Starting phenix.real_space_refine on Thu Mar 5 14:46:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6klo_0713/03_2026/6klo_0713.cif Found real_map, /net/cci-nas-00/data/ceres_data/6klo_0713/03_2026/6klo_0713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6klo_0713/03_2026/6klo_0713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6klo_0713/03_2026/6klo_0713.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6klo_0713/03_2026/6klo_0713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6klo_0713/03_2026/6klo_0713.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 38 5.16 5 C 14584 2.51 5 N 3834 2.21 5 O 4805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23275 Number of models: 1 Model: "" Number of chains: 15 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: "H" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3220 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 20, 'TRANS': 375} 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: 5.33, per 1000 atoms: 0.23 Number of scatterers: 23275 At special positions: 0 Unit cell: (146.9, 148.03, 178.54, 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 38 16.00 O 4805 8.00 N 3834 7.00 C 14584 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 1.1 seconds 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5556 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 57 sheets defined 24.6% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 226 through 233 Processing helix chain 'A' and resid 245 through 250 removed outlier: 4.017A pdb=" N GLU A 250 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.607A 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 Processing helix chain 'A' and resid 505 through 512 removed outlier: 3.563A pdb=" N VAL A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 555 Processing helix chain 'A' and resid 571 through 575 removed outlier: 3.808A pdb=" N VAL A 575 " --> pdb=" O GLU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 591 Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.508A pdb=" N LYS B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 249 removed outlier: 3.793A pdb=" N ALA B 249 " --> pdb=" O ASP B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 424 through 428 Processing helix chain 'B' and resid 462 through 470 Processing helix chain 'B' and resid 502 through 510 removed outlier: 4.677A pdb=" N SER B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLN B 508 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 555 Processing helix chain 'B' and resid 580 through 591 Processing helix chain 'B' and resid 598 through 602 Processing helix chain 'C' and resid 226 through 233 Processing helix chain 'C' and resid 245 through 250 removed outlier: 4.084A pdb=" N GLU C 250 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 277 Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 424 through 428 removed outlier: 3.786A 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 502 through 511 removed outlier: 4.697A pdb=" N SER C 507 " --> pdb=" O SER C 503 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN C 508 " --> pdb=" O ASN C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 555 Processing helix chain 'C' and resid 580 through 592 removed outlier: 3.974A pdb=" N LYS C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 602 Processing helix chain 'D' and resid 226 through 233 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.795A pdb=" N ALA D 249 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU D 250 " --> pdb=" O SER D 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 246 through 250' Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 424 through 428 removed outlier: 3.687A 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 502 through 510 removed outlier: 4.462A pdb=" N SER D 507 " --> pdb=" O SER D 503 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLN D 508 " --> pdb=" O ASN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 555 Processing helix chain 'D' and resid 580 through 592 removed outlier: 3.749A pdb=" N LYS D 592 " --> pdb=" O LYS D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 602 Processing helix chain 'E' and resid 226 through 233 Processing helix chain 'E' and resid 245 through 250 removed outlier: 3.651A pdb=" N ALA E 249 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU E 250 " --> pdb=" O SER E 247 " (cutoff:3.500A) 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: 3.711A 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 502 through 510 removed outlier: 4.697A pdb=" N SER E 507 " --> pdb=" O SER E 503 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLN E 508 " --> pdb=" O ASN E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 554 Processing helix chain 'E' and resid 580 through 592 removed outlier: 4.113A pdb=" N LYS E 592 " --> pdb=" O LYS E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 602 Processing helix chain 'F' and resid 226 through 233 Processing helix chain 'F' and resid 245 through 250 removed outlier: 3.521A pdb=" N PHE F 248 " --> pdb=" O ASN F 245 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA F 249 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU F 250 " --> pdb=" O SER F 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 245 through 250' Processing helix chain 'F' and resid 271 through 277 Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 424 through 428 removed outlier: 3.585A pdb=" N ILE F 428 " --> pdb=" O ASP F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 470 Processing helix chain 'F' and resid 502 through 512 removed outlier: 4.770A pdb=" N SER F 507 " --> pdb=" O SER F 503 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN F 508 " --> pdb=" O ASN F 504 " (cutoff:3.500A) removed outlier: 3.794A 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 571 through 575 removed outlier: 3.826A pdb=" N VAL F 575 " --> pdb=" O GLU F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 593 removed outlier: 3.962A pdb=" N LYS F 592 " --> pdb=" O LYS F 588 " (cutoff:3.500A) removed outlier: 4.495A 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 233 Processing helix chain 'G' and resid 245 through 249 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: 3.543A 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 510 removed outlier: 4.590A pdb=" N SER G 507 " --> pdb=" O SER G 503 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLN G 508 " --> pdb=" O ASN G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 555 Processing helix chain 'G' and resid 571 through 575 removed outlier: 3.920A pdb=" N VAL G 575 " --> pdb=" O GLU G 572 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 593 removed outlier: 4.068A pdb=" N TYR G 593 " --> pdb=" O GLU G 589 " (cutoff:3.500A) Processing helix chain 'G' and resid 598 through 602 Processing helix chain 'H' and resid 19 through 28 Processing helix chain 'H' and resid 32 through 56 removed outlier: 4.079A pdb=" N LYS H 44 " --> pdb=" O GLU H 40 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLU H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLN H 48 " --> pdb=" O LYS H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 59 No H-bonds generated for 'chain 'H' and resid 57 through 59' Processing helix chain 'H' and resid 60 through 66 Processing helix chain 'H' and resid 69 through 81 Processing helix chain 'H' and resid 96 through 101 Processing helix chain 'H' and resid 115 through 126 Processing helix chain 'H' and resid 216 through 228 removed outlier: 3.662A pdb=" N GLY H 220 " --> pdb=" O ASP H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 235 Processing helix chain 'H' and resid 236 through 248 Processing helix chain 'H' and resid 249 through 259 removed outlier: 4.392A pdb=" N ALA H 253 " --> pdb=" O GLY H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 266 Processing helix chain 'H' and resid 268 through 281 Processing helix chain 'H' and resid 298 through 302 removed outlier: 3.971A pdb=" N GLU H 301 " --> pdb=" O GLY H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 312 removed outlier: 3.510A pdb=" N TYR H 311 " --> pdb=" O SER H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 368 through 372 removed outlier: 3.813A pdb=" N ILE H 372 " --> pdb=" O LEU H 369 " (cutoff:3.500A) 