Starting phenix.real_space_refine on Wed May 6 01:20:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vej_65009/05_2026/9vej_65009.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vej_65009/05_2026/9vej_65009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vej_65009/05_2026/9vej_65009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vej_65009/05_2026/9vej_65009.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vej_65009/05_2026/9vej_65009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vej_65009/05_2026/9vej_65009.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 21 9.91 5 S 82 5.16 5 C 20929 2.51 5 N 5571 2.21 5 O 6918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33521 Number of models: 1 Model: "" Number of chains: 15 Chain: "B" Number of atoms: 4344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4344 Classifications: {'peptide': 560} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 539} Chain: "A" Number of atoms: 4344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4344 Classifications: {'peptide': 560} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 539} Chain: "C" Number of atoms: 4344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4344 Classifications: {'peptide': 560} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 539} Chain: "D" Number of atoms: 4344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4344 Classifications: {'peptide': 560} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 539} Chain: "E" Number of atoms: 4344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4344 Classifications: {'peptide': 560} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 539} Chain: "F" Number of atoms: 4344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4344 Classifications: {'peptide': 560} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 539} Chain: "G" Number of atoms: 4344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4344 Classifications: {'peptide': 560} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 539} Chain: "H" Number of atoms: 3092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3092 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 9, 'TRANS': 379} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.96, per 1000 atoms: 0.21 Number of scatterers: 33521 At special positions: 0 Unit cell: (188.16, 186.48, 222.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 21 19.99 S 82 16.00 O 6918 8.00 N 5571 7.00 C 20929 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: 2.28 Conformation dependent library (CDL) restraints added in 1.1 seconds 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8046 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 76 sheets defined 17.9% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 253 through 260 removed outlier: 3.578A pdb=" N GLY B 260 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 286 Processing helix chain 'B' and resid 293 through 297 removed outlier: 3.520A pdb=" N PHE B 297 " --> pdb=" O LYS B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.955A pdb=" N GLN B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 554 Processing helix chain 'B' and resid 582 through 595 Processing helix chain 'B' and resid 605 through 609 Processing helix chain 'B' and resid 668 through 674 Processing helix chain 'B' and resid 760 through 764 removed outlier: 3.555A pdb=" N LEU B 764 " --> pdb=" O PRO B 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 241 Processing helix chain 'A' and resid 253 through 260 removed outlier: 3.565A pdb=" N GLY A 260 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 504 through 512 removed outlier: 4.078A pdb=" N GLN A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 554 Processing helix chain 'A' and resid 582 through 595 Processing helix chain 'A' and resid 605 through 609 Processing helix chain 'A' and resid 668 through 674 Processing helix chain 'A' and resid 766 through 771 removed outlier: 3.559A pdb=" N GLN A 770 " --> pdb=" O ASP A 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 254 through 259 removed outlier: 4.114A pdb=" N SER C 258 " --> pdb=" O ASP C 254 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 254 through 259' Processing helix chain 'C' and resid 279 through 286 Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 504 through 512 removed outlier: 3.879A pdb=" N GLN C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 554 Processing helix chain 'C' and resid 582 through 595 Processing helix chain 'C' and resid 605 through 609 Processing helix chain 'C' and resid 668 through 674 Processing helix chain 'C' and resid 766 through 771 removed outlier: 4.143A pdb=" N GLN C 770 " --> pdb=" O ASP C 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 241 Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.579A pdb=" N SER D 258 " --> pdb=" O SER D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 286 Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.201A pdb=" N THR D 429 " --> pdb=" O SER D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 504 through 512 removed outlier: 4.046A pdb=" N GLN D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 554 Processing helix chain 'D' and resid 582 through 595 Processing helix chain 'D' and resid 605 through 609 Processing helix chain 'D' and resid 668 through 674 Processing helix chain 'D' and resid 766 through 771 Processing helix chain 'E' and resid 234 through 241 Processing helix chain 'E' and resid 253 through 260 removed outlier: 3.586A pdb=" N GLY E 260 " --> pdb=" O ALA E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 286 Processing helix chain 'E' and resid 293 through 297 Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 504 through 512 removed outlier: 4.159A pdb=" N GLN E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 554 Processing helix chain 'E' and resid 582 through 595 Processing helix chain 