttpt) REVERT: E 318 GLN cc_start: 0.7912 (mt0) cc_final: 0.7698 (mt0) REVERT: E 543 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7432 (mm-30) REVERT: F 304 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7309 (mm-30) REVERT: F 317 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7517 (m-30) REVERT: F 367 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: F 576 GLU cc_start: 0.7842 (tt0) cc_final: 0.7276 (mt-10) REVERT: G 303 MET cc_start: 0.9244 (ttp) cc_final: 0.8863 (ttp) REVERT: G 317 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7472 (m-30) REVERT: G 608 MET cc_start: 0.8668 (mtt) cc_final: 0.8352 (mmm) outliers start: 47 outliers final: 25 residues processed: 192 average time/residue: 0.5569 time to fit residues: 122.3714 Evaluate side-chains 186 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 A residue 568 ILE 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 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 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: 0.6980 chunk 228 optimal weight: 4.9990 chunk 188 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 370 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 = 0.3334 r_free = 0.3334 target = 0.114929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.093933 restraints weight = 26893.532| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.70 r_work: 0.2970 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20370 Z= 0.163 Angle : 0.530 5.564 27615 Z= 0.296 Chirality : 0.046 0.129 3115 Planarity : 0.005 0.054 3619 Dihedral : 5.679 43.216 2757 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.15 % Allowed : 13.75 % Favored : 84.10 % 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: -1.77 (0.15), residues: 2548 helix: -0.86 (0.24), residues: 448 sheet: -0.38 (0.19), residues: 651 loop : -1.68 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 324 TYR 0.017 0.001 TYR F 438 PHE 0.020 0.002 PHE F 248 TRP 0.007 0.001 TRP E 374 HIS 0.001 0.000 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (20370) covalent geometry : angle 0.52998 / 0.30 (27615) hydrogen bonds : bond 0.03451 / 2.22 ( 654) hydrogen bonds : angle 4.92792 / 3.38 ( 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 217 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 169 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: B 262 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8303 (tp30) REVERT: B 451 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.8728 (ptm) REVERT: B 608 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.7357 (mmm) REVERT: C 576 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6599 (pt0) REVERT: D 251 GLN cc_start: 0.8169 (mp10) cc_final: 0.7938 (mp10) REVERT: D 279 SER cc_start: 0.8760 (m) cc_final: 0.8459 (p) REVERT: E 318 GLN cc_start: 0.7929 (mt0) cc_final: 0.7706 (mt0) REVERT: E 543 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7469 (mm-30) REVERT: F 304 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7237 (mm-30) REVERT: F 576 GLU cc_start: 0.7836 (tt0) cc_final: 0.7277 (mt-10) REVERT: G 303 MET cc_start: 0.9230 (ttp) cc_final: 0.8836 (ttp) REVERT: G 317 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7432 (m-30) REVERT: G 491 SER cc_start: 0.7561 (OUTLIER) cc_final: 0.7356 (p) REVERT: G 608 MET cc_start: 0.8575 (mtt) cc_final: 0.8308 (mmm) outliers start: 48 outliers final: 26 residues processed: 195 average time/residue: 0.6058 time to fit residues: 134.5472 Evaluate side-chains 186 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 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 568 ILE Chi-restraints excluded: chain B residue 608 MET 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 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 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 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 Chi-restraints excluded: chain G residue 576 GLU 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: 0.9990 chunk 64 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 247 optimal weight: 2.