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: 6.757A pdb=" N ASN A 391 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU A 306 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN A 389 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE A 308 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR A 387 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 437 through 438 removed outlier: 4.584A 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 325 removed outlier: 3.662A pdb=" N SER A 323 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 369 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A 325 " --> pdb=" O GLN A 367 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR G 326 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS G 320 " --> pdb=" O TRP A 374 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR F 321 " --> pdb=" O GLY F 371 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER F 323 " --> pdb=" O SER F 369 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER F 369 " --> pdb=" O SER F 323 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER E 369 " --> pdb=" O SER E 323 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR D 326 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN E 370 " --> pdb=" O ARG D 324 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 321 " --> pdb=" O GLY D 371 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA D 325 " --> pdb=" O GLN D 367 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP D 368 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN D 370 " --> pdb=" O ARG C 324 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG C 324 " --> pdb=" O ASN D 370 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER C 369 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 322 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER B 323 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN B 370 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG A 324 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 416 through 422 removed outlier: 6.784A pdb=" N LEU A 411 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR A 420 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR A 409 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS A 422 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR A 403 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 6.755A 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: 6.784A pdb=" N LEU A 411 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR A 420 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR A 409 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS A 422 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL A 405 " --> pdb=" O SER A 483 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N SER A 483 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLN A 481 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR A 409 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR A 479 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 411 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU A 477 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU A 413 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE A 475 " --> pdb=" O LEU A 413 " (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: 9.140A pdb=" N ILE A 610 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER A 515 " --> pdb=" O ILE A 610 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE A 612 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.339A 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: 6.783A pdb=" N ASN B 391 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU B 306 " --> pdb=" O ASN B 389 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN B 389 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 308 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 6.291A 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: 6.783A pdb=" N ASN B 391 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU B 306 " --> pdb=" O ASN B 389 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN B 389 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 308 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR B 387 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 4.582A 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: 3.559A pdb=" N GLU B 416 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 411 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR B 420 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR B 409 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS B 422 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYR B 403 " --> pdb=" O ASN B 431 " (cutoff:3.500A) removed outlier: 6.800A 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: 3.559A pdb=" N GLU B 416 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 411 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR B 420 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR B 409 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS B 422 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LYS B 404 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY B 484 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR B 406 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL B 482 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR B 408 " --> pdb=" O THR B 480 " (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: 9.183A pdb=" N ILE B 610 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER B 515 " --> pdb=" O ILE B 610 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE B 612 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 6.283A 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 removed outlier: 3.694A pdb=" N LEU B 562 " --> pdb=" O ASN B 559 " (cutoff:3.500A) 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: 6.727A pdb=" N ASN C 391 " --> pdb=" O GLU C 304 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU C 306 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN C 389 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE C 308 " --> pdb=" O TYR C 387 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR C 387 " --> pdb=" O ILE C 308 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 299 through 310 removed outlier: 6.727A pdb=" N ASN C 391 " --> pdb=" O GLU C 304 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU C 306 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN C 389 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE C 308 " --> pdb=" O TYR C 387 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR C 387 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 4.555A 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: 6.829A pdb=" N LEU C 411 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR C 420 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR C 409 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LYS C 422 " --> pdb=" O PRO C 407 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL C 405 " --> pdb=" O SER C 483 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER C 483 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLN C 481 " --> pdb=" O PRO C 407 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR C 409 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR C 479 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU C 411 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU C 477 " --> pdb=" O LEU C 411 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AC5, first strand: chain 'C' and resid 524 through 530 Processing sheet with id=AC6, first strand: chain 'C' and resid 557 through 559 removed outlier: 3.603A pdb=" N LEU C 562 " --> pdb=" O ASN C 559 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 234 through 237 Processing sheet with id=AC8, first strand: chain 'D' and resid 299 through 310 removed outlier: 6.806A pdb=" N ASN D 391 " --> pdb=" O GLU D 304 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU D 306 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN D 389 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE D 308 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR D 387 " --> pdb=" O ILE D 308 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 299 through 310 removed outlier: 6.806A pdb=" N ASN D 391 " --> pdb=" O