Starting phenix.real_space_refine on Sun Sep 29 18:45:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klo_0713/09_2024/6klo_0713.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klo_0713/09_2024/6klo_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klo_0713/09_2024/6klo_0713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klo_0713/09_2024/6klo_0713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klo_0713/09_2024/6klo_0713.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klo_0713/09_2024/6klo_0713.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 13.49, per 1000 atoms: 0.58 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: 5.46 Conformation dependent library (CDL) restraints added in 2.8 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: 3.32 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: 8.99 Time building geometry restraints manager: 6.42 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: 2.330 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: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.280 Process input model: 52.110 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.110 ------------------------------------------------------------------------------- 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= 0.304 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 : 5.62 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (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 TRP 0.008 0.001 TRP H 223 HIS 0.002 0.001 HIS H 157 PHE 0.016 0.002 PHE A 248 TYR 0.017 0.001 TYR F 438 ARG 0.006 0.000 ARG D 606 *********************** 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 fitting. rotamer outliers: 3 poor density : 360 time to evaluate : 2.874 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: 1.4479 time to fit residues: 594.9993 Evaluate side-chains 216 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 214 time to evaluate : 2.610 ------------------------------------------------------------------------------- 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 245 optimal weight: 0.0870 chunk 220 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 148 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 228 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 264 optimal weight: 4.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN A 534 GLN B 391 ASN B 492 GLN ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23656 Z= 0.168 Angle : 0.526 7.327 32056 Z= 0.289 Chirality : 0.046 0.150 3595 Planarity : 0.004 0.048 4197 Dihedral : 5.129 28.672 3184 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.31 % Allowed : 10.14 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.14), residues: 2942 helix: -1.02 (0.20), residues: 568 sheet: -0.61 (0.17), residues: 764 loop : -1.86 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 374 HIS 0.005 0.001 HIS H 157 PHE 0.024 0.001 PHE C 248 TYR 0.013 0.001 TYR H 368 ARG 0.005 0.000 ARG F 528 *********************** 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 296 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 262 time to evaluate : 2.647 Fit side-chains REVERT: A 441 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8157 (ttpp) REVERT: A 593 TYR cc_start: 0.7901 (m-80) cc_final: 0.7513 (m-80) REVERT: B 281 ASP cc_start: 0.8342 (t0) cc_final: 0.8103 (t0) REVERT: B 289 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7196 (ptp-170) REVERT: B 303 MET cc_start: 0.9076 (ttp) cc_final: 0.8874 (ttp) REVERT: B 311 ASN cc_start: 0.8612 (p0) cc_final: 0.8288 (p0) REVERT: B 533 GLU cc_start: 0.8212 (tt0) cc_final: 0.7984 (tt0) REVERT: C 296 TYR cc_start: 0.8788 (t80) cc_final: 0.8471 (t80) REVERT: C 489 LYS cc_start: 0.7723 (mttp) cc_final: 0.7509 (mttt) REVERT: D 375 ASN cc_start: 0.8272 (m110) cc_final: 0.7989 (m110) REVERT: D 463 TYR cc_start: 0.8571 (t80) cc_final: 0.8363 (t80) REVERT: E 620 ASN cc_start: 0.5126 (p0) cc_final: 0.4616 (p0) REVERT: H 143 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7568 (mt-10) REVERT: H 180 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: H 182 ASP cc_start: 0.8242 (t70) cc_final: 0.8035 (t0) REVERT: H 339 THR cc_start: 0.7540 (p) cc_final: 0.7279 (t) REVERT: H 347 SER cc_start: 0.6681 (m) cc_final: 0.5997 (t) outliers start: 34 outliers final: 12 residues processed: 287 average time/residue: 1.3928 time to fit residues: 456.1752 Evaluate side-chains 226 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 211 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 619 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 452 ASP Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 180 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 264 optimal weight: 7.9990 chunk 285 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 chunk 262 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 212 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 ASN C 318 