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3378 r_free = 0.3378 target = 0.117889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.097171 restraints weight = 26644.042| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.68 r_work: 0.2984 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1470 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= 0.146 Angle : 0.510 5.074 27615 Z= 0.285 Chirality : 0.045 0.135 3115 Planarity : 0.005 0.052 3619 Dihedral : 5.496 42.641 2757 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.33 % Allowed : 14.78 % 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: -1.55 (0.15), residues: 2548 helix: -0.68 (0.24), residues: 448 sheet: -0.09 (0.19), residues: 644 loop : -1.62 (0.14), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 324 TYR 0.016 0.001 TYR F 438 PHE 0.019 0.002 PHE F 248 TRP 0.007 0.001 TRP C 374 HIS 0.001 0.000 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (20370) covalent geometry : angle 0.50951 / 0.28 (27615) hydrogen bonds : bond 0.03249 / 2.10 ( 654) hydrogen bonds : angle 4.76603 / 3.27 ( 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 215 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7412 (mt-10) REVERT: B 262 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8305 (tp30) REVERT: B 608 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7135 (mmm) REVERT: C 367 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7055 (tm-30) REVERT: C 576 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6591 (pt0) REVERT: D 251 GLN cc_start: 0.8120 (mp10) cc_final: 0.7866 (mp10) REVERT: D 279 SER cc_start: 0.8760 (m) cc_final: 0.8451 (p) REVERT: E 318 GLN cc_start: 0.7834 (mt0) cc_final: 0.7601 (mt0) REVERT: E 543 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7488 (mm-30) REVERT: E 588 LYS cc_start: 0.7628 (ttpt) cc_final: 0.7021 (ttmm) REVERT: F 304 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7186 (mm-30) REVERT: F 367 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: F 379 SER cc_start: 0.8616 (OUTLIER) cc_final: 0.8340 (p) REVERT: F 576 GLU cc_start: 0.7825 (tt0) cc_final: 0.7262 (mt-10) REVERT: G 303 MET cc_start: 0.9227 (ttp) cc_final: 0.8835 (ttp) REVERT: G 317 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7534 (m-30) REVERT: G 491 SER cc_start: 0.7526 (OUTLIER) cc_final: 0.7249 (p) REVERT: G 608 MET cc_start: 0.8517 (mtt) cc_final: 0.8308 (mmm) outliers start: 52 outliers final: 24 residues processed: 192 average time/residue: 0.6262 time to fit residues: 136.9651 Evaluate side-chains 183 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 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 B residue 608 MET Chi-restraints excluded: chain C residue 286 LEU 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 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 376 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 G residue 286 LEU Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain G residue 491 SER Chi-restraints excluded: chain G residue 523 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 234 optimal weight: 0.9980 chunk 210 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3384 r_free = 0.3384 target = 0.118285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.097456 restraints weight = 26313.609| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.70 r_work: 0.2987 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1580 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= 0.136 Angle : 0.498 4.818 27615 Z= 0.278 Chirality : 0.045 0.152 3115 Planarity : 0.005 0.051 3619 Dihedral : 5.379 42.307 2757 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.37 % Allowed : 15.14 % Favored : 82.49 % 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: -1.40 (0.15), residues: 2548 helix: -0.55 (0.24), residues: 448 sheet: 0.08 (0.19), residues: 644 loop : -1.56 (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 0.018 0.001 PHE F 248 TRP 0.008 0.001 TRP C 374 HIS 0.001 0.000 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (20370) covalent geometry : angle 0.49827 / 0.28 (27615) hydrogen bonds : bond 0.03122 / 2.02 ( 654) hydrogen bonds : angle 4.65394 / 3.20 ( 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 219 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 166 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7385 (mt-10) REVERT: B 262 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8330 (tp30) REVERT: B 451 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8746 (ptm) REVERT: C 367 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7058 (tm-30) REVERT: C 576 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6597 (pt0) REVERT: D 251 GLN cc_start: 0.8096 (mp10) cc_final: 0.7823 (mp10) REVERT: D 279 SER cc_start: 0.8744 (m) cc_final: 0.8450 (p) REVERT: E 304 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.7835 (mm-30) REVERT: E 318 GLN cc_start: 0.7802 (mt0) cc_final: 0.7556 (mt0) REVERT: E 543 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: E 588 LYS cc_start: 0.7620 (ttpt) cc_final: 0.7017 (ttmm) REVERT: F 304 