'E' and resid 605 through 609 Processing helix chain 'E' and resid 668 through 675 Processing helix chain 'E' and resid 760 through 764 Processing helix chain 'E' and resid 766 through 770 Processing helix chain 'F' and resid 234 through 241 Processing helix chain 'F' and resid 253 through 257 Processing helix chain 'F' and resid 279 through 286 Processing helix chain 'F' and resid 293 through 297 Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 504 through 512 removed outlier: 4.012A pdb=" N GLN F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 554 Processing helix chain 'F' and resid 582 through 595 Processing helix chain 'F' and resid 605 through 609 Processing helix chain 'F' and resid 668 through 674 Processing helix chain 'F' and resid 766 through 771 removed outlier: 3.545A pdb=" N GLN F 770 " --> pdb=" O ASP F 766 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 241 Processing helix chain 'G' and resid 254 through 259 removed outlier: 4.058A pdb=" N SER G 258 " --> pdb=" O ASP G 254 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 254 through 259' Processing helix chain 'G' and resid 279 through 286 Processing helix chain 'G' and resid 293 through 297 Processing helix chain 'G' and resid 463 through 472 Processing helix chain 'G' and resid 504 through 512 removed outlier: 4.054A pdb=" N GLN G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 554 Processing helix chain 'G' and resid 582 through 595 Processing helix chain 'G' and resid 605 through 609 Processing helix chain 'G' and resid 668 through 675 removed outlier: 3.557A pdb=" N LEU G 675 " --> pdb=" O ALA G 671 " (cutoff:3.500A) Processing helix chain 'G' and resid 760 through 764 Processing helix chain 'G' and resid 769 through 773 removed outlier: 3.628A pdb=" N ILE G 772 " --> pdb=" O ILE G 769 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE G 773 " --> pdb=" O GLN G 770 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 769 through 773' Processing helix chain 'H' and resid 74 through 80 removed outlier: 3.597A pdb=" N LYS H 80 " --> pdb=" O TRP H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 104 removed outlier: 3.693A pdb=" N LYS H 103 " --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 119 through 133 Processing helix chain 'H' and resid 134 through 136 No H-bonds generated for 'chain 'H' and resid 134 through 136' Processing helix chain 'H' and resid 166 through 178 Processing helix chain 'H' and resid 275 through 290 removed outlier: 5.984A pdb=" N GLY H 286 " --> pdb=" O LYS H 282 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N TRP H 287 " --> pdb=" O ASN H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 304 Processing helix chain 'H' and resid 307 through 316 Processing helix chain 'H' and resid 324 through 337 removed outlier: 4.278A pdb=" N GLN H 328 " --> pdb=" O LYS H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 352 through 357 Processing helix chain 'H' and resid 366 through 375 Processing helix chain 'H' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'B' and resid 242 through 245 Processing sheet with id=AA2, first strand: chain 'B' and resid 307 through 318 removed outlier: 6.427A pdb=" N ASN B 392 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL B 314 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN B 390 " --> pdb=" O VAL B 314 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU B 316 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR B 388 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 437 through 439 removed outlier: 3.551A pdb=" N GLU B 437 " --> pdb=" O ASN B 397 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE B 460 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 321 through 348 removed outlier: 4.014A pdb=" N PHE B 355 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE A 355 " --> pdb=" O PHE G 348 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE G 355 " --> pdb=" O PHE F 348 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE F 355 " --> pdb=" O PHE E 348 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE D 355 " --> pdb=" O PHE C 348 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE C 355 " --> pdb=" O PHE B 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 418 through 423 removed outlier: 5.573A pdb=" N THR B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU B 414 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA B 420 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR B 404 " --> pdb=" O ASN B 432 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASN B 432 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 418 through 423 removed outlier: 5.573A pdb=" N THR B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU B 414 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA B 420 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE B 403 " --> pdb=" O TYR B 487 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR B 487 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLU B 405 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY B 485 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS B 407 " --> pdb=" O THR B 483 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N THR B 483 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR B 409 " --> pdb=" O ASN B 481 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLY B 485 " --> pdb=" O GLU B 501 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLU B 501 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TYR B 487 " --> pdb=" O GLY B 499 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 524 through 530 Processing sheet with id=AA8, first strand: chain 'B' and resid 558 through 561 Processing sheet with id=AA9, first strand: chain 'B' and resid 624 through 626 Processing sheet with id=AB1, first strand: chain 'B' and resid 624 through 626 removed outlier: 4.365A pdb=" N VAL B 751 " --> pdb=" O SER