GLN E 582 ASN F 494 GLN H 146 ASN H 199 GLN H 233 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1430 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= 0.209 Angle : 0.520 6.766 32056 Z= 0.285 Chirality : 0.046 0.149 3595 Planarity : 0.004 0.048 4197 Dihedral : 5.026 29.153 3182 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.85 % Allowed : 11.95 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.14), residues: 2942 helix: -0.44 (0.21), residues: 571 sheet: -0.19 (0.18), residues: 764 loop : -1.70 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 374 HIS 0.003 0.001 HIS F 313 PHE 0.025 0.001 PHE C 248 TYR 0.017 0.001 TYR F 296 ARG 0.003 0.000 ARG F 528 *********************** 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 277 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 229 time to evaluate : 2.686 Fit side-chains REVERT: A 441 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8141 (ttpp) REVERT: B 289 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7197 (ptp-170) REVERT: B 303 MET cc_start: 0.9026 (ttp) cc_final: 0.8817 (ttp) REVERT: B 311 ASN cc_start: 0.8643 (p0) cc_final: 0.8366 (p0) REVERT: B 384 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7883 (mm-30) REVERT: B 533 GLU cc_start: 0.8212 (tt0) cc_final: 0.7973 (tt0) REVERT: C 296 TYR cc_start: 0.8778 (t80) cc_final: 0.8459 (t80) REVERT: C 489 LYS cc_start: 0.7696 (mttp) cc_final: 0.7430 (mttt) REVERT: D 463 TYR cc_start: 0.8590 (t80) cc_final: 0.8387 (t80) REVERT: E 620 ASN cc_start: 0.5135 (p0) cc_final: 0.4618 (p0) REVERT: F 320 LYS cc_start: 0.7626 (tttt) cc_final: 0.7409 (tttt) REVERT: G 384 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7438 (tp30) REVERT: G 489 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7457 (mttp) REVERT: G 532 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7897 (ptmm) REVERT: H 143 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7527 (mt-10) REVERT: H 180 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7909 (tp30) REVERT: H 234 LYS cc_start: 0.7346 (tmmt) cc_final: 0.7100 (pttt) REVERT: H 339 THR cc_start: 0.7723 (p) cc_final: 0.7501 (t) REVERT: H 347 SER cc_start: 0.6841 (m) cc_final: 0.6189 (t) outliers start: 48 outliers final: 17 residues processed: 260 average time/residue: 1.3767 time to fit residues: 408.8563 Evaluate side-chains 235 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 211 time to evaluate : 2.680 ------------------------------------------------------------------------------- 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 602 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain E residue 315 SER 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 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 532 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 233 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 126 optimal weight: 0.4980 chunk 177 optimal weight: 4.9990 chunk 265 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 251 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 ASN B 582 ASN E 582 ASN F 494 GLN G 534 GLN H 233 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23656 Z= 0.225 Angle : 0.523 8.326 32056 Z= 0.286 Chirality : 0.046 0.168 3595 Planarity : 0.004 0.051 4197 Dihedral : 5.023 28.397 3182 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.77 % Allowed : 12.84 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.14), residues: 2942 helix: -0.21 (0.22), residues: 571 sheet: 0.05 (0.18), residues: 764 loop : -1.60 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 374 HIS 0.003 0.001 HIS F 313 PHE 0.024 0.001 PHE C 248 TYR 0.020 0.001 TYR F 296 ARG 0.003 0.000 ARG C 289 *********************** 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 255 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 209 time to evaluate : 2.895 Fit side-chains REVERT: A 441 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8127 (ttpp) REVERT: A 562 LEU cc_start: 0.7857 (tp) cc_final: 0.7605 (tt) REVERT: B 281 ASP cc_start: 0.8432 (t0) cc_final: 0.8116 (t0) REVERT: B 289 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7392 (ptp-170) REVERT: B 311 ASN cc_start: 0.8718 (p0) cc_final: 0.8435 (p0) REVERT: B 384 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7836 (mm-30) REVERT: C 296 TYR cc_start: 0.8784 (t80) cc_final: 0.8472 (t80) REVERT: C 489 LYS cc_start: 0.7747 (mttp) cc_final: 0.7534 (mttt) REVERT: D 463 TYR cc_start: 0.8605 (t80) cc_final: 0.8402 (t80) REVERT: E 372 GLU cc_start: 0.7581 (pt0) cc_final: 0.7359 (pt0) REVERT: E 620 ASN cc_start: 0.5123 (p0) cc_final: 0.4636 (p0) REVERT: F 562 LEU cc_start: 0.7600 (pt) cc_final: 0.7060 (mt) REVERT: G 384 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7412 (tp30) REVERT: G 489 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7451 (mttp) REVERT: G 532 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7897 (ptmt) REVERT: H 143 