Starting phenix.real_space_refine on Sat Sep 28 18:59:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klx_0721/09_2024/6klx_0721.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klx_0721/09_2024/6klx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klx_0721/09_2024/6klx_0721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klx_0721/09_2024/6klx_0721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klx_0721/09_2024/6klx_0721.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klx_0721/09_2024/6klx_0721.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 12.59, per 1000 atoms: 0.63 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: 4.73 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.73 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: 7.05 Time building geometry restraints manager: 5.53 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: 0.00 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: 2.700 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: 0.030 Extract box with map and model: 0.830 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 46.180 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.090 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:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 20370 Z= 0.507 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.007 0.002 TRP E 374 HIS 0.002 0.001 HIS C 313 PHE 0.020 0.003 PHE F 248 TYR 0.023 0.002 TYR F 438 ARG 0.003 0.000 ARG C 527 *********************** 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 fitting. rotamer outliers: 3 poor density : 233 time to evaluate : 2.325 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: 0.7026 (tm-30) REVERT: A 589 GLU cc_start: 0.7992 (pp20) cc_final: 0.7446 (pp20) REVERT: B 608 MET cc_start: 0.8557 (mtt) cc_final: 0.8315 (mmm) REVERT: C 564 TYR cc_start: 0.7826 (m-80) cc_final: 0.7499 (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: 0.6971 (tm-30) REVERT: E 597 LYS cc_start: 0.7704 (mttt) cc_final: 0.7494 (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: 0.6984 (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: 1.3773 time to fit residues: 366.5576 Evaluate side-chains 169 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 2.324 ------------------------------------------------------------------------------- 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 212 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 370 ASN A 449 ASN A 485 ASN B 224 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN D 224 ASN ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 ASN G 582 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.0919 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= 0.344 Angle : 0.604 6.766 27615 Z= 0.336 Chirality : 0.048 0.143 3115 Planarity : 0.006 0.055 3619 Dihedral : 6.214 43.498 2760 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.39 % Allowed : 10.34 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.14), residues: 2548 helix: -1.80 (0.22), residues: 448 sheet: -1.10 (0.18), residues: 637 loop : -1.96 (0.14), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 374 HIS 0.002 0.001 HIS C 313 PHE 0.027 0.002 PHE B 248 TYR 0.020 0.002 TYR F 438 ARG 0.011 0.000 ARG B 324 *********************** 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 207 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 451 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8326 (ptm) REVERT: C 543 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7015 (mm-30) REVERT: D 279 SER cc_start: 0.8610 (m) cc_final: 0.8378 (p) REVERT: D 318 GLN cc_start: 0.7193 (mt0) cc_final: 0.6947 (mt0) REVERT: D 320 LYS cc_start: 0.7744 (mttm) cc_final: 0.7507 (tppt) REVERT: D 441 LYS cc_start: 0.8045 (ttpp) cc_final: 0.7723 (ttpt) REVERT: D 526 GLU cc_start: 0.8000 (tt0) cc_final: 0.7789 (tt0) REVERT: E 318 GLN cc_start: 0.7285 (mt0) cc_final: 0.7046 (mt0) REVERT: E 367 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7020 (tm-30) REVERT: E 543 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6927 (mm-30) REVERT: F 317 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.7072 (m-30) REVERT: F 576 GLU cc_start: 0.7344 (tt0) cc_final: 0.7002 (mt-10) REVERT: G 303 MET cc_start: 0.9016 (ttp) cc_final: 0.8531 (ttp) outliers start: 31 outliers final: 10 residues processed: 194 average time/residue: 1.1928 time to fit residues: 265.5093 Evaluate side-chains 175 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 160 time to evaluate : 2.455 ------------------------------------------------------------------------------- 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 367 GLN 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 523 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 229 optimal weight: 0.4980 chunk 247 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 449 