B 684 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER B 684 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE B 753 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR B 682 " --> pdb=" O ILE B 753 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLU B 755 " --> pdb=" O ASN B 680 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ASN B 680 " --> pdb=" O GLU B 755 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 679 " --> pdb=" O ASN B 727 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 638 through 641 removed outlier: 3.609A pdb=" N ALA B 663 " --> pdb=" O ILE B 738 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 242 through 245 Processing sheet with id=AB4, first strand: chain 'A' and resid 307 through 318 removed outlier: 6.489A pdb=" N ASN A 392 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL A 314 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASN A 390 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU A 316 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR A 388 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 438 through 439 removed outlier: 4.555A pdb=" N ILE A 460 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 417 through 423 removed outlier: 6.799A pdb=" N PHE A 412 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TYR A 404 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASN A 432 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 417 through 423 removed outlier: 6.799A pdb=" N PHE A 412 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE A 403 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N TYR A 487 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLU A 405 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY A 485 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS A 407 " --> pdb=" O THR A 483 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N THR A 483 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR A 409 " --> pdb=" O ASN A 481 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLY A 485 " --> pdb=" O GLU A 501 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLU A 501 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR A 487 " --> pdb=" O GLY A 499 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 524 through 530 Processing sheet with id=AB9, first strand: chain 'A' and resid 558 through 561 Processing sheet with id=AC1, first strand: chain 'A' and resid 624 through 626 removed outlier: 6.650A pdb=" N ASP A 750 " --> pdb=" O LYS A 654 " (cutoff:3.500A) removed outlier: 12.488A pdb=" N LYS A 654 " --> pdb=" O ASP A 750 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 624 through 626 removed outlier: 4.224A pdb=" N VAL A 751 " --> pdb=" O SER A 684 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER A 684 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE A 753 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR A 682 " --> pdb=" O ILE A 753 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLU A 755 " --> pdb=" O ASN A 680 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ASN A 680 " --> pdb=" O GLU A 755 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 638 through 641 removed outlier: 3.734A pdb=" N ALA A 663 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASP A 734 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL A 697 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER A 708 " --> pdb=" O VAL A 697 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL A 699 " --> pdb=" O ILE A 706 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 242 through 245 Processing sheet with id=AC5, first strand: chain 'C' and resid 307 through 318 removed outlier: 6.502A pdb=" N ASN C 392 " --> pdb=" O GLU C 312 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL C 314 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN C 390 " --> pdb=" O VAL C 314 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU C 316 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR C 388 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 438 through 439 removed outlier: 4.590A pdb=" N ILE C 460 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 417 through 423 removed outlier: 5.452A pdb=" N THR C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU C 414 " --> pdb=" O THR C 418 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 420 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR C 404 " --> pdb=" O ASN C 432 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASN C 432 " --> pdb=" O TYR C 404 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 417 through 423 removed outlier: 5.452A pdb=" N THR C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU C 414 " --> pdb=" O THR C 418 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 420 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE C 403 " --> pdb=" O TYR C 487 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N TYR C 487 " --> pdb=" O ILE C 403 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLU C 405 " --> pdb=" O GLY C 485 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY C 485 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS C 407 " --> pdb=" O THR C 483 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N THR C 483 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR C 409 " --> pdb=" O ASN C 481 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY C 500 " --> pdb=" O TYR C 487 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ILE C 489 " --> pdb=" O THR C 498 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N THR C 498 " --> pdb=" O ILE C 489 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 524 through 530 Processing sheet with id=AD1, first strand: chain 'C' and resid 558 through 561 Processing sheet with id=AD2, first strand: chain 'C' and resid 624 through 626 removed outlier: 6.458A pdb=" N ASP C 750 " --> pdb=" O LYS C 654 " (cutoff:3.500A) removed outlier: 12.300A pdb=" N LYS C 654 " --> pdb=" O ASP C 750 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 624 through 626 removed outlier: 5.073A pdb=" N TRP C 748 " --> pdb=" O LYS C 688 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LYS C 688 " --> pdb=" O TRP C 748 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ASP C 750 " --> pdb=" O TYR C 686 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR C 686 " --> pdb=" O ASP C 750 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 638 through 641 removed outlier: 3.874A pdb=" N ALA C 663 " --> pdb=" O ILE C 738 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ASP C 734 " --> pdb=" O LEU C 667 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 697 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER C 708 " --> pdb=" O VAL C 697 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL C 699 " --> pdb=" O ILE C 706 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 242 through 245 Processing sheet with id=AD6, first strand: chain 'D' and resid 307 through 318 removed outlier: 6.483A pdb=" N ASN D 392 " --> pdb=" O GLU D 312 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL D 314 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN D 390 " --> pdb=" O VAL D 314 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU D 316 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR D 388 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 438 through 439 removed outlier: 4.540A pdb=" N ILE D 460 " --> pdb=" O LEU D 389 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 418 through 423 removed outlier: 5.453A pdb=" N THR D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU D 414 " --> pdb=" O THR D 418 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA D 420 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR D 404 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN D 432 " --> pdb=" O TYR D 404 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 418 through 423 removed outlier: 5.453A pdb=" N THR D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU D 414 " --> pdb=" O THR D 418 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA D 420 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ILE D 403 " --> pdb=" O TYR D 487 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N TYR D 487 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU D 405 " --> pdb=" O GLY D 485 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY D 485 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS D 407 " --> pdb=" O THR D 483 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR D 483 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR D 409 " --> pdb=" O ASN D 481 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLY D 485 " --> pdb=" O GLU D 501 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU D 501 " --> pdb=" O GLY D 485 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N TYR D 487 " --> pdb=" O GLY D 499 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 524 through 530 Processing sheet with id=AE2, first strand: chain 'D' and resid 558 through 561 Processing sheet with id=AE3, first strand: chain 'D' and resid 624 through 626 removed outlier: 6.450A pdb=" N ASP D 750 " --> pdb=" O LYS D 654 " (cutoff:3.500A) removed outlier: 12.333A pdb=" N LYS D 654 " --> pdb=" O ASP D 750 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 624 through 626 removed outlier: 4.242A pdb=" N VAL D 751 " --> pdb=" O SER D 684 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER D 684 " --> pdb=" O VAL D 751 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE D 753 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR D 682 " --> pdb=" O ILE D 753 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLU D 755 " --> pdb=" O ASN D 680 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ASN D 680 " --> pdb=" O GLU D 755 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 638 through 641 removed outlier: 3.809A pdb=" N ALA D 663 " --> pdb=" O ILE D 738 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL D 697 " --> pdb=" O SER D 708 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER D 708 " --> pdb=" O VAL D 697 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL D 699 " --> pdb=" O ILE D 706 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 242 through 245 Processing sheet with id=AE7, first strand: chain 'E' and resid 307 through 318 removed outlier: 6.467A pdb=" N ASN E 392 " --> pdb=" O GLU E 312 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL E 314 " --> pdb=" O ASN E 390 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN E 390 " --> pdb=" O VAL E 314 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU E 316 " --> pdb=" O TYR E 388 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TYR E 388 " --> pdb=" O LEU E 316 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 438 through 439 removed outlier: 4.535A pdb=" N ILE E 460 " --> pdb=" O LEU E 389 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 417 through 423 removed outlier: 6.757A pdb=" N PHE E 412 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N TYR E 404 " --> pdb=" O ASN E 432 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASN E 432 " --> pdb=" O TYR E 404 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 417 through 423 removed outlier: 6.757A pdb=" N PHE E 412 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE E 403 " --> pdb=" O TYR E 487 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TYR E 487 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU E 405 " --> pdb=" O GLY E 485 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY E 485 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYS E 407 " --> pdb=" O THR E 483 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR E 483 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR E 409 " --> pdb=" O ASN