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7534 (mt-10) REVERT: H 180 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7868 (tp30) REVERT: H 234 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7017 (ptmt) REVERT: H 284 LEU cc_start: 0.6789 (pt) cc_final: 0.6483 (pp) REVERT: H 339 THR cc_start: 0.7686 (p) cc_final: 0.7473 (t) outliers start: 46 outliers final: 21 residues processed: 241 average time/residue: 1.4354 time to fit residues: 394.2494 Evaluate side-chains 232 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 203 time to evaluate : 2.605 ------------------------------------------------------------------------------- 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 289 ARG Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 619 THR 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 315 SER 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 602 VAL 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 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 598 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 0.1980 chunk 159 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 209 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 240 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 ASN C 318 GLN E 582 ASN F 494 GLN F 508 GLN G 534 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1666 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= 0.181 Angle : 0.497 7.880 32056 Z= 0.271 Chirality : 0.045 0.145 3595 Planarity : 0.004 0.051 4197 Dihedral : 4.850 26.796 3182 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.62 % Allowed : 13.53 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.14), residues: 2942 helix: -0.06 (0.22), residues: 578 sheet: 0.32 (0.18), residues: 757 loop : -1.56 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 374 HIS 0.003 0.001 HIS F 313 PHE 0.020 0.001 PHE C 248 TYR 0.020 0.001 TYR F 296 ARG 0.004 0.000 ARG G 457 *********************** 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 264 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 222 time to evaluate : 2.912 Fit side-chains REVERT: A 562 LEU cc_start: 0.7745 (tp) cc_final: 0.7417 (tt) REVERT: B 289 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7474 (ptp-170) REVERT: B 311 ASN cc_start: 0.8643 (p0) cc_final: 0.8430 (p0) REVERT: B 384 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7793 (mm-30) REVERT: B 589 GLU cc_start: 0.8048 (pp20) cc_final: 0.7418 (tm-30) REVERT: C 296 TYR cc_start: 0.8736 (t80) cc_final: 0.8358 (t80) REVERT: C 489 LYS cc_start: 0.7663 (mttp) cc_final: 0.7380 (mttt) REVERT: D 463 TYR cc_start: 0.8568 (t80) cc_final: 0.8367 (t80) REVERT: E 289 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8089 (ptp90) REVERT: E 620 ASN cc_start: 0.5089 (p0) cc_final: 0.4621 (p0) REVERT: G 384 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7406 (tp30) REVERT: G 489 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7475 (mttm) REVERT: H 180 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7824 (tp30) REVERT: H 219 LYS cc_start: 0.6927 (tptt) cc_final: 0.6713 (tptp) REVERT: H 234 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.7034 (pttt) outliers start: 42 outliers final: 23 residues processed: 251 average time/residue: 1.4624 time to fit residues: 420.0267 Evaluate side-chains 228 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 198 time to evaluate : 2.537 ------------------------------------------------------------------------------- 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 498 GLU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 315 SER 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 289 ARG 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 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 94 optimal weight: 2.9990 chunk 253 optimal weight: 0.0570 chunk 55 optimal weight: 0.8980 chunk 165 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 281 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 93 optimal weight: 0.2980 chunk 147 optimal weight: 3.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 ASN C 318 GLN D 251 GLN E 582 ASN F 494 GLN G 455 ASN G 534 GLN H 233 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23656 Z= 0.162 Angle : 0.490 8.311 32056 Z= 0.267 Chirality : 0.045 0.142 3595 Planarity : 0.004 0.052 4197 Dihedral : 4.710 26.140 3182 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.58 % Allowed : 14.57 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 2942 helix: 0.04 (0.22), residues: 578 sheet: 0.54 (0.18), residues: 757 loop : -1.50 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 374 HIS 0.003 0.001 HIS F 313 PHE 0.019 0.001 PHE C 248 TYR 0.020 0.001 TYR F 296 ARG 0.004 0.000 ARG G 457 *********************** 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 263 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 222 time to evaluate : 2.531 Fit side-chains REVERT: A 441 