ASN B 224 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN C 620 ASN D 224 ASN ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN G 224 ASN G 582 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 20370 Z= 0.444 Angle : 0.638 7.219 27615 Z= 0.352 Chirality : 0.050 0.158 3115 Planarity : 0.006 0.061 3619 Dihedral : 6.269 43.634 2760 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.28 % Allowed : 13.03 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.15), residues: 2548 helix: -1.36 (0.23), residues: 448 sheet: -0.79 (0.19), residues: 637 loop : -1.83 (0.14), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 374 HIS 0.002 0.001 HIS C 313 PHE 0.030 0.003 PHE F 248 TYR 0.022 0.002 TYR F 438 ARG 0.005 0.001 ARG B 324 *********************** 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 220 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 169 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 608 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.6524 (mmm) REVERT: C 367 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7114 (tm-30) REVERT: C 543 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7053 (mm-30) REVERT: D 303 MET cc_start: 0.8991 (ttm) cc_final: 0.8733 (ttp) REVERT: D 441 LYS cc_start: 0.8063 (ttpp) cc_final: 0.7785 (ttpt) REVERT: E 318 GLN cc_start: 0.7412 (mt0) cc_final: 0.7141 (mt0) REVERT: E 367 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7132 (tm-30) REVERT: E 543 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6898 (mm-30) REVERT: E 588 LYS cc_start: 0.7585 (ttpt) cc_final: 0.7050 (ttmm) REVERT: F 304 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7134 (mm-30) REVERT: F 318 GLN cc_start: 0.7396 (mt0) cc_final: 0.6982 (mt0) REVERT: F 576 GLU cc_start: 0.7369 (tt0) cc_final: 0.7001 (mt-10) REVERT: G 303 MET cc_start: 0.9002 (ttp) cc_final: 0.8500 (ttp) REVERT: G 608 MET cc_start: 0.8580 (mtt) cc_final: 0.8217 (mmm) outliers start: 51 outliers final: 26 residues processed: 196 average time/residue: 1.2814 time to fit residues: 285.9042 Evaluate side-chains 187 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 156 time to evaluate : 2.614 ------------------------------------------------------------------------------- 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 491 SER Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 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 388 ILE Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 310 THR Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 367 GLN 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 F residue 304 GLU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 451 MET Chi-restraints excluded: chain G residue 491 SER Chi-restraints excluded: chain G residue 523 GLN Chi-restraints excluded: chain G residue 576 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 230 optimal weight: 0.3980 chunk 243 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 218 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 449 ASN B 224 ASN B 485 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 620 ASN D 224 ASN D 318 GLN D 367 GLN D 485 ASN D 582 ASN E 485 ASN F 485 ASN G 224 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1356 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= 0.219 Angle : 0.519 5.114 27615 Z= 0.291 Chirality : 0.045 0.135 3115 Planarity : 0.005 0.063 3619 Dihedral : 5.746 43.041 2760 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.37 % Allowed : 14.51 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.15), residues: 2548 helix: -0.91 (0.24), residues: 448 sheet: -0.43 (0.19), residues: 651 loop : -1.70 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 374 HIS 0.001 0.001 HIS G 313 PHE 0.017 0.001 PHE B 248 TYR 0.015 0.001 TYR F 438 ARG 0.002 0.000 ARG B 324 *********************** 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 226 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 173 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7201 (mt-10) REVERT: B 262 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7870 (tp30) REVERT: B 451 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8320 (ptm) REVERT: B 608 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.6627 (mmm) REVERT: C 576 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.6141 (pt0) REVERT: D 279 SER cc_start: 0.8593 (m) cc_final: 0.8370 (p) REVERT: D 441 LYS cc_start: 0.8028 (ttpp) cc_final: 0.7675 (ttpt) REVERT: E 318 GLN cc_start: 0.7289 (mt0) cc_final: 0.7087 (mt0) REVERT: E 543 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7006 (mm-30) REVERT: E 588 LYS cc_start: 0.7628 (ttpt) cc_final: 0.7073 (ttmm) REVERT: F 304 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.6924 (mm-30) REVERT: F 317 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7094 (m-30) REVERT: F 576 GLU cc_start: 0.7324 (tt0) cc_final: 0.6982 (mt-10) REVERT: G 303 MET cc_start: 0.8965 (ttp) cc_final: 0.8459 (ttp) outliers start: 53 outliers final: 25 residues processed: 201 average time/residue: 1.2471 time to fit residues: 286.2349 Evaluate side-chains 185 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 2.343 ------------------------------------------------------------------------------- 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 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 310 THR Chi-restraints excluded: chain C residue 441 LYS 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 388 ILE Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain E residue 310 THR Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 568 ILE 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 451 MET Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain G residue 286 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 370 ASN A 449 ASN B 224 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN D 224 ASN D 318 GLN ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 20370 Z= 0.417 Angle : 0.609 6.793 27615 Z= 0.337 Chirality : 0.049 0.168 3115 Planarity : 0.006 0.062 3619 Dihedral : 5.987 43.285 2757 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.42 % Allowed : 15.49 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.15), residues: 2548 helix: -0.90 (0.24), residues: 448 sheet: -0.39 (0.20), residues: 651 loop : -1.70 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 374 HIS 0.002 0.001 HIS C 313 PHE 0.028 0.002 PHE F 248 TYR 0.022 0.002 TYR F 438 ARG 0.003 0.000 ARG B 393 *********************** 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 220 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 166 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: B 451 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8369 (ptm) REVERT: B 608 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.6477 (mmm) REVERT: C 576 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.6008 (pt0) REVERT: D 441 LYS cc_start: 0.8024 (ttpp) cc_final: 0.7820 (ttpm) REVERT: E 304 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7606 (mm-30) REVERT: E 318 GLN cc_start: 0.7448 (mt0) cc_final: 0.7164 (mt0) REVERT: E 543 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6949 (mm-30) REVERT: E 588 LYS cc_start: 0.7666 (ttpt) cc_final: 0.7109 (ttmm) REVERT: F 304 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7111 (mm-30) REVERT: F 317 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.7064 (m-30) REVERT: F 491 SER cc_start: 0.7177 (OUTLIER) cc_final: 0.6938 (p) REVERT: F 576 GLU cc_start: 0.7363 (tt0) cc_final: 0.7006 (mt-10) REVERT: G 303 MET cc_start: 0.8981 (ttp) cc_final: 0.8542 (ttp) outliers start: 54 outliers final: 32 residues processed: 196 average time/residue: 1.1899 time to fit residues: 267.0916 Evaluate side-chains 196 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 155 time to evaluate : 2.365 ------------------------------------------------------------------------------- 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 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 B residue 608 MET Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 441 LYS 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 388 ILE Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 310 THR Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 451 MET Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 568 ILE Chi-restraints excluded: chain F residue 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 321 THR Chi-restraints excluded: chain G residue 399 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.8980 chunk 219 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 128 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 449 ASN B 224 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 620 ASN D 224 ASN D 318 GLN ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 ASN ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1530 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= 0.184 Angle : 0.500 4.679 27615 Z= 0.281 Chirality : 0.044 0.127 3115 Planarity : 0.005 0.057 3619 Dihedral : 5.496 42.829 2757 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.33 % Allowed : 15.