GLU D 304 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU D 306 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN D 389 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE D 308 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR D 387 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE D 459 " --> pdb=" O ILE D 388 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 416 through 422 removed outlier: 6.775A pdb=" N LEU D 411 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR D 420 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR D 409 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS D 422 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR D 403 " --> pdb=" O ASN D 431 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN D 431 " --> pdb=" O TYR D 403 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 416 through 422 removed outlier: 6.775A pdb=" N LEU D 411 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR D 420 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR D 409 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS D 422 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL D 405 " --> pdb=" O SER D 483 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER D 483 " --> pdb=" O VAL D 405 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLN D 481 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR D 409 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR D 479 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU D 411 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU D 477 " --> pdb=" O LEU D 411 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 488 through 489 Processing sheet with id=AD4, first strand: chain 'D' and resid 524 through 530 removed outlier: 9.155A pdb=" N ILE D 610 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N SER D 515 " --> pdb=" O ILE D 610 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE D 612 " --> pdb=" O SER D 515 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE D 517 " --> pdb=" O ILE D 612 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 557 through 559 Processing sheet with id=AD6, first strand: chain 'E' and resid 234 through 236 Processing sheet with id=AD7, first strand: chain 'E' and resid 299 through 310 removed outlier: 6.763A pdb=" N ASN E 391 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU E 306 " --> pdb=" O ASN E 389 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN E 389 " --> pdb=" O LEU E 306 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE E 308 " --> pdb=" O TYR E 387 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR E 387 " --> pdb=" O ILE E 308 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 299 through 310 removed outlier: 6.763A pdb=" N ASN E 391 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU E 306 " --> pdb=" O ASN E 389 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN E 389 " --> pdb=" O LEU E 306 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE E 308 " --> pdb=" O TYR E 387 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR E 387 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE E 459 " --> pdb=" O ILE E 388 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 416 through 422 removed outlier: 5.422A pdb=" N THR E 417 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU E 413 " --> pdb=" O THR E 417 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA E 419 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR E 403 " --> pdb=" O ASN E 431 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN E 431 " --> pdb=" O TYR E 403 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 416 through 422 removed outlier: 5.422A pdb=" N THR E 417 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU E 413 " --> pdb=" O THR E 417 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA E 419 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS E 404 " --> pdb=" O GLY E 484 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY E 484 " --> pdb=" O LYS E 404 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR E 406 " --> pdb=" O VAL E 482 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL E 482 " --> pdb=" O THR E 406 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR E 408 " --> pdb=" O THR E 480 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 524 through 530 removed outlier: 9.196A pdb=" N ILE E 610 " --> pdb=" O SER E 513 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N SER E 515 " --> pdb=" O ILE E 610 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE E 612 " --> pdb=" O SER E 515 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE E 517 " --> pdb=" O ILE E 612 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 557 through 559 Processing sheet with id=AE4, first strand: chain 'F' and resid 234 through 237 Processing sheet with id=AE5, first strand: chain 'F' and resid 299 through 310 removed outlier: 6.766A pdb=" N ASN F 391 " --> pdb=" O GLU F 304 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU F 306 " --> pdb=" O ASN F 389 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN F 389 " --> pdb=" O LEU F 306 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE F 308 " --> pdb=" O TYR F 387 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR F 387 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 299 through 310 removed outlier: 6.766A pdb=" N ASN F 391 " --> pdb=" O GLU F 304 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU F 306 " --> pdb=" O ASN F 389 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN F 389 " --> pdb=" O LEU F 306 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE F 308 " --> pdb=" O TYR F 387 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR F 387 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE F 459 " --> pdb=" O ILE F 388 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 416 through 422 removed outlier: 6.736A pdb=" N LEU F 411 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR F 420 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N THR F 409 " --> pdb=" O THR F 420 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYS F 422 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL F 405 " --> pdb=" O SER F 483 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER F 483 " --> pdb=" O VAL F 405 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLN F 481 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR F 409 " --> pdb=" O THR F 479 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR F 479 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU F 411 " --> pdb=" O LEU F 477 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU F 477 " --> pdb=" O LEU F 411 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 524 through 530 Processing sheet with id=AE9, first strand: chain 'F' and resid 557 through 559 removed outlier: 3.901A pdb=" N LEU F 562 " --> pdb=" O ASN F 559 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 234 through 237 Processing sheet with id=AF2, first strand: chain 'G' and resid 299 through 301 removed outlier: 3.650A pdb=" N GLU G 436 " --> pdb=" O ASN G 396 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 305 through 310 removed outlier: 3.718A pdb=" N ASN G 305 " --> pdb=" O ASN G 391 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE G 459 " --> pdb=" O ILE G 388 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 417 through 422 removed outlier: 6.815A pdb=" N LEU G 411 " --> pdb=" O LEU G 418 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR G 420 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N THR G 409 " --> pdb=" O THR G 420 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS G 422 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TYR G 403 " --> pdb=" O ASN G 431 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN G 431 " --> pdb=" O TYR G 403 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 417 through 422 removed outlier: 6.815A pdb=" N LEU G 411 " --> pdb=" O LEU G 418 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR G 420 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N THR G 409 " --> pdb=" O THR G 420 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS G 422 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL G 405 " --> pdb=" O SER G 483 