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7139 (mm-30) REVERT: F 317 ASP cc_start: 0.7957 (t0) cc_final: 0.7518 (m-30) REVERT: F 367 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: F 379 SER cc_start: 0.8610 (OUTLIER) cc_final: 0.8386 (p) REVERT: F 576 GLU cc_start: 0.7815 (tt0) cc_final: 0.7260 (mt-10) REVERT: G 303 MET cc_start: 0.9217 (ttp) cc_final: 0.8824 (ttp) outliers start: 53 outliers final: 37 residues processed: 197 average time/residue: 0.6025 time to fit residues: 135.6248 Evaluate side-chains 203 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain G residue 568 ILE Chi-restraints excluded: chain G residue 588 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 74 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 218 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3369 r_free = 0.3369 target = 0.117236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.096447 restraints weight = 26585.256| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.68 r_work: 0.2987 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1606 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= 0.142 Angle : 0.501 5.178 27615 Z= 0.279 Chirality : 0.045 0.127 3115 Planarity : 0.005 0.051 3619 Dihedral : 5.354 42.126 2757 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.69 % Allowed : 15.32 % Favored : 82.00 % 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: -1.33 (0.15), residues: 2548 helix: -0.45 (0.24), residues: 448 sheet: 0.09 (0.19), residues: 651 loop : -1.52 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 324 TYR 0.017 0.001 TYR F 438 PHE 0.018 0.002 PHE F 248 TRP 0.006 0.001 TRP A 374 HIS 0.001 0.000 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (20370) covalent geometry : angle 0.50061 / 0.28 (27615) hydrogen bonds : bond 0.03118 / 2.01 ( 654) hydrogen bonds : angle 4.62584 / 3.18 ( 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 223 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 163 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: B 262 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8306 (tp30) REVERT: B 451 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8761 (ptm) REVERT: C 367 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7073 (tm-30) REVERT: C 576 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6586 (pt0) REVERT: D 251 GLN cc_start: 0.8068 (mp10) cc_final: 0.7773 (mp10) REVERT: D 279 SER cc_start: 0.8757 (m) cc_final: 0.8466 (p) REVERT: E 304 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.7848 (mm-30) REVERT: E 543 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7471 (mm-30) REVERT: E 588 LYS cc_start: 0.7622 (ttpt) cc_final: 0.7019 (ttmm) REVERT: F 286 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8554 (tp) REVERT: F 304 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7135 (mm-30) REVERT: F 379 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8381 (p) REVERT: F 576 GLU cc_start: 0.7828 (tt0) cc_final: 0.7280 (mt-10) REVERT: G 303 MET cc_start: 0.9212 (ttp) cc_final: 0.8808 (ttp) outliers start: 60 outliers final: 33 residues processed: 199 average time/residue: 0.5985 time to fit residues: 135.6445 Evaluate side-chains 193 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 441 LYS Chi-restraints excluded: chain B residue 451 MET 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 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 399 THR 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 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 523 GLN Chi-restraints excluded: chain G residue 588 LYS 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: 2.9990 chunk 80 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 178 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 236 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3389 r_free = 0.3389 target = 0.118714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.097861 restraints weight = 26479.791| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.69 r_work: 0.2998 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20370 Z= 0.127 Angle : 0.488 5.150 27615 Z= 0.272 Chirality : 0.044 0.125 3115 Planarity : 0.005 0.051 3619 Dihedral : 5.262 41.781 2757 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.15 % Allowed : 16.17 % Favored : 81.68 % 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: -1.19 (0.15), residues: 2548 helix: -0.34 (0.25), residues: 448 sheet: 0.30 (0.19), residues: 644 loop : -1.49 (0.14), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 527 TYR 0.014 0.001 TYR F 438 PHE 0.017 0.001 PHE