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8049 (ttpp) REVERT: A 564 TYR cc_start: 0.8056 (m-10) cc_final: 0.7854 (m-10) REVERT: B 281 ASP cc_start: 0.8451 (t0) cc_final: 0.8187 (t0) REVERT: B 289 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7671 (ptp-170) REVERT: B 384 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7785 (mm-30) REVERT: B 589 GLU cc_start: 0.8031 (pp20) cc_final: 0.7448 (tm-30) REVERT: C 296 TYR cc_start: 0.8687 (t80) cc_final: 0.8470 (t80) REVERT: C 489 LYS cc_start: 0.7587 (mttp) cc_final: 0.7305 (mttt) REVERT: D 320 LYS cc_start: 0.8064 (mttm) cc_final: 0.7804 (mttp) REVERT: E 289 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8079 (ptp90) REVERT: E 620 ASN cc_start: 0.5240 (p0) cc_final: 0.4783 (p0) REVERT: F 562 LEU cc_start: 0.7648 (pt) cc_final: 0.6984 (mt) REVERT: G 446 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8083 (mt) REVERT: G 489 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7483 (mttm) REVERT: H 180 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7884 (tp30) REVERT: H 234 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7009 (ptmm) REVERT: H 258 LEU cc_start: 0.5674 (OUTLIER) cc_final: 0.5442 (mm) outliers start: 41 outliers final: 20 residues processed: 252 average time/residue: 1.3619 time to fit residues: 393.4931 Evaluate side-chains 232 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 203 time to evaluate : 2.670 ------------------------------------------------------------------------------- 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 B residue 289 ARG Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 619 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 315 SER 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 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 571 ASP Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 233 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 0.0770 chunk 31 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 237 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 280 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN C 318 GLN D 251 GLN E 582 ASN F 494 GLN G 534 GLN H 233 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23656 Z= 0.200 Angle : 0.504 8.196 32056 Z= 0.275 Chirality : 0.045 0.169 3595 Planarity : 0.004 0.052 4197 Dihedral : 4.772 27.090 3182 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.46 % Allowed : 15.11 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 2942 helix: 0.08 (0.22), residues: 578 sheet: 0.62 (0.18), residues: 757 loop : -1.48 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 374 HIS 0.003 0.001 HIS F 313 PHE 0.021 0.001 PHE C 248 TYR 0.021 0.001 TYR F 296 ARG 0.003 0.000 ARG C 289 *********************** 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 248 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 210 time to evaluate : 2.917 Fit side-chains REVERT: A 441 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8047 (ttpp) REVERT: B 289 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7680 (ptp-170) REVERT: B 384 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7805 (mm-30) REVERT: B 589 GLU cc_start: 0.8031 (pp20) cc_final: 0.7449 (tm-30) REVERT: C 296 TYR cc_start: 0.8729 (t80) cc_final: 0.8520 (t80) REVERT: C 489 LYS cc_start: 0.7623 (mttp) cc_final: 0.7319 (mttt) REVERT: E 620 ASN cc_start: 0.5249 (p0) cc_final: 0.4798 (p0) REVERT: F 562 LEU cc_start: 0.7565 (pt) cc_final: 0.6895 (mt) REVERT: G 384 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: G 446 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8124 (mt) REVERT: G 489 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7506 (mttm) REVERT: H 180 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7887 (tp30) REVERT: H 234 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.7019 (ptmt) REVERT: H 258 LEU cc_start: 0.5611 (OUTLIER) cc_final: 0.5383 (mm) outliers start: 38 outliers final: 24 residues processed: 235 average time/residue: 1.4147 time to fit residues: 382.2014 Evaluate side-chains 233 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 2.739 ------------------------------------------------------------------------------- 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 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 321 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain E residue 315 SER 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 589 GLU 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 571 ASP Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 233 ASN 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 173 optimal weight: 0.0670 chunk 112 optimal weight: 0.0060 chunk 167 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 178 optimal weight: 0.4980 chunk 191 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 overall best weight: 0.6936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 ASN C 318 GLN D 251 GLN E 582 ASN F 