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER G 483 " --> pdb=" O VAL G 405 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLN G 481 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR G 409 " --> pdb=" O THR G 479 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR G 479 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU G 411 " --> pdb=" O LEU G 477 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU G 477 " --> pdb=" O LEU G 411 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 488 through 489 Processing sheet with id=AF7, first strand: chain 'G' and resid 524 through 530 removed outlier: 9.050A pdb=" N ILE G 610 " --> pdb=" O SER G 513 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER G 515 " --> pdb=" O ILE G 610 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE G 612 " --> pdb=" O SER G 515 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE G 517 " --> pdb=" O ILE G 612 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 557 through 559 Processing sheet with id=AF9, first strand: chain 'H' and resid 89 through 95 removed outlier: 3.976A pdb=" N LEU H 154 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS H 159 " --> pdb=" O ALA H 205 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ILE H 207 " --> pdb=" O LYS H 159 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LYS H 198 " --> pdb=" O VAL H 194 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL H 194 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR H 200 " --> pdb=" O ARG H 192 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG H 192 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS H 202 " --> pdb=" O ILE H 190 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE H 190 " --> pdb=" O LYS H 202 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU H 204 " --> pdb=" O ASP H 188 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER H 184 " --> pdb=" O VAL H 208 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 136 through 139 Processing sheet with id=AG2, first strand: chain 'H' and resid 291 through 297 removed outlier: 3.565A pdb=" N ILE H 354 " --> pdb=" O SER H 297 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE H 355 " --> pdb=" O LEU H 407 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA H 409 " --> pdb=" O ILE H 355 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ARG H 357 " --> pdb=" O ALA H 409 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU H 411 " --> pdb=" O ARG H 357 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN H 359 " --> pdb=" O LEU H 411 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR H 410 " --> pdb=" O ILE H 391 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE H 391 " --> pdb=" O THR H 410 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 339 through 340 866 hydrogen bonds defined for protein. 2217 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.38 Time building geometry restraints manager: 2.50 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: 7627 1.34 - 1.45: 3155 1.45 - 1.57: 12805 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 23656 Sorted by residual: bond pdb=" CA ALA C 288 " pdb=" C ALA C 288 " ideal model delta sigma weight residual 1.523 1.488 0.035 1.80e-02 3.09e+03 3.75e+00 bond pdb=" CA HIS B 313 " pdb=" CB HIS B 313 " ideal model delta sigma weight residual 1.526 1.499 0.028 1.53e-02 4.27e+03 3.24e+00 bond pdb=" CG PRO A 439 " pdb=" CD PRO A 439 " ideal model delta sigma weight residual 1.512 1.469 0.043 2.70e-02 1.37e+03 2.51e+00 bond pdb=" CG PRO E 439 " pdb=" CD PRO E 439 " ideal model delta sigma weight residual 1.512 1.470 0.042 2.70e-02 1.37e+03 2.40e+00 bond pdb=" CG PRO F 439 " pdb=" CD PRO F 439 " ideal model delta sigma weight residual 1.512 1.470 0.042 2.70e-02 1.37e+03 2.37e+00 ... (remaining 23651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 30822 1.38 - 2.75: 1048 2.75 - 4.13: 167 4.13 - 5.51: 16 5.51 - 6.89: 3 Bond angle restraints: 32056 Sorted by residual: angle pdb=" N VAL B 602 " pdb=" CA VAL B 602 " pdb=" C VAL B 602 " ideal model delta sigma weight residual 110.21 106.58 3.63 1.13e+00 7.83e-01 1.03e+01 angle pdb=" C SER B 247 " pdb=" N PHE B 248 " pdb=" CA PHE B 248 " ideal model delta sigma weight residual 123.25 118.02 5.23 1.69e+00 3.50e-01 9.58e+00 angle pdb=" N VAL G 602 " pdb=" CA VAL G 602 " pdb=" C VAL G 602 " ideal model delta sigma weight residual 110.05 106.73 3.32 1.09e+00 8.42e-01 9.25e+00 angle pdb=" CA LEU A 604 " pdb=" C LEU A 604 " pdb=" N GLU A 605 " ideal model delta sigma weight residual 114.17 118.17 -4.00 1.45e+00 4.76e-01 7.62e+00 angle pdb=" CA ALA C 288 " pdb=" C ALA C 288 " pdb=" N ARG C 289 " ideal model delta sigma weight residual 118.27 122.51 -4.24 1.59e+00 3.96e-01 7.13e+00 ... (remaining 32051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 13159 16.95 - 33.90: 1029 33.90 - 50.85: 170 50.85 - 67.80: 43 67.80 - 84.75: 19 Dihedral angle restraints: 14420 sinusoidal: 5744 harmonic: 8676 Sorted by residual: dihedral pdb=" CA GLU G 605 " pdb=" C GLU G 605 " pdb=" N ARG G 606 " pdb=" CA ARG G 606 " ideal model delta harmonic sigma weight residual 180.00 147.74 32.26 0 5.00e+00 4.00e-02 4.16e+01 dihedral pdb=" CA VAL A 602 " pdb=" C VAL A 602 " pdb=" N LYS A 603 " pdb=" CA LYS A 603 " ideal model delta harmonic sigma weight residual 180.00 -152.33 -27.67 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA VAL F 602 " pdb=" C VAL F 602 " pdb=" N LYS F 603 " pdb=" CA LYS F 603 " ideal model delta harmonic sigma weight residual -180.00 -153.60 -26.40 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 14417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2194 0.036 - 0.073: 908 0.073 - 0.109: 343 0.109 - 0.145: 143 0.145 - 0.181: 7 Chirality restraints: 3595 Sorted by residual: chirality pdb=" CB THR A 406 " pdb=" CA THR A 406 " pdb=" OG1 THR A 406 " pdb=" CG2 THR A 406 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.22e-01 chirality pdb=" CA ASN E 224 " pdb=" N ASN E 224 " pdb=" C ASN E 224 " pdb=" CB ASN E 224 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA ASN F 224 " pdb=" N ASN F 224 " pdb=" C ASN F 224 " pdb=" CB ASN F 224 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 3592 not shown) Planarity restraints: 4197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 268 " -0.037 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO C 269 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 269 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 269 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 438 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO F 439 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO F 439 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 439 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 268 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO G 269 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 269 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 269 " 0.028 5.00e-02 4.00e+02 ... (remaining 4194 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1552 2.73 - 3.27: 22562 3.27 - 3.81: 37179 3.81 - 4.36: 48743 4.36 - 4.90: 82670 Nonbonded interactions: 192706 Sorted by model distance: nonbonded pdb=" OE1 GLU B 230 " pdb=" OG SER B 258 " model vdw 2.185 3.040 nonbonded pdb=" O ILE D 509 " pdb=" OG SER D 513 " model vdw 2.231 3.040 nonbonded pdb=" OD1 ASP C 221 " pdb="CA CA C1002 " model vdw 2.242 2.510 nonbonded pdb=" OE1 GLU C 230 " pdb=" OG SER C 258 " model vdw 2.246 3.040 nonbonded pdb=" O ILE E 225 " pdb="CA CA E1002 " model vdw 2.249 2.510 ... (remaining 192701 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.370 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23656 Z= 0.206 Angle : 0.600 6.886 32056 Z= 0.348 Chirality : 0.048 0.181 3595 Planarity : 0.005 0.055 4197 Dihedral : 13.062 84.749 8864 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.12 % Allowed : 2.93 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.13), residues: 2942 helix: -2.44 (0.17), residues: 554 sheet: -1.54 (0.17), residues: 792 loop : -2.23 (0.13), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 606 TYR 0.017 0.001 TYR F 438 PHE 0.016 0.002 PHE A 248 TRP 0.008 0.001 TRP H 223 HIS 0.002 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00468 (23656) covalent geometry : angle 0.59995 (32056) hydrogen