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.15), residues: 2548 helix: -0.63 (0.24), residues: 448 sheet: -0.02 (0.20), residues: 644 loop : -1.60 (0.14), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 374 HIS 0.001 0.000 HIS G 313 PHE 0.015 0.001 PHE F 248 TYR 0.014 0.001 TYR B 438 ARG 0.002 0.000 ARG B 324 *********************** 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 221 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 169 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7142 (mt-10) REVERT: B 451 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8401 (ptm) REVERT: C 576 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5963 (pt0) REVERT: D 279 SER cc_start: 0.8582 (m) cc_final: 0.8363 (p) REVERT: D 289 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.8246 (mtm-85) REVERT: D 441 LYS cc_start: 0.8031 (ttpp) cc_final: 0.7811 (ttpm) REVERT: E 304 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7549 (mm-30) REVERT: E 318 GLN cc_start: 0.7244 (mt0) cc_final: 0.7014 (mt0) REVERT: E 543 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7073 (mm-30) REVERT: E 588 LYS cc_start: 0.7630 (ttpt) cc_final: 0.7082 (ttmm) REVERT: F 286 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8248 (tp) REVERT: F 304 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.6774 (mm-30) REVERT: F 317 ASP cc_start: 0.7325 (t0) cc_final: 0.7071 (m-30) REVERT: F 491 SER cc_start: 0.7111 (OUTLIER) cc_final: 0.6699 (p) REVERT: F 576 GLU cc_start: 0.7299 (tt0) cc_final: 0.6966 (mt-10) REVERT: G 303 MET cc_start: 0.8945 (ttp) cc_final: 0.8424 (ttp) outliers start: 52 outliers final: 28 residues processed: 200 average time/residue: 1.2095 time to fit residues: 277.7999 Evaluate side-chains 193 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 157 time to evaluate : 2.423 ------------------------------------------------------------------------------- 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 242 VAL 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 568 ILE Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 441 LYS 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 388 ILE Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 310 THR Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 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 F residue 451 MET Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain G residue 286 LEU 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 576 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 205 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 242 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 370 ASN A 449 ASN B 224 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN D 224 ASN D 318 GLN ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN G 582 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1611 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= 0.206 Angle : 0.500 4.897 27615 Z= 0.279 Chirality : 0.045 0.125 3115 Planarity : 0.005 0.056 3619 Dihedral : 5.383 42.625 2757 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.51 % Allowed : 15.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.15), residues: 2548 helix: -0.51 (0.24), residues: 448 sheet: 0.15 (0.20), residues: 644 loop : -1.56 (0.14), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 374 HIS 0.001 0.000 HIS F 313 PHE 0.017 0.002 PHE F 248 TYR 0.016 0.001 TYR F 438 ARG 0.002 0.000 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 163 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7111 (mt-10) REVERT: B 451 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8447 (ptm) REVERT: C 367 GLN cc_start: 0.7668 (tm-30) cc_final: 0.7173 (tm-30) REVERT: C 576 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5962 (pt0) REVERT: D 251 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.6712 (mt0) REVERT: D 279 SER cc_start: 0.8631 (m) cc_final: 0.8428 (p) REVERT: D 441 LYS cc_start: 0.8074 (ttpp) cc_final: 0.7801 (ttpm) REVERT: E 304 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7576 (mm-30) REVERT: E 318 GLN cc_start: 0.7257 (mt0) cc_final: 0.7028 (mt0) REVERT: E 543 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7070 (mm-30) REVERT: E 588 LYS cc_start: 0.7637 (ttpt) cc_final: 0.7067 (ttmm) REVERT: F 304 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.6754 (mm-30) REVERT: F 379 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.8159 (p) REVERT: F 576 GLU cc_start: 0.7315 (tt0) cc_final: 0.6996 (mt-10) REVERT: G 303 MET cc_start: 0.8954 (ttp) cc_final: 0.8434 (ttp) outliers start: 56 outliers final: 32 residues processed: 196 average time/residue: 1.2547 time to fit residues: 279.7954 Evaluate side-chains 194 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 154 time to evaluate : 2.301 ------------------------------------------------------------------------------- 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 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 251 GLN Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 310 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 568 ILE Chi-restraints excluded: chain E residue 579 PHE Chi-restraints excluded: chain F residue 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 523 GLN Chi-restraints excluded: chain G residue 568 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.2980 chunk 96 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 220 optimal weight: 