E 579 TRP 0.007 0.001 TRP E 374 HIS 0.001 0.000 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (20370) covalent geometry : angle 0.48798 / 0.27 (27615) hydrogen bonds : bond 0.03004 / 1.94 ( 654) hydrogen bonds : angle 4.54021 / 3.12 ( 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 215 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7372 (mt-10) REVERT: B 262 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8323 (tp30) REVERT: B 451 MET cc_start: 0.9219 (ptp) cc_final: 0.8769 (ptm) REVERT: C 367 GLN cc_start: 0.7785 (tm-30) cc_final: 0.7078 (tm-30) REVERT: C 576 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6585 (pt0) REVERT: D 251 GLN cc_start: 0.8056 (mp10) cc_final: 0.7758 (mp10) REVERT: D 279 SER cc_start: 0.8749 (m) cc_final: 0.8464 (p) REVERT: E 304 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7813 (mm-30) REVERT: E 543 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7512 (mm-30) REVERT: E 588 LYS cc_start: 0.7605 (ttpt) cc_final: 0.7013 (ttmm) REVERT: F 286 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8517 (tp) REVERT: F 304 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.6981 (mm-30) REVERT: F 317 ASP cc_start: 0.7942 (t0) cc_final: 0.7463 (m-30) REVERT: F 367 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: F 379 SER cc_start: 0.8600 (OUTLIER) cc_final: 0.8386 (p) REVERT: F 576 GLU cc_start: 0.7816 (tt0) cc_final: 0.7270 (mt-10) REVERT: G 303 MET cc_start: 0.9217 (ttp) cc_final: 0.8814 (ttp) REVERT: G 446 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8240 (pp) outliers start: 48 outliers final: 33 residues processed: 197 average time/residue: 0.5898 time to fit residues: 132.6076 Evaluate side-chains 197 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 C residue 310 THR 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 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 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 F residue 451 MET 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 446 LEU Chi-restraints excluded: chain G residue 568 ILE Chi-restraints excluded: chain G residue 588 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 54 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 G 582 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.097115 restraints weight = 26537.729| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.68 r_work: 0.2984 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20370 Z= 0.157 Angle : 0.511 5.541 27615 Z= 0.284 Chirality : 0.045 0.126 3115 Planarity : 0.005 0.052 3619 Dihedral : 5.366 41.560 2757 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.28 % Allowed : 16.21 % 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: -1.21 (0.15), residues: 2548 helix: -0.33 (0.24), residues: 448 sheet: 0.22 (0.20), residues: 651 loop : -1.48 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 393 TYR 0.017 0.001 TYR F 438 PHE 0.020 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/Z covalent geometry : bond 0.00377 / 0.16 (20370) covalent geometry : angle 0.51074 / 0.28 (27615) hydrogen bonds : bond 0.03180 / 2.05 ( 654) hydrogen bonds : angle 4.62764 / 3.18 ( 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 208 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: B 262 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8312 (tp30) REVERT: B 441 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7901 (ttpm) REVERT: B 451 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8813 (ptm) REVERT: C 576 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6404 (pt0) REVERT: D 251 GLN cc_start: 0.8087 (mp10) cc_final: 0.7864 (mp10) REVERT: D 279 SER cc_start: 0.8761 (m) cc_final: 0.8469 (p) REVERT: E 304 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.7814 (mm-30) REVERT: E 543 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7475 (mm-30) REVERT: E 588 LYS cc_start: 0.7622 (ttpt) cc_final: 0.7030 (ttmm) REVERT: F 286 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8534 (tp) REVERT: F 304 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7172 (mm-30) REVERT: F 379 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8380 (p) REVERT: F 576 GLU cc_start: 0.7842 (tt0) cc_final: 0.7288 (mt-10) REVERT: G 303 MET cc_start: 0.9216 (ttp) cc_final: 0.8817 (ttp) outliers start: 51 outliers final: 38 residues processed: 187 average time/residue: 0.5833 time to fit residues: 124.8122 Evaluate side-chains 200 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 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 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 