E 481 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N GLY E 485 " --> pdb=" O GLU E 501 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLU E 501 " --> pdb=" O GLY E 485 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N TYR E 487 " --> pdb=" O GLY E 499 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 524 through 530 Processing sheet with id=AF3, first strand: chain 'E' and resid 558 through 561 Processing sheet with id=AF4, first strand: chain 'E' and resid 624 through 626 removed outlier: 6.654A pdb=" N ASP E 750 " --> pdb=" O LYS E 654 " (cutoff:3.500A) removed outlier: 12.478A pdb=" N LYS E 654 " --> pdb=" O ASP E 750 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 624 through 626 removed outlier: 4.243A pdb=" N VAL E 751 " --> pdb=" O SER E 684 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER E 684 " --> pdb=" O VAL E 751 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE E 753 " --> pdb=" O TYR E 682 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR E 682 " --> pdb=" O ILE E 753 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLU E 755 " --> pdb=" O ASN E 680 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ASN E 680 " --> pdb=" O GLU E 755 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL E 679 " --> pdb=" O ASN E 727 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 639 through 641 removed outlier: 3.914A pdb=" N ALA E 663 " --> pdb=" O ILE E 738 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 242 through 245 Processing sheet with id=AF8, first strand: chain 'F' and resid 307 through 318 removed outlier: 6.486A pdb=" N ASN F 392 " --> pdb=" O GLU F 312 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL F 314 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN F 390 " --> pdb=" O VAL F 314 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU F 316 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR F 388 " --> pdb=" O LEU F 316 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 438 through 439 removed outlier: 4.539A pdb=" N ILE F 460 " --> pdb=" O LEU F 389 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 417 through 423 removed outlier: 5.447A pdb=" N THR F 418 " --> pdb=" O LEU F 414 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU F 414 " --> pdb=" O THR F 418 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA F 420 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR F 404 " --> pdb=" O ASN F 432 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN F 432 " --> pdb=" O TYR F 404 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 417 through 423 removed outlier: 5.447A pdb=" N THR F 418 " --> pdb=" O LEU F 414 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU F 414 " --> pdb=" O THR F 418 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA F 420 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE F 403 " --> pdb=" O TYR F 487 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR F 487 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLU F 405 " --> pdb=" O GLY F 485 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY F 485 " --> pdb=" O GLU F 405 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LYS F 407 " --> pdb=" O THR F 483 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N THR F 483 " --> pdb=" O LYS F 407 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR F 409 " --> pdb=" O ASN F 481 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLY F 485 " --> pdb=" O GLU F 501 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLU F 501 " --> pdb=" O GLY F 485 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR F 487 " --> pdb=" O GLY F 499 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 524 through 530 Processing sheet with id=AG4, first strand: chain 'F' and resid 558 through 561 Processing sheet with id=AG5, first strand: chain 'F' and resid 624 through 626 removed outlier: 6.456A pdb=" N ASP F 750 " --> pdb=" O LYS F 654 " (cutoff:3.500A) removed outlier: 12.303A pdb=" N LYS F 654 " --> pdb=" O ASP F 750 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 624 through 626 removed outlier: 5.071A pdb=" N TRP F 748 " --> pdb=" O LYS F 688 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LYS F 688 " --> pdb=" O TRP F 748 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ASP F 750 " --> pdb=" O TYR F 686 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR F 686 " --> pdb=" O ASP F 750 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 638 through 641 removed outlier: 3.785A pdb=" N VAL F 697 " --> pdb=" O LYS F 709 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 242 through 245 Processing sheet with id=AG9, first strand: chain 'G' and resid 307 through 318 removed outlier: 6.495A pdb=" N ASN G 392 " --> pdb=" O GLU G 312 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL G 314 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASN G 390 " --> pdb=" O VAL G 314 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU G 316 " --> pdb=" O TYR G 388 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR G 388 " --> pdb=" O LEU G 316 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 438 through 439 removed outlier: 4.551A pdb=" N ILE G 460 " --> pdb=" O LEU G 389 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 417 through 423 removed outlier: 6.797A pdb=" N PHE G 412 " --> pdb=" O ILE G 419 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N TYR G 404 " --> pdb=" O ASN G 432 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASN G 432 " --> pdb=" O TYR G 404 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 417 through 423 removed outlier: 6.797A pdb=" N PHE G 412 " --> pdb=" O ILE G 419 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ILE G 403 " --> pdb=" O TYR G 487 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N TYR G 487 " --> pdb=" O ILE G 403 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLU G 405 " --> pdb=" O GLY G 485 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLY G 485 " --> pdb=" O GLU G 405 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS G 407 " --> pdb=" O THR G 483 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR G 483 " --> pdb=" O LYS G 407 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR G 409 " --> pdb=" O ASN G 481 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLY G 485 " --> pdb=" O GLU G 501 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLU G 501 " --> pdb=" O GLY G 485 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR G 487 " --> pdb=" O GLY G 499 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 524 through 530 Processing sheet with id=AH5, first strand: chain 'G' and resid 558 through 561 Processing sheet with id=AH6, first strand: chain 'G' and resid 624 through 626 removed outlier: 6.784A pdb=" N ASP G 750 " --> pdb=" O LYS G 654 " (cutoff:3.500A) removed outlier: 12.549A pdb=" N LYS G 654 " --> pdb=" O ASP G 750 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 624 through 626 removed outlier: 4.200A pdb=" N VAL G 751 " --> pdb=" O SER G 684 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER G 684 " --> pdb=" O VAL G 751 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE G 753 " --> pdb=" O TYR G 682 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR G 682 " --> pdb=" O ILE G 753 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLU G 755 " --> pdb=" O ASN G 680 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASN G 680 " --> pdb=" O GLU G 755 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL G 679 " --> pdb=" O ASN G 727 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 638 through 641 removed outlier: 3.760A pdb=" N ALA G 663 " --> pdb=" O ILE G 738 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 142 through 148 removed outlier: 6.959A pdb=" N ILE H 261 " --> pdb=" O VAL H 242 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL H 242 " --> pdb=" O ILE H 261 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LYS H 263 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU H 240 " --> pdb=" O LYS H 263 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 160 through 161 Processing sheet with id=AI2, first strand: chain 'H' and resid 188 through 191 Processing sheet with id=AI3, first strand: chain 'H' and resid 345 through 351 removed outlier: 3.673A pdb=" N ILE H 402 " --> pdb=" O CYS H 351 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE H 403 " --> pdb=" O ILE H 455 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA H 457 " --> pdb=" O ILE H 403 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG H 405 " --> pdb=" O ALA H 457 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU H 459 " --> pdb=" O ARG H 405 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLN H 407 " --> pdb=" O LEU H 459 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR H 458 " --> pdb=" O ILE H 439 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE H 439 " --> pdb=" O THR H 458 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 385 through 388 removed outlier: 3.619A pdb=" N MET H 385 " --> pdb=" O LEU H 431 " (cutoff:3.500A) 1507 hydrogen bonds defined for protein. 3990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.23 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10620 1.33 - 1.45: 4989 1.45 - 1.57: 18348 1.57 - 1.69: 0 1.69 - 1.81: 162 Bond restraints: 34119 Sorted by residual: bond pdb=" CA LEU F 683 " pdb=" C LEU F 683 " ideal model delta sigma weight residual 1.522 1.493 0.029 1.20e-02 6.94e+03 5.72e+00 bond pdb=" CA SER C 757 " pdb=" C SER C 757 " ideal model delta sigma weight residual 1.523 1.506 0.017 8.20e-03 1.49e+04 4.44e+00 bond pdb=" CA ALA C 666 " pdb=" C ALA C 666 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.28e-02 6.10e+03 4.01e+00 bond pdb=" CA MET B 311 " pdb=" C MET B 311 " ideal model delta sigma weight residual 1.523 1.499 0.025 1.24e-02 6.50e+03 3.97e+00 bond pdb=" C ILE C 244 " pdb=" O ILE C 244 " ideal model delta sigma weight residual 1.237 1.216 0.021 1.07e-02 8.73e+03 3.78e+00 ... (remaining 34114 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 45447 1.86 - 3.72: 715 3.72 - 5.58: 68 5.58 - 7.44: 22 7.44 - 9.30: 3 Bond angle restraints: 46255 Sorted by residual: angle pdb=" N ASN A 715 " pdb=" CA ASN A 715 " pdb=" C ASN A 715 " ideal model delta sigma weight residual 113.61 106.56 7.05 1.50e+00 4.44e-01 2.21e+01 angle pdb=" C LYS H 269 " pdb=" CA LYS H 269 " pdb=" CB LYS H 269 " ideal model delta sigma weight residual 117.23 111.20 6.03 1.36e+00 5.41e-01 1.96e+01 angle pdb=" N TYR H 307 " pdb=" CA TYR H 307 " pdb=" C TYR H 307 " ideal model delta sigma weight residual 113.12 107.72 5.40 1.25e+00 6.40e-01 1.86e+01 angle pdb=" C GLN H 305 " pdb=" CA GLN H 305 " pdb=" CB GLN H 305 " ideal model delta sigma weight residual 115.79 110.85 4.94 1.19e+00 7.06e-01 1.72e+01 angle pdb=" N ILE G 637 " pdb=" CA ILE G 637 " pdb=" C ILE G 637 " ideal model delta sigma weight residual 112.96 108.86 4.10 1.00e+00 1.00e+00 1.68e+01 ... (remaining 46250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 18781 17.45 - 34.89: 1502 34.89 - 52.34: 289 52.34 - 69.78: 48 69.78 - 87.23: 18 Dihedral angle restraints: 20638 sinusoidal: 8066 harmonic: 12572 Sorted by residual: dihedral pdb=" CA ASN H 163 " pdb=" C ASN H 163 " pdb=" N THR H 164 " pdb=" CA THR H 164 " ideal model delta harmonic sigma weight residual 180.00 -162.18 -17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA TYR C 573 " pdb=" C TYR C 573 " pdb=" N GLU C 574 " pdb=" CA GLU C 574 " ideal model delta harmonic sigma weight residual -180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASN A 432 " pdb=" C ASN A 432 " pdb=" N ILE A 433 " pdb=" CA ILE A 433 " ideal model delta harmonic sigma weight residual 180.00 162.51 17.49 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 