bonds : bond 0.18519 ( 829) hydrogen bonds : angle 7.77414 ( 2217) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 360 time to evaluate : 0.932 Fit side-chains REVERT: B 311 ASN cc_start: 0.8730 (p0) cc_final: 0.8412 (p0) REVERT: C 372 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7175 (mt-10) REVERT: C 489 LYS cc_start: 0.7819 (mttp) cc_final: 0.7545 (mttt) REVERT: D 463 TYR cc_start: 0.8628 (t80) cc_final: 0.8397 (t80) REVERT: F 414 ASP cc_start: 0.7778 (t0) cc_final: 0.7563 (t0) REVERT: H 44 LYS cc_start: 0.6841 (ptpp) cc_final: 0.6610 (pptt) REVERT: H 56 ARG cc_start: 0.8367 (ttp80) cc_final: 0.7891 (ppt-90) REVERT: H 63 GLN cc_start: 0.6564 (mt0) cc_final: 0.6349 (mt0) REVERT: H 182 ASP cc_start: 0.8320 (t70) cc_final: 0.8105 (t0) REVERT: H 347 SER cc_start: 0.6503 (m) cc_final: 0.6278 (m) outliers start: 3 outliers final: 2 residues processed: 363 average time/residue: 0.7003 time to fit residues: 286.6474 Evaluate side-chains 216 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 214 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain H residue 233 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN B 391 ASN B 492 GLN B 582 ASN C 318 GLN D 590 GLN E 582 ASN F 494 GLN G 449 ASN G 534 GLN G 559 ASN H 199 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.118293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.084825 restraints weight = 32727.297| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.00 r_work: 0.2824 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23656 Z= 0.207 Angle : 0.585 7.141 32056 Z= 0.321 Chirality : 0.048 0.167 3595 Planarity : 0.005 0.054 4197 Dihedral : 5.507 31.778 3184 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.73 % Allowed : 10.06 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.14), residues: 2942 helix: -1.16 (0.20), residues: 570 sheet: -0.63 (0.18), residues: 750 loop : -1.93 (0.13), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 528 TYR 0.017 0.001 TYR D 438 PHE 0.031 0.002 PHE C 248 TRP 0.012 0.001 TRP B 374 HIS 0.006 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00489 (23656) covalent geometry : angle 0.58481 (32056) hydrogen bonds : bond 0.04065 ( 829) hydrogen bonds : angle 5.31071 ( 2217) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 441 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8668 (ttpp) REVERT: A 451 MET cc_start: 0.9273 (ptm) cc_final: 0.9034 (ptt) REVERT: B 281 ASP cc_start: 0.8866 (t0) cc_final: 0.8592 (t0) REVERT: B 286 LEU cc_start: 0.9068 (pt) cc_final: 0.8820 (pt) REVERT: B 289 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7597 (ptp-170) REVERT: B 324 ARG cc_start: 0.7729 (ttt90) cc_final: 0.7515 (tpt-90) REVERT: B 533 GLU cc_start: 0.8822 (tt0) cc_final: 0.8594 (tt0) REVERT: C 489 LYS cc_start: 0.8234 (mttp) cc_final: 0.7723 (mttt) REVERT: C 561 GLU cc_start: 0.8224 (tp30) cc_final: 0.7973 (tp30) REVERT: D 289 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8633 (ptp90) REVERT: D 463 TYR cc_start: 0.8909 (t80) cc_final: 0.8690 (t80) REVERT: E 464 ASP cc_start: 0.8692 (m-30) cc_final: 0.8200 (t0) REVERT: E 620 ASN cc_start: 0.5242 (p0) cc_final: 0.4781 (p0) REVERT: G 532 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7971 (ptmm) REVERT: G 585 GLU cc_start: 0.8096 (pp20) cc_final: 0.7623 (tp30) REVERT: H 143 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8004 (mt-10) REVERT: H 180 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: H 182 ASP cc_start: 0.8449 (t70) cc_final: 0.8227 (t0) REVERT: H 196 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8424 (mm-30) REVERT: H 339 THR cc_start: 0.7533 (p) cc_final: 0.7271 (t) REVERT: H 347 SER cc_start: 0.6683 (m) cc_final: 0.6042 (t) outliers start: 45 outliers final: 22 residues processed: 259 average time/residue: 0.7261 time to fit residues: 212.7930 Evaluate side-chains 232 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain D residue 289 ARG Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 590 GLN Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 589 GLU Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 452 ASP Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 532 LYS Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain G residue 582 ASN Chi-restraints excluded: chain G residue 598 LYS Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 196 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 33 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 280 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 234 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 ASN B 582 ASN E 582 ASN F 370 ASN F 494 GLN G 534 GLN H 233 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.087328 restraints weight = 32683.735| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.01 r_work: 0.2838 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23656 Z= 0.130 Angle : 0.513 6.846 32056 Z= 0.283 Chirality : 0.046 0.152 3595 Planarity : 0.004 0.052 4197 Dihedral : 5.091 27.790 3182 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.77 % Allowed : 11.80 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.14), residues: 2942 helix: -0.48 (0.21), residues: 571 sheet: -0.22 (0.18), residues: 764 loop : -1.73 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 528 TYR 0.014 0.001 TYR F 438 PHE 0.023 0.001 PHE C 248 TRP 0.013 0.001 TRP B 374 HIS 0.003 0.001 HIS F 313 Details of bonding type rmsd covalent geometry : bond 0.00296 (23656) covalent geometry : angle 0.51305 (32056) hydrogen bonds : bond 0.03338 ( 829) hydrogen bonds : angle 4.94101 ( 2217) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 441 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8590 (ttpp) REVERT: A 451 MET cc_start: 0.9254 (ptm) cc_final: 0.9033 (ptt) REVERT: A 562 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7293 (tp) REVERT: A 589 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8170 (tp30) REVERT: B 289 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7620 (ptp-170) REVERT: B 376 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8282 (t) REVERT: B 533 GLU cc_start: 0.8779 (tt0) cc_final: 0.8540 (tt0) REVERT: C 296 TYR cc_start: 0.9165 (t80) cc_final: 0.8833 (t80) REVERT: C 489 LYS cc_start: 0.8188 (mttp) cc_final: 0.7662 (mttt) REVERT: C 561 GLU cc_start: 0.8285 (tp30) cc_final: 0.8036 (tp30) REVERT: D 463 TYR cc_start: 0.8862 (t80) cc_final: 0.8601 (t80) REVERT: E 452 ASP cc_start: 0.8176 (t0) cc_final: 0.7973 (t0) REVERT: E 620 ASN cc_start: 0.5350 (p0) cc_final: 0.4917 (p0) REVERT: F 564 TYR cc_start: 0.8301 (m-10) cc_final: 0.8073 (m-80) REVERT: G 489 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7393 (mttp) REVERT: H 143 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7972 (mt-10) REVERT: H 180 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7891 (tp30) REVERT: H 182 ASP cc_start: 0.8458 (t70) cc_final: 0.8211 (t0) REVERT: H 196 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8406 (mm-30) REVERT: H 234 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.7116 (pttt) REVERT: H 347 SER cc_start: 0.6797 (m) cc_final: 0.6194 (t) outliers start: 46 outliers final: 17 residues processed: 267 average time/residue: 0.6368 time to fit residues: 194.0934 Evaluate side-chains 235 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 590 GLN Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 602 VAL Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 196 GLU Chi-restraints excluded: chain H residue 233 ASN Chi-restraints excluded: chain H residue 234 LYS Chi-restraints excluded: chain H residue 285 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 ASN B 582 ASN C 318 GLN C 500 ASN E 582 ASN F 494 GLN F 508 GLN G 534 GLN H 233 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.117670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.084015 restraints weight = 32889.722| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.01 r_work: 0.2807 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 23656 Z= 0.245 Angle : 0.589 9.407 32056 Z= 0.321 Chirality : 0.049 0.172 3595 Planarity : 0.005 0.056 4197 Dihedral : 5.402 31.275 3182 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.12 % Allowed : 12.72 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.14), residues: 2942 helix: -0.33 (0.21), residues: 571 sheet: -0.25 (0.18), residues: 792 loop : -1.62 (0.14), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 457 TYR 0.020 0.002 TYR D 438 PHE 0.028 0.002 PHE C 248 TRP 0.014 0.001 TRP B 374 HIS 0.004 0.001 HIS F 313 Details of bonding type rmsd covalent geometry : bond 0.00584 (23656) covalent geometry : angle 0.58852 (32056) hydrogen bonds : bond 0.03782 ( 829) hydrogen bonds : angle 5.02441 ( 2217) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 214 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 441 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8623 (ttpp) REVERT: A 451 MET cc_start: 0.9286 (ptm) cc_final: 0.9053 (ptt) REVERT: A 562 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7537 (tp) REVERT: B 281 ASP cc_start: 0.8841 (t0) cc_final: 0.8476 (t0) REVERT: B 286 LEU cc_start: 0.9097 (pt) cc_final: 0.8849 (pt) REVERT: B 289 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7633 (ptp-170) REVERT: B 533 GLU cc_start: 0.8821 (tt0) cc_final: 0.8593 (tt0) REVERT: B 589 GLU cc_start: 0.8341 (pp20) cc_final: 0.7521 (tm-30) REVERT: C 489 LYS cc_start: 0.8208 (mttp) cc_final: 0.7635 (mttt) REVERT: C 561 GLU cc_start: 0.8212 (tp30) cc_final: 0.8000 (tp30) REVERT: D 463 TYR cc_start: 0.8925 (t80) cc_final: 0.8706 (t80) REVERT: E 620 ASN cc_start: 0.5281 (p0) cc_final: 0.4853 (p0) REVERT: F 320 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7489 (mtpp) REVERT: G 384 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: G 532 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8026 (ptmm) REVERT: H 37 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7455 (pp20) REVERT: H 180 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7886 (tp30) REVERT: H 182 ASP cc_start: 0.8422 (t70) cc_final: 0.8193 (t0) REVERT: H 196 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8527 (mm-30) REVERT: H 234 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.6973 (pttt) outliers start: 55 outliers final: 27 residues processed: 249 average time/residue: 0.6651 time to fit residues: 187.7643 Evaluate side-chains 229 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain E residue 254 LYS Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 590 GLN Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 602 VAL Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 532 LYS Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain G residue 582 ASN Chi-restraints excluded: chain G residue 598 LYS Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 196 GLU Chi-restraints excluded: chain H residue 234 LYS Chi-restraints excluded: chain H residue 285 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 264 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 235 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 chunk 284 optimal weight: 9.9990 chunk 186 optimal weight: 0.5980 chunk 101 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 GLN B 582 ASN E 582 ASN F 222 ASN F 494 GLN G 534 GLN H 233 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.120474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.087131 restraints weight = 32545.101| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.00 r_work: 0.2860 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23656 Z= 0.118 Angle : 0.503 7.333 32056 Z= 0.276 Chirality : 0.045 0.149 3595 Planarity : 0.004 0.055 4197 Dihedral : 4.940 27.465 3180 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.66 % Allowed : 13.88 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.14), residues: 2942 helix: -0.07 (0.22), residues: 571 sheet: 0.27 (0.18), residues: 757 loop : -1.59 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 457 TYR 0.013 0.001 TYR F 296 PHE 0.020 0.001 PHE B 248 TRP 0.016 0.001 TRP B 374 HIS 0.003 0.001 HIS F 313 Details of bonding type rmsd covalent geometry : bond 0.00269 (23656) covalent geometry : angle 0.50297 (32056) hydrogen bonds : bond 0.02996 ( 829) hydrogen bonds : angle 4.76957 ( 2217) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.9273 (ptm) cc_final: 0.9058 (ptt) REVERT: A 562 LEU cc_start: 0.7657 (tp) cc_final: 0.7453 (tp) REVERT: B 289 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7920 (ptp-170) REVERT: B 376 THR cc_start: 0.8519 (p) cc_final: 0.8293 (t) REVERT: B 589 GLU cc_start: 0.8312 (pp20) cc_final: 0.7514 (tm-30) REVERT: B 605 GLU cc_start: 0.8131 (pt0) cc_final: 0.7647 (pp20) REVERT: C 289 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8169 (mtp180) REVERT: C 296 TYR cc_start: 0.9135 (t80) cc_final: 0.8775 (t80) REVERT: C 489 LYS cc_start: 0.8050 (mttp) cc_final: 0.7515 (mttt) REVERT: D 318 GLN cc_start: 0.7997 (mt0) cc_final: 0.7758 (mt0) REVERT: D 463 TYR cc_start: 0.8865 (t80) cc_final: 0.8648 (t80) REVERT: E 289 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8349 (ptp90) REVERT: E 464 ASP cc_start: 0.8640 (m-30) cc_final: 0.8246 (t0) REVERT: E 620 ASN cc_start: 0.5558 (p0) cc_final: 0.5194 (p0) REVERT: F 564 TYR cc_start: 0.8334 (m-10) cc_final: 0.8081 (m-80) REVERT: G 384 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8287 (tp30) REVERT: G 489 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7419 (mttp) REVERT: G 585 GLU cc_start: 0.8064 (pp20) cc_final: 0.7586 (tp30) REVERT: H 180 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7931 (tp30) REVERT: H 182 ASP cc_start: 0.8490 (t70) cc_final: 0.8235 (t0) REVERT: H 219 LYS cc_start: 0.6856 (tptt) cc_final: 0.6633 (tptp) REVERT: H 234 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6905 (pttt) outliers start: 43 outliers final: 21 residues processed: 245 average time/residue: 0.6541 time to fit residues: 182.5605 Evaluate side-chains 224 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 602 VAL Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 234 LYS Chi-restraints excluded: chain H residue 285 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 237 optimal weight: 1.9990 chunk 209 optimal weight: 0.0670 chunk 157 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 214 optimal weight: 0.0050 chunk 58 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.8136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 ASN E 582 ASN F 222 ASN F 494 GLN G 534 GLN H 233 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.086360 restraints weight = 32877.830| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.01 r_work: 0.2837 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23656 Z= 0.123 Angle : 0.505 8.767 32056 Z= 0.276 Chirality : 0.045 0.146 3595 Planarity : 0.004 0.055 4197 Dihedral : 4.859 27.209 3180 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.58 % Allowed : 14.46 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 2942 helix: 0.01 (0.22), residues: 578 sheet: 0.48 (0.18), residues: 757 loop : -1.58 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 457 TYR 0.019 0.001 TYR F 296 PHE 0.020 0.001 PHE C 248 TRP 0.019 0.001 TRP B 374 HIS 0.003 0.001 HIS F 313 Details of bonding type rmsd covalent geometry : bond 0.00284 (23656) covalent geometry : angle 0.50513 (32056) hydrogen bonds : bond 0.02999 ( 829) hydrogen bonds : angle 4.70398 ( 2217) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 441 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8530 (ttpp) REVERT: A 451 MET cc_start: 0.9311 (ptm) cc_final: 0.9091 (ptt) REVERT: A 562 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7386 (tp) REVERT: B 281 ASP cc_start: 0.8840 (t0) cc_final: 0.8415 (t0) REVERT: B 289 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7792 (ptp-170) REVERT: B 376 THR cc_start: 0.8457 (p) cc_final: 0.8224 (t) REVERT: B 589 GLU cc_start: 0.8326 (pp20) cc_final: 0.7519 (tm-30) REVERT: B 605 GLU cc_start: 0.8101 (pt0) cc_final: 0.7572 (pp20) REVERT: C 289 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8093 (mtp180) REVERT: C 296 TYR cc_start: 0.9127 (t80) cc_final: 0.8754 (t80) REVERT: C 489 LYS cc_start: 0.7953 (mttp) cc_final: 0.7401 (mttt) REVERT: D 318 GLN cc_start: 0.7961 (mt0) cc_final: 0.7749 (mt0) REVERT: D 463 TYR cc_start: 0.8827 (t80) cc_final: 0.8614 (t80) REVERT: E 620 ASN cc_start: 0.5587 (p0) cc_final: 0.5259 (p0) REVERT: F 564 TYR cc_start: 0.8260 (m-10) cc_final: 0.7982 (m-80) REVERT: G 446 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8364 (mt) REVERT: G 489 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7327 (mttp) REVERT: G 532 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7917 (ptmt) REVERT: G 585 GLU cc_start: 0.8063 (pp20) cc_final: 0.7593 (tp30) REVERT: H 82 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7819 (mtmm) REVERT: H 180 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7886 (tp30) REVERT: H 182 ASP cc_start: 0.8492 (t70) cc_final: 0.8257 (t0) REVERT: H 234 LYS cc_start: 0.7482 (tmmt) cc_final: 0.6925 (ptmm) outliers start: 41 outliers final: 24 residues processed: 233 average time/residue: 0.6977 time to fit residues: 184.3701 Evaluate side-chains 233 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 602 VAL Chi-restraints excluded: chain F residue 619 THR Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 532 LYS Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 285 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 104 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 289 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 ASN E 582 ASN F 222 ASN F 494 GLN G 534 GLN H 233 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.119063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.085001 restraints weight = 32878.135| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.02 r_work: 0.2813 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23656 Z= 0.172 Angle : 0.535 8.033 32056 Z= 0.292 Chirality : 0.047 0.161 3595 Planarity : 0.004 0.055 4197 Dihedral : 5.020 28.546 3180 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.85 % Allowed : 14.65 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.14), residues: 2942 helix: 0.01 (0.22), residues: 571 sheet: 0.51 (0.18), residues: 757 loop : -1.51 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 289 TYR 0.024 0.001 TYR F 296 PHE 0.023 0.002 PHE C 248 TRP 0.015 0.001 TRP B 374 HIS 0.003 0.001 HIS F 313 Details of bonding type rmsd covalent geometry : bond 0.00405 (23656) covalent geometry : angle 0.53453 (32056) hydrogen bonds : bond 0.03258 ( 829) hydrogen bonds : angle 4.77840 ( 2217) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 441 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8565 (ttpp) REVERT: A 451 MET cc_start: 0.9312 (ptm) cc_final: 0.9079 (ptt) REVERT: A 562 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7414 (tp) REVERT: B 281 ASP cc_start: 0.8818 (t0) cc_final: 0.8496 (t0) REVERT: B 589 GLU cc_start: 0.8325 (pp20) cc_final: 0.7505 (tm-30) REVERT: B 605 GLU cc_start: 0.8179 (pt0) cc_final: 0.7726 (pp20) REVERT: C 289 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8146 (mtp180) REVERT: C 296 TYR cc_start: 0.9189 (t80) cc_final: 0.8896 (t80) REVERT: C 489 LYS cc_start: 0.7978 (mttp) cc_final: 0.7417 (mttt) REVERT: D 463 TYR cc_start: 0.8892 (t80) cc_final: 0.8688 (t80) REVERT: E 441 LYS cc_start: 0.9180 (ttpp) cc_final: 0.8975 (tttm) REVERT: E 464 ASP cc_start: 0.8650 (m-30) cc_final: 0.8184 (t0) REVERT: E 548 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8273 (mt-10) REVERT: E 620 ASN cc_start: 0.5616 (p0) cc_final: 0.5288 (p0) REVERT: F 564 TYR cc_start: 0.8282 (m-10) cc_final: 0.8000 (m-80) REVERT: G 446 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8494 (mt) REVERT: G 489 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7443 (mttp) REVERT: G 532 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7964 (ptmt) REVERT: G 585 GLU cc_start: 0.7956 (pp20) cc_final: 0.7646 (tp30) REVERT: H 56 ARG cc_start: 0.8099 (tmm160) cc_final: 0.7347 (ptm160) REVERT: H 180 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7893 (tp30) REVERT: H 182 ASP cc_start: 0.8491 (t70) cc_final: 0.8244 (t0) REVERT: H 234 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6857 (pttt) REVERT: H 258 LEU cc_start: 0.5620 (OUTLIER) cc_final: 0.5381 (mm) outliers start: 48 outliers final: 29 residues processed: 235 average time/residue: 0.6899 time to fit residues: 184.0407 Evaluate side-chains 236 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 602 VAL Chi-restraints excluded: chain F residue 619 THR Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 532 LYS Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 234 LYS Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 285 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 0.4980 chunk 166 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 222 optimal weight: 0.8980 chunk 258 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 ASN E 582 ASN F 222 ASN F 494 GLN G 534 GLN H 233 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.086326 restraints weight = 32657.541| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.03 r_work: 0.2833 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23656 Z= 0.124 Angle : 0.509 8.873 32056 Z= 0.278 Chirality : 0.045 0.164 3595 Planarity : 0.004 0.054 4197 Dihedral : 4.851 27.269 3180 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.73 % Allowed : 15.07 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.14), residues: 2942 helix: 0.05 (0.22), residues: 578 sheet: 0.63 (0.18), residues: 757 loop : -1.52 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 56 TYR 0.021 0.001 TYR F 296 PHE 0.019 0.001 PHE C 248 TRP 0.014 0.001 TRP B 374 HIS 0.003 0.001 HIS F 313 Details of bonding type rmsd covalent geometry : bond 0.00286 (23656) covalent geometry : angle 0.50918 (32056) hydrogen bonds : bond 0.02956 ( 829) hydrogen bonds : angle 4.69132 ( 2217) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 213 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 441 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8528 (ttpp) REVERT: A 451 MET cc_start: 0.9299 (ptm) cc_final: 0.9076 (ptt) REVERT: B 281 ASP cc_start: 0.8784 (t0) cc_final: 0.8466 (t0) REVERT: B 376 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8263 (t) REVERT: B 589 GLU cc_start: 0.8322 (pp20) cc_final: 0.7491 (tm-30) REVERT: B 605 GLU cc_start: 0.8164 (pt0) cc_final: 0.7652 (pp20) REVERT: C 289 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8166 (mtp180) REVERT: C 296 TYR cc_start: 0.9132 (t80) cc_final: 0.8775 (t80) REVERT: C 489 LYS cc_start: 0.7950 (mttp) cc_final: 0.7370 (mttt) REVERT: D 463 TYR cc_start: 0.8854 (t80) cc_final: 0.8646 (t80) REVERT: E 441 LYS cc_start: 0.9154 (ttpp) cc_final: 0.8951 (tttm) REVERT: E 464 ASP cc_start: 0.8618 (m-30) cc_final: 0.8212 (t0) REVERT: E 548 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8261 (mt-10) REVERT: E 620 ASN cc_start: 0.5582 (p0) cc_final: 0.5260 (p0) REVERT: F 564 TYR cc_start: 0.8251 (m-10) cc_final: 0.7957 (m-80) REVERT: G 384 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: G 446 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8379 (mt) REVERT: G 489 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7357 (mttp) REVERT: G 532 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7946 (ptmt) REVERT: G 585 GLU cc_start: 0.7971 (pp20) cc_final: 0.7597 (tp30) REVERT: H 56 ARG cc_start: 0.8147 (tmm160) cc_final: 0.7451 (ptm160) REVERT: H 180 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7918 (tp30) REVERT: H 182 ASP cc_start: 0.8481 (t70) cc_final: 0.8228 (t0) REVERT: H 234 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.6916 (ptmm) outliers start: 45 outliers final: 30 residues processed: 240 average time/residue: 0.6859 time to fit residues: 186.5121 Evaluate side-chains 243 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 441 LYS Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain E residue 254 LYS Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 602 VAL Chi-restraints excluded: chain F residue 619 THR Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 532 LYS Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 234 LYS Chi-restraints excluded: chain H residue 285 THR Chi-restraints excluded: chain H residue 347 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 63 optimal weight: 0.9980 chunk 235 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 chunk 275 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 254 optimal weight: 0.9990 chunk 270 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 ASN E 582 ASN F 222 ASN F 494 GLN G 534 GLN H 233 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.118481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.084420 restraints weight = 33040.194| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.00 r_work: 