494 GLN G 534 GLN H 233 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23656 Z= 0.169 Angle : 0.500 8.422 32056 Z= 0.272 Chirality : 0.045 0.162 3595 Planarity : 0.004 0.053 4197 Dihedral : 4.712 26.159 3182 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.58 % Allowed : 15.34 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 2942 helix: 0.13 (0.22), residues: 578 sheet: 0.71 (0.18), residues: 757 loop : -1.45 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 374 HIS 0.003 0.001 HIS F 313 PHE 0.019 0.001 PHE C 248 TYR 0.026 0.001 TYR A 564 ARG 0.003 0.000 ARG C 289 *********************** 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 247 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 2.732 Fit side-chains REVERT: A 564 TYR cc_start: 0.7903 (m-10) cc_final: 0.7685 (m-80) REVERT: B 289 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7680 (ptp-170) REVERT: B 384 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7798 (mm-30) REVERT: B 589 GLU cc_start: 0.8000 (pp20) cc_final: 0.7386 (tm-30) REVERT: C 489 LYS cc_start: 0.7571 (mttp) cc_final: 0.7298 (mttt) REVERT: E 620 ASN cc_start: 0.5231 (p0) cc_final: 0.4783 (p0) REVERT: F 451 MET cc_start: 0.8445 (ptm) cc_final: 0.8219 (ptt) REVERT: F 562 LEU cc_start: 0.7573 (pt) cc_final: 0.6892 (mt) REVERT: F 589 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7795 (pt0) REVERT: G 384 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: G 446 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8065 (mt) REVERT: G 489 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7532 (mttm) REVERT: H 180 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7884 (tp30) REVERT: H 234 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.7070 (pttt) REVERT: H 258 LEU cc_start: 0.5603 (OUTLIER) cc_final: 0.5375 (mm) outliers start: 41 outliers final: 29 residues processed: 232 average time/residue: 1.3530 time to fit residues: 359.9091 Evaluate side-chains 232 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 194 time to evaluate : 2.690 ------------------------------------------------------------------------------- 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 498 GLU Chi-restraints excluded: chain A residue 558 LYS 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 321 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain E residue 315 SER 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 589 GLU 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 452 ASP Chi-restraints excluded: chain G residue 489 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 233 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 7.9990 chunk 268 optimal weight: 6.9990 chunk 245 optimal weight: 0.5980 chunk 261 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 113 optimal weight: 0.1980 chunk 205 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 260 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 ASN C 318 GLN D 251 GLN E 582 ASN F 494 GLN G 534 GLN H 233 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1851 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= 0.239 Angle : 0.524 8.463 32056 Z= 0.285 Chirality : 0.046 0.179 3595 Planarity : 0.004 0.054 4197 Dihedral : 4.853 26.965 3182 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.66 % Allowed : 15.23 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 2942 helix: 0.10 (0.22), residues: 578 sheet: 0.71 (0.18), residues: 757 loop : -1.47 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 374 HIS 0.003 0.001 HIS C 313 PHE 0.022 0.002 PHE C 248 TYR 0.025 0.001 TYR F 296 ARG 0.003 0.000 ARG C 289 *********************** 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 247 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 204 time to evaluate : 2.904 Fit side-chains REVERT: A 441 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8056 (ttpp) REVERT: B 384 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7761 (mm-30) REVERT: B 589 GLU cc_start: 0.8016 (pp20) cc_final: 0.7394 (tm-30) REVERT: C 489 LYS cc_start: 0.7611 (mttp) cc_final: 0.7309 (mttt) REVERT: E 620 ASN cc_start: 0.5265 (p0) cc_final: 0.4819 (p0) REVERT: F 562 LEU cc_start: 0.7601 (pt) cc_final: 0.6936 (mt) REVERT: G 384 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: G 446 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8209 (mt) REVERT: G 489 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7572 (mttm) REVERT: H 56 ARG cc_start: 0.7864 (ttp-170) cc_final: 0.7283 (ptm160) REVERT: H 180 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7882 (tp30) REVERT: H 234 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.7072 (ptmt) REVERT: H 258 LEU cc_start: 0.5559 (OUTLIER) cc_final: 0.5330 (mm) outliers start: 43 outliers final: 29 residues processed: 230 average time/residue: 1.4361 time to fit residues: 383.0178 Evaluate side-chains 235 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 198 time to evaluate : 2.737 ------------------------------------------------------------------------------- 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 498 GLU Chi-restraints excluded: chain A residue 558 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 376 THR Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 619 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 315 SER Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 218 LEU 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 289 ARG Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 452 ASP Chi-restraints excluded: chain G residue 489 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 233 ASN 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 171 optimal weight: 1.9990 chunk 276 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 289 optimal weight: 7.9990 chunk 266 optimal weight: 0.9990 chunk 230 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 ASN C 318 GLN D 251 GLN E 582 ASN F 222 ASN F 494 GLN G 534 GLN H 233 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23656 Z= 0.236 Angle : 0.530 8.720 32056 Z= 0.288 Chirality : 0.046 0.182 3595 Planarity : 0.004 0.054 4197 Dihedral : 4.864 27.172 3180 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.50 % Allowed : 15.61 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 2942 helix: 0.09 (0.22), residues: 578 sheet: 0.72 (0.18), residues: 757 loop : -1.47 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 231 HIS 0.002 0.001 HIS C 313 PHE 0.022 0.001 PHE C 248 TYR 0.026 0.001 TYR F 296 ARG 0.004 0.000 ARG G 457 ********************** 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 236 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 197 time to evaluate : 2.501 Fit side-chains REVERT: A 441 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8056 (ttpp) REVERT: B 384 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7756 (mm-30) REVERT: B 589 GLU cc_start: 0.8018 (pp20) cc_final: 0.7497 (tm-30) REVERT: C 489 LYS cc_start: 0.7617 (mttp) cc_final: 0.7310 (mttt) REVERT: E 620 ASN cc_start: 0.5274 (p0) cc_final: 0.4831 (p0) REVERT: F 218 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8288 (mp) REVERT: F 562 LEU cc_start: 0.7618 (pt) cc_final: 0.6949 (mt) REVERT: G 384 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: G 446 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8212 (mt) REVERT: G 489 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7571 (mttm) REVERT: G 498 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7212 (tp30) REVERT: H 82 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8122 (mtmm) REVERT: H 180 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7879 (tp30) REVERT: H 234 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.7061 (ptmt) REVERT: H 258 LEU cc_start: 0.5560 (OUTLIER) cc_final: 0.5332 (mm) outliers start: 39 outliers final: 28 residues processed: 222 average time/residue: 1.3981 time to fit residues: 353.8776 Evaluate side-chains 230 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 192 time to evaluate : 2.727 ------------------------------------------------------------------------------- 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 498 GLU Chi-restraints excluded: chain A residue 558 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 376 THR Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 619 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 315 SER Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 218 LEU 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 289 ARG Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 452 ASP Chi-restraints excluded: chain G residue 489 LYS 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 233 ASN 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 183 optimal weight: 2.9990 chunk 245 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 212 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 237 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 ASN C 318 GLN D 251 GLN 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 = 0.120772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.086629 restraints weight = 32590.479| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.03 r_work: 0.2843 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23656 Z= 0.182 Angle : 0.511 8.739 32056 Z= 0.278 Chirality : 0.045 0.178 3595 Planarity : 0.004 0.054 4197 Dihedral : 4.763 26.661 3180 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.43 % Allowed : 15.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 2942 helix: 0.10 (0.22), residues: 578 sheet: 0.78 (0.18), residues: 757 loop : -1.45 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 374 HIS 0.002 0.001 HIS C 313 PHE 0.019 0.001 PHE C 248 TYR 0.024 0.001 TYR F 296 ARG 0.006 0.000 ARG C 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7620.27 seconds wall clock time: 134 minutes 50.78 seconds (8090.78 seconds total)