20635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3036 0.035 - 0.069: 1391 0.069 - 0.104: 532 0.104 - 0.138: 213 0.138 - 0.173: 14 Chirality restraints: 5186 Sorted by residual: chirality pdb=" CG LEU D 288 " pdb=" CB LEU D 288 " pdb=" CD1 LEU D 288 " pdb=" CD2 LEU D 288 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CA VAL C 697 " pdb=" N VAL C 697 " pdb=" C VAL C 697 " pdb=" CB VAL C 697 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CB ILE B 753 " pdb=" CA ILE B 753 " pdb=" CG1 ILE B 753 " pdb=" CG2 ILE B 753 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.25e-01 ... (remaining 5183 not shown) Planarity restraints: 5998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 656 " 0.020 2.00e-02 2.50e+03 2.39e-02 9.99e+00 pdb=" CG PHE C 656 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE C 656 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 656 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 PHE C 656 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE C 656 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 656 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 656 " -0.015 2.00e-02 2.50e+03 1.87e-02 6.12e+00 pdb=" CG PHE A 656 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 656 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 656 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 656 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 656 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 656 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 715 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" C ASN C 715 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN C 715 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN C 716 " 0.013 2.00e-02 2.50e+03 ... (remaining 5995 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 173 2.63 - 3.20: 29013 3.20 - 3.76: 48169 3.76 - 4.33: 72761 4.33 - 4.90: 120963 Nonbonded interactions: 271079 Sorted by model distance: nonbonded pdb=" OD2 ASP B 749 " pdb="CA CA B 903 " model vdw 2.062 2.510 nonbonded pdb=" OE2 GLU C 238 " pdb="CA CA C 902 " model vdw 2.078 2.510 nonbonded pdb=" OE2 GLU E 238 " pdb="CA CA E 902 " model vdw 2.091 2.510 nonbonded pdb=" OE2 GLU G 238 " pdb="CA CA G 902 " model vdw 2.091 2.510 nonbonded pdb=" OE2 GLU A 238 " pdb="CA CA A 902 " model vdw 2.096 2.510 ... (remaining 271074 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: 10.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.740 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 29.180 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 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:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 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 0.049 34119 Z= 0.213 Angle : 0.609 9.299 46255 Z= 0.351 Chirality : 0.047 0.173 5186 Planarity : 0.004 0.041 5998 Dihedral : 13.282 87.228 12592 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.12), residues: 4293 helix: -0.47 (0.21), residues: 674 sheet: 0.81 (0.13), residues: 1446 loop : -1.42 (0.12), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 180 TYR 0.020 0.001 TYR H 313 PHE 0.053 0.002 PHE C 656 TRP 0.030 0.001 TRP C 640 HIS 0.004 0.001 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00477 (34119) covalent geometry : angle 0.60883 (46255) hydrogen bonds : bond 0.12743 ( 1458) hydrogen bonds : angle 6.13261 ( 3990) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: B 365 GLU cc_start: 0.7617 (tt0) cc_final: 0.7372 (tt0) REVERT: B 660 ASN cc_start: 0.8515 (t0) cc_final: 0.7994 (t0) REVERT: B 714 ASN cc_start: 0.8677 (m-40) cc_final: 0.7868 (p0) REVERT: B 737 TYR cc_start: 0.7718 (m-80) cc_final: 0.6978 (m-80) REVERT: A 287 ASP cc_start: 0.8792 (t0) cc_final: 0.8468 (OUTLIER) REVERT: A 334 TRP cc_start: 0.6773 (m-10) cc_final: 0.5734 (t60) REVERT: A 365 GLU cc_start: 0.7318 (pt0) cc_final: 0.6908 (pt0) REVERT: A 559 LYS cc_start: 0.8757 (ttpp) cc_final: 0.7877 (pmmt) REVERT: A 642 ASN cc_start: 0.8024 (m-40) cc_final: 0.7611 (t0) REVERT: C 276 ASP cc_start: 0.9124 (p0) cc_final: 0.8780 (p0) REVERT: C 327 GLU cc_start: 0.8284 (tt0) cc_final: 0.7860 (tt0) REVERT: C 369 GLN cc_start: 0.7542 (mt0) cc_final: 0.6753 (mt0) REVERT: C 672 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7796 (mtmm) REVERT: D 327 GLU cc_start: 0.8051 (tt0) cc_final: 0.7578 (tm-30) REVERT: D 657 GLN cc_start: 0.7496 (tm-30) cc_final: 0.6870 (tp40) REVERT: D 698 GLU cc_start: 0.8097 (tt0) cc_final: 0.7852 (tt0) REVERT: E 365 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6739 (mt-10) REVERT: E 375 LYS cc_start: 0.7974 (ptpt) cc_final: 0.7555 (ptmt) REVERT: E 523 ARG cc_start: 0.7986 (ptm-80) cc_final: 0.7760 (ptt180) REVERT: E 559 LYS cc_start: 0.8297 (ptpp) cc_final: 0.7900 (ptpp) REVERT: E 578 MET cc_start: 0.8322 (tpt) cc_final: 0.8050 (tpt) REVERT: E 656 PHE cc_start: 0.7824 (m-80) cc_final: 0.7601 (m-10) REVERT: F 369 GLN cc_start: 0.8003 (mt0) cc_final: 0.7766 (mt0) REVERT: F 559 LYS cc_start: 0.8801 (ptpt) cc_final: 0.8126 (pmmt) REVERT: F 654 LYS cc_start: 0.6957 (mmmm) cc_final: 0.6720 (mptt) REVERT: F 735 LYS cc_start: 0.8457 (pttt) cc_final: 0.8115 (ptpp) REVERT: G 719 GLN cc_start: 0.8608 (tt0) cc_final: 0.8160 (tt0) REVERT: H 79 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8719 (mm-30) REVERT: H 102 ASN cc_start: 0.8912 (m110) cc_final: 0.8495 (t0) REVERT: H 259 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8582 (mt-10) REVERT: H 289 LYS cc_start: 0.8351 (ptpp) cc_final: 0.7864 (mtmm) REVERT: H 317 GLN cc_start: 0.8452 (mp10) cc_final: 0.8131 (mp10) REVERT: H 428 GLU cc_start: 0.8841 (pp20) cc_final: 0.8439 (tm-30) outliers start: 0 outliers final: 1 residues processed: 346 average time/residue: 0.7089 time to fit residues: 290.9417 Evaluate side-chains 330 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 ASN B 272 HIS B 333 ASN B 507 GLN B 568 ASN B 616 ASN B 660 