0.6980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 449 ASN B 224 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 620 ASN D 224 ASN D 318 GLN ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20370 Z= 0.343 Angle : 0.566 6.656 27615 Z= 0.313 Chirality : 0.047 0.140 3115 Planarity : 0.005 0.058 3619 Dihedral : 5.711 42.782 2757 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.46 % Allowed : 16.21 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.15), residues: 2548 helix: -0.57 (0.24), residues: 448 sheet: -0.01 (0.20), residues: 651 loop : -1.56 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 374 HIS 0.002 0.000 HIS F 313 PHE 0.025 0.002 PHE F 248 TYR 0.020 0.002 TYR F 438 ARG 0.005 0.000 ARG D 289 *********************** 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 216 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 161 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7247 (mt-10) REVERT: B 451 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8453 (ptm) REVERT: C 576 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5837 (pt0) REVERT: D 279 SER cc_start: 0.8659 (m) cc_final: 0.8395 (p) REVERT: D 441 LYS cc_start: 0.8068 (ttpp) cc_final: 0.7785 (ttpm) REVERT: E 304 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7662 (mm-30) REVERT: E 318 GLN cc_start: 0.7294 (mt0) cc_final: 0.7069 (mt0) REVERT: E 543 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7034 (mm-30) REVERT: E 588 LYS cc_start: 0.7645 (ttpt) cc_final: 0.7103 (ttmm) REVERT: F 286 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8418 (tp) REVERT: F 304 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7058 (mm-30) REVERT: F 576 GLU cc_start: 0.7352 (tt0) cc_final: 0.7019 (mt-10) REVERT: G 303 MET cc_start: 0.8989 (ttp) cc_final: 0.8561 (ttp) outliers start: 55 outliers final: 35 residues processed: 190 average time/residue: 1.2038 time to fit residues: 261.9719 Evaluate side-chains 199 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 2.509 ------------------------------------------------------------------------------- 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 479 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 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 388 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 388 ILE Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 310 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 451 MET Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 568 ILE Chi-restraints excluded: chain E residue 579 PHE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 304 GLU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain G residue 286 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 chunk 226 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 449 ASN B 224 ASN B 582 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 620 ASN D 224 ASN D 318 GLN ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 ASN ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20370 Z= 0.290 Angle : 0.541 5.938 27615 Z= 0.301 Chirality : 0.046 0.134 3115 Planarity : 0.005 0.057 3619 Dihedral : 5.631 42.493 2757 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.15 % Allowed : 16.66 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.15), residues: 2548 helix: -0.50 (0.24), residues: 448 sheet: 0.29 (0.21), residues: 595 loop : -1.52 (0.14), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 374 HIS 0.001 0.000 HIS F 313 PHE 0.021 0.002 PHE F 248 TYR 0.018 0.001 TYR F 438 ARG 0.005 0.000 ARG D 289 *********************** 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 206 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 158 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7263 (mt-10) REVERT: B 451 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8450 (ptm) REVERT: C 576 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5825 (pt0) REVERT: D 279 SER cc_start: 0.8646 (m) cc_final: 0.8402 (p) REVERT: D 441 LYS cc_start: 0.8079 (ttpp) cc_final: 0.7806 (ttpm) REVERT: E 304 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7625 (mm-30) REVERT: E 318 GLN cc_start: 0.7281 (mt0) cc_final: 0.7057 (mt0) REVERT: E 543 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7074 (mm-30) REVERT: E 588 LYS cc_start: 0.7640 (ttpt) cc_final: 0.7101 (ttmm) REVERT: F 286 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8400 (tp) REVERT: F 304 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7014 (mm-30) REVERT: F 576 GLU cc_start: 0.7346 (tt0) cc_final: 0.7016 (mt-10) REVERT: G 303 MET cc_start: 0.8979 (ttp) cc_final: 0.8482 (ttp) outliers start: 48 outliers final: 37 residues processed: 188 average time/residue: 1.2770 time to fit residues: 275.0261 Evaluate side-chains 201 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 157 time to evaluate : 2.443 ------------------------------------------------------------------------------- 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 479 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 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 388 ILE Chi-restraints excluded: chain C residue 563 LEU 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 388 ILE Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 310 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 568 ILE Chi-restraints excluded: chain E residue 579 PHE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 304 GLU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain G residue 286 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.0070 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 166 optimal weight: 0.6980 chunk 251 optimal weight: 2.9990 chunk 231 optimal weight: 0.0570 chunk 199 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 449 ASN B 224 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN D 224 ASN D 367 GLN D 582 ASN ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20370 Z= 0.137 Angle : 0.464 4.344 27615 Z= 0.260 Chirality : 0.043 0.126 3115 Planarity : 0.005 0.053 3619 Dihedral : 5.030 41.115 2757 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.79 % Allowed : 17.11 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.15), residues: 2548 helix: -0.22 (0.25), residues: 448 sheet: 0.43 (0.20), residues: 644 loop : -1.42 (0.14), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 374 HIS 0.001 0.000 HIS G 313 PHE 0.015 0.001 PHE E 579 TYR 0.013 0.001 TYR C 438 ARG 0.002 0.000 ARG D 289 ********************** 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 224 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 184 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7409 (pt) REVERT: B 451 MET cc_start: 0.8938 (ptp) cc_final: 0.8434 (ptm) REVERT: C 576 GLU cc_start: 0.6099 (OUTLIER) cc_final: 0.5788 (pt0) REVERT: D 441 LYS cc_start: 0.7984 (ttpp) cc_final: 0.7689 (ttpm) REVERT: E 318 GLN cc_start: 0.7259 (mt0) cc_final: 0.7046 (mt0) REVERT: E 543 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6923 (mm-30) REVERT: F 286 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8337 (pt) REVERT: F 304 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.6406 (mm-30) REVERT: F 317 ASP cc_start: 0.7300 (t0) cc_final: 0.7079 (m-30) REVERT: F 379 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.8122 (p) REVERT: F 576 GLU cc_start: 0.7265 (tt0) cc_final: 0.6944 (mt-10) REVERT: G 303 MET cc_start: 0.8921 (ttp) cc_final: 0.8507 (ttp) outliers start: 40 outliers final: 22 residues processed: 210 average time/residue: 1.2099 time to fit residues: 291.1477 Evaluate side-chains 188 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 2.638 ------------------------------------------------------------------------------- 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 367 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 479 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 388 ILE Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 522 SER 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 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 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 F residue 379 SER Chi-restraints excluded: chain F residue 399 THR Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 399 THR 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 212 optimal weight: 0.0470 chunk 61 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 29 optimal weight: 0.0870 chunk 55 optimal weight: 0.4980 chunk 200 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 0.0770 chunk 175 optimal weight: 0.5980 overall best weight: 0.2614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 449 ASN B 224 ASN B 620 ASN C 224 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 485 ASN C 620 ASN D 224 ASN ** 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 = 0.3438 r_free = 0.3438 target = 0.122511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.102049 restraints weight = 26178.623| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.69 r_work: 0.3060 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20370 Z= 0.126 Angle : 0.455 4.603 27615 Z= 0.253 Chirality : 0.043 0.149 3115 Planarity : 0.004 0.054 3619 Dihedral : 4.743 39.828 2757 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.34 % Allowed : 18.27 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.16), residues: 2548 helix: 0.06 (0.25), residues: 448 sheet: 0.76 (0.20), residues: 651 loop : -1.32 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 244 HIS 0.003 0.001 HIS F 313 PHE 0.015 0.001 PHE E 579 TYR 0.013 0.001 TYR C 438 ARG 0.002 0.000 ARG G 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5637.75 seconds wall clock time: 100 minutes 27.88 seconds (6027.88 seconds total)