0.2806 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23656 Z= 0.201 Angle : 0.560 8.255 32056 Z= 0.305 Chirality : 0.048 0.183 3595 Planarity : 0.005 0.056 4197 Dihedral : 5.124 29.430 3180 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.77 % Allowed : 15.38 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.14), residues: 2942 helix: 0.01 (0.22), residues: 571 sheet: 0.64 (0.18), residues: 750 loop : -1.49 (0.14), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 457 TYR 0.026 0.001 TYR F 296 PHE 0.024 0.002 PHE C 248 TRP 0.013 0.001 TRP B 374 HIS 0.003 0.001 HIS F 313 Details of bonding type rmsd covalent geometry : bond 0.00478 (23656) covalent geometry : angle 0.55996 (32056) hydrogen bonds : bond 0.03387 ( 829) hydrogen bonds : angle 4.82985 ( 2217) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 207 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 441 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8575 (ttpp) REVERT: A 451 MET cc_start: 0.9305 (ptm) cc_final: 0.9059 (ptt) REVERT: A 562 LEU cc_start: 0.7899 (tp) cc_final: 0.7674 (tt) REVERT: B 605 GLU cc_start: 0.8320 (pt0) cc_final: 0.7836 (pp20) REVERT: C 289 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8117 (mtp180) REVERT: C 296 TYR cc_start: 0.9208 (t80) cc_final: 0.8903 (t80) REVERT: C 489 LYS cc_start: 0.7969 (mttp) cc_final: 0.7390 (mttt) REVERT: D 463 TYR cc_start: 0.8870 (t80) cc_final: 0.8660 (t80) REVERT: E 376 THR cc_start: 0.8794 (m) cc_final: 0.8336 (t) REVERT: E 441 LYS cc_start: 0.9164 (ttpp) cc_final: 0.8959 (tttm) REVERT: E 464 ASP cc_start: 0.8632 (m-30) cc_final: 0.8144 (t0) REVERT: E 548 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8256 (mt-10) REVERT: E 620 ASN cc_start: 0.5631 (p0) cc_final: 0.5313 (p0) REVERT: F 564 TYR cc_start: 0.8248 (m-10) cc_final: 0.7955 (m-80) REVERT: G 384 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: G 446 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8532 (mt) REVERT: G 489 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8057 (mttt) REVERT: G 498 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8119 (tp30) REVERT: G 532 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7938 (ptmt) REVERT: G 585 GLU cc_start: 0.7931 (pp20) cc_final: 0.7541 (tp30) REVERT: H 56 ARG cc_start: 0.8054 (tmm160) cc_final: 0.7424 (ptm160) REVERT: H 180 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7909 (tp30) REVERT: H 182 ASP cc_start: 0.8435 (t70) cc_final: 0.8177 (t0) REVERT: H 234 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6947 (ptmt) REVERT: H 258 LEU cc_start: 0.5449 (OUTLIER) cc_final: 0.5216 (mm) outliers start: 46 outliers final: 30 residues processed: 235 average time/residue: 0.6693 time to fit residues: 178.6174 Evaluate side-chains 237 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain E residue 254 LYS Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 602 VAL Chi-restraints excluded: chain F residue 619 THR Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 532 LYS Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 234 LYS Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 285 THR Chi-restraints excluded: chain H residue 347 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 101 optimal weight: 0.9980 chunk 276 optimal weight: 5.9990 chunk 274 optimal weight: 20.0000 chunk 196 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 269 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 168 optimal weight: 0.6980 chunk 203 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 ASN E 582 ASN F 222 ASN F 494 GLN G 534 GLN H 233 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.086105 restraints weight = 32781.660| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.03 r_work: 0.2832 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23656 Z= 0.129 Angle : 0.519 9.077 32056 Z= 0.283 Chirality : 0.046 0.189 3595 Planarity : 0.004 0.054 4197 Dihedral : 4.878 27.387 3180 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.54 % Allowed : 15.77 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.14), residues: 2942 helix: 0.04 (0.22), residues: 578 sheet: 0.70 (0.18), residues: 757 loop : -1.51 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 457 TYR 0.023 0.001 TYR F 296 PHE 0.019 0.001 PHE C 248 TRP 0.012 0.001 TRP B 374 HIS 0.002 0.001 HIS F 313 Details of bonding type rmsd covalent geometry : bond 0.00300 (23656) covalent geometry : angle 0.51938 (32056) hydrogen bonds : bond 0.02956 ( 829) hydrogen bonds : angle 4.69064 ( 2217) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 451 MET cc_start: 0.9309 (ptm) cc_final: 0.9094 (ptt) REVERT: B 281 ASP cc_start: 0.8910 (t0) cc_final: 0.8557 (t0) REVERT: B 589 GLU cc_start: 0.8296 (pp20) cc_final: 0.7494 (tm-30) REVERT: B 605 GLU cc_start: 0.8191 (pt0) cc_final: 0.7683 (pp20) REVERT: C 289 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8166 (mtp180) REVERT: C 296 TYR cc_start: 0.9162 (t80) cc_final: 0.8805 (t80) REVERT: C 489 LYS cc_start: 0.7911 (mttp) cc_final: 0.7301 (mttt) REVERT: D 463 TYR cc_start: 0.8863 (t80) cc_final: 0.8658 (t80) REVERT: E 376 THR cc_start: 0.8746 (m) cc_final: 0.8306 (t) REVERT: E 441 LYS cc_start: 0.9126 (ttpp) cc_final: 0.8918 (tttm) REVERT: E 464 ASP cc_start: 0.8619 (m-30) cc_final: 0.8213 (t0) REVERT: E 548 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8247 (mt-10) REVERT: E 620 ASN cc_start: 0.5587 (p0) cc_final: 0.5271 (p0) REVERT: F 564 TYR cc_start: 0.8241 (m-10) cc_final: 0.7951 (m-80) REVERT: G 384 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8215 (tt0) REVERT: G 446 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8381 (mt) REVERT: G 489 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7436 (mttt) REVERT: G 498 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8102 (tp30) REVERT: G 532 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7944 (ptmt) REVERT: G 585 GLU cc_start: 0.7932 (pp20) cc_final: 0.7547 (tp30) REVERT: H 56 ARG cc_start: 0.8105 (tmm160) cc_final: 0.7362 (ptm160) REVERT: H 180 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7921 (tp30) REVERT: H 182 ASP cc_start: 0.8406 (t70) cc_final: 0.8170 (t0) REVERT: H 234 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6934 (ptmm) REVERT: H 258 LEU cc_start: 0.5470 (OUTLIER) cc_final: 0.5236 (mm) outliers start: 40 outliers final: 28 residues processed: 235 average time/residue: 0.6613 time to fit residues: 177.2899 Evaluate side-chains 239 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain E residue 254 LYS Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 602 VAL Chi-restraints excluded: chain F residue 619 THR Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 532 LYS Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 234 LYS Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 285 THR Chi-restraints excluded: chain H residue 347 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 276 optimal weight: 5.9990 chunk 127 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 112 optimal weight: 0.3980 chunk 91 optimal weight: 0.0020 chunk 256 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 ASN B 582 ASN F 222 ASN F 494 GLN G 455 ASN G 534 GLN H 233 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.122354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.088196 restraints weight = 33010.985| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.05 r_work: 0.2856 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23656 Z= 0.102 Angle : 0.498 8.610 32056 Z= 0.270 Chirality : 0.045 0.165 3595 Planarity : 0.004 0.054 4197 Dihedral : 4.636 26.305 3180 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.23 % Allowed : 16.19 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.15), residues: 2942 helix: 0.12 (0.22), residues: 578 sheet: 0.86 (0.18), residues: 757 loop : -1.46 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 457 TYR 0.021 0.001 TYR F 296 PHE 0.017 0.001 PHE B 248 TRP 0.014 0.001 TRP B 374 HIS 0.003 0.001 HIS F 313 Details of bonding type rmsd covalent geometry : bond 0.00232 (23656) covalent geometry : angle 0.49767 (32056) hydrogen bonds : bond 0.02730 ( 829) hydrogen bonds : angle 4.55941 ( 2217) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8534.28 seconds wall clock time: 145 minutes 50.25 seconds (8750.25 seconds total)