399 THR 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 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 F residue 451 MET 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 446 LEU Chi-restraints excluded: chain G residue 568 ILE Chi-restraints excluded: chain G residue 588 LYS 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: 0.0970 chunk 218 optimal weight: 4.9990 chunk 132 optimal weight: 0.1980 chunk 161 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 192 optimal weight: 0.8980 chunk 175 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN A 449 ASN B 224 ASN B 620 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.100296 restraints weight = 26393.780| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.68 r_work: 0.3032 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20370 Z= 0.094 Angle : 0.459 4.381 27615 Z= 0.256 Chirality : 0.043 0.125 3115 Planarity : 0.004 0.050 3619 Dihedral : 4.973 40.621 2757 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.97 % Allowed : 16.52 % 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: -0.98 (0.15), residues: 2548 helix: -0.14 (0.25), residues: 448 sheet: 0.51 (0.19), residues: 644 loop : -1.40 (0.14), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 289 TYR 0.013 0.001 TYR C 438 PHE 0.016 0.001 PHE E 579 TRP 0.008 0.001 TRP A 374 HIS 0.001 0.000 HIS G 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.09 (20370) covalent geometry : angle 0.45913 / 0.26 (27615) hydrogen bonds : bond 0.02705 / 1.75 ( 654) hydrogen bonds : angle 4.30519 / 2.96 ( 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 220 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7206 (mt-10) REVERT: A 568 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7427 (pt) REVERT: A 608 MET cc_start: 0.8417 (mmm) cc_final: 0.8131 (mtt) REVERT: B 451 MET cc_start: 0.9196 (ptp) cc_final: 0.8778 (ptm) REVERT: B 588 LYS cc_start: 0.7940 (ptmt) cc_final: 0.7552 (pptt) REVERT: C 576 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6444 (pt0) REVERT: D 251 GLN cc_start: 0.7999 (mp10) cc_final: 0.7732 (mp10) REVERT: D 279 SER cc_start: 0.8766 (m) cc_final: 0.8501 (p) REVERT: E 543 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7387 (mm-30) REVERT: F 304 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.6711 (mm-30) REVERT: F 317 ASP cc_start: 0.7899 (t0) cc_final: 0.7459 (m-30) REVERT: F 367 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7331 (tm-30) REVERT: F 576 GLU cc_start: 0.7813 (tt0) cc_final: 0.7242 (mt-10) REVERT: G 303 MET cc_start: 0.9194 (ttp) cc_final: 0.8780 (ttp) outliers start: 44 outliers final: 24 residues processed: 203 average time/residue: 0.5708 time to fit residues: 132.7495 Evaluate side-chains 189 residues out of total 2233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 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 C residue 310 THR 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 399 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 543 GLU 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 G residue 286 LEU 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: 2.9990 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 0.0060 chunk 238 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN A 449 ASN B 224 ASN B 620 ASN C 251 GLN ** 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 = 0.3346 r_free = 0.3346 target = 0.115702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.094768 restraints weight = 26854.768| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.66 r_work: 0.2963 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 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 : 0.005 0.041 20370 Z= 0.217 Angle : 0.559 5.710 27615 Z= 0.309 Chirality : 0.047 0.138 3115 Planarity : 0.005 0.055 3619 Dihedral : 5.507 41.037 2757 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.66 % Allowed : 17.29 % Favored : 81.06 % 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: -1.16 (0.15), residues: 2548 helix: -0.30 (0.24), residues: 448 sheet: 0.29 (0.20), residues: 651 loop : -1.47 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 393 TYR 0.021 0.002 TYR F 438 PHE 0.025 0.002 PHE F 248 TRP 0.004 0.001 TRP C 502 HIS 0.001 0.000 HIS F 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 (20370) covalent geometry : angle 0.55857 / 0.31 (27615) hydrogen bonds : bond 0.03521 / 2.26 ( 654) hydrogen bonds : angle 4.76705 / 3.27 ( 1743) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5866.38 seconds wall clock time: 101 minutes 7.81 seconds (6067.81 seconds total)