ASN B 662 ASN B 677 GLN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 GLN B 731 ASN A 272 HIS A 362 GLN A 507 GLN A 568 ASN A 584 ASN A 715 ASN C 246 ASN C 272 HIS C 568 ASN C 616 ASN C 660 ASN C 677 GLN C 680 ASN C 715 ASN C 779 GLN D 246 ASN D 272 HIS D 333 ASN D 362 GLN D 369 GLN D 432 ASN D 568 ASN D 716 GLN E 246 ASN E 272 HIS E 392 ASN E 568 ASN E 584 ASN E 616 ASN E 647 ASN E 676 ASN E 680 ASN E 719 GLN E 731 ASN F 246 ASN F 272 HIS F 432 ASN F 473 ASN F 616 ASN F 647 ASN F 680 ASN F 745 ASN G 246 ASN G 272 HIS G 392 ASN G 568 ASN G 677 GLN ** G 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 731 ASN H 107 ASN H 172 GLN H 283 ASN H 295 GLN H 328 GLN H 407 GLN H 438 HIS Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.121887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.067642 restraints weight = 49124.248| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.16 r_work: 0.2666 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 34119 Z= 0.174 Angle : 0.534 7.010 46255 Z= 0.294 Chirality : 0.046 0.154 5186 Planarity : 0.004 0.038 5998 Dihedral : 4.667 19.042 4592 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.41 % Allowed : 10.60 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.12), residues: 4293 helix: -0.24 (0.21), residues: 688 sheet: 1.03 (0.13), residues: 1425 loop : -1.27 (0.12), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 180 TYR 0.016 0.001 TYR C 336 PHE 0.020 0.001 PHE A 656 TRP 0.013 0.001 TRP D 748 HIS 0.004 0.001 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00427 (34119) covalent geometry : angle 0.53416 (46255) hydrogen bonds : bond 0.03663 ( 1458) hydrogen bonds : angle 4.98260 ( 3990) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 351 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 365 GLU cc_start: 0.7221 (tt0) cc_final: 0.7003 (tt0) REVERT: B 660 ASN cc_start: 0.8509 (t0) cc_final: 0.7945 (t0) REVERT: B 714 ASN cc_start: 0.8639 (m-40) cc_final: 0.7926 (p0) REVERT: B 737 TYR cc_start: 0.7700 (m-80) cc_final: 0.7115 (m-80) REVERT: A 287 ASP cc_start: 0.8945 (t0) cc_final: 0.8544 (t0) REVERT: A 334 TRP cc_start: 0.6594 (m-10) cc_final: 0.5712 (t60) REVERT: A 365 GLU cc_start: 0.6704 (pt0) cc_final: 0.6419 (pt0) REVERT: A 559 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8094 (pttm) REVERT: A 642 ASN cc_start: 0.8034 (m-40) cc_final: 0.7610 (t0) REVERT: A 747 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.6471 (m-80) REVERT: C 225 ASP cc_start: 0.8402 (m-30) cc_final: 0.8020 (p0) REVERT: C 276 ASP cc_start: 0.9066 (p0) cc_final: 0.8690 (p0) REVERT: C 327 GLU cc_start: 0.8365 (tt0) cc_final: 0.7941 (tt0) REVERT: C 369 GLN cc_start: 0.7327 (mt0) cc_final: 0.6594 (mt0) REVERT: C 773 PHE cc_start: 0.5224 (OUTLIER) cc_final: 0.4919 (m-10) REVERT: D 327 GLU cc_start: 0.8102 (tt0) cc_final: 0.7608 (tm-30) REVERT: D 698 GLU cc_start: 0.8121 (tt0) cc_final: 0.7881 (tt0) REVERT: E 375 LYS cc_start: 0.7749 (ptpt) cc_final: 0.7315 (ptmm) REVERT: E 559 LYS cc_start: 0.8210 (ptpp) cc_final: 0.7809 (ptpp) REVERT: E 578 MET cc_start: 0.8295 (tpt) cc_final: 0.8041 (tpt) REVERT: E 672 LYS cc_start: 0.8297 (mtmt) cc_final: 0.7973 (mtmm) REVERT: F 369 GLN cc_start: 0.7487 (mt0) cc_final: 0.7240 (mt0) REVERT: F 559 LYS cc_start: 0.8544 (ptpt) cc_final: 0.7801 (pmmt) REVERT: F 654 LYS cc_start: 0.6702 (mmmm) cc_final: 0.6484 (mptp) REVERT: F 735 LYS cc_start: 0.8414 (pttt) cc_final: 0.8048 (mtmm) REVERT: G 719 GLN cc_start: 0.8442 (tt0) cc_final: 0.8052 (tt0) REVERT: H 102 ASN cc_start: 0.8842 (m110) cc_final: 0.8209 (t0) REVERT: H 317 GLN cc_start: 0.8129 (mp10) cc_final: 0.7869 (mp10) REVERT: H 428 GLU cc_start: 0.8215 (pp20) cc_final: 0.7743 (tm-30) outliers start: 53 outliers final: 14 residues processed: 374 average time/residue: 0.6673 time to fit residues: 298.6586 Evaluate side-chains 343 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 327 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 685 MET Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain C residue 773 PHE Chi-restraints excluded: chain E residue 685 MET Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 747 TYR Chi-restraints excluded: chain F residue 679 VAL Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain G residue 651 THR Chi-restraints excluded: chain G residue 738 ILE Chi-restraints excluded: chain G residue 759 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 20 optimal weight: 0.7980 chunk 206 optimal weight: 0.2980 chunk 82 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 372 optimal weight: 0.7980 chunk 256 optimal weight: 1.9990 chunk 342 optimal weight: 0.8980 chunk 227 optimal weight: 0.0040 chunk 275 optimal weight: 5.9990 chunk 264 optimal weight: 9.9990 chunk 370 optimal weight: 0.0370 overall best weight: 0.3870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 432 ASN B 507 GLN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN A 507 GLN A 584 ASN A 616 ASN C 432 ASN C 493 HIS C 660 ASN D 362 GLN D 369 GLN E 333 ASN E 432 ASN E 584 ASN E 676 ASN E 719 GLN E 760 ASN F 308 ASN F 333 ASN F 362 GLN F 770 GLN G 432 ASN G 680 ASN H 172 GLN H 295 GLN H 328 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.125412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.072026 restraints weight = 48968.402| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.17 r_work: 0.2762 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 34119 Z= 0.081 Angle : 0.457 7.362 46255 Z= 0.250 Chirality : 0.043 0.149 5186 Planarity : 0.003 0.031 5998 Dihedral : 4.034 15.710 4592 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.22 % Allowed : 11.53 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.12), residues: 4293 helix: 0.17 (0.21), residues: 681 sheet: 1.20 (0.13), residues: 1418 loop : -1.09 (0.12), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 180 TYR 0.023 0.001 TYR G 664 PHE 0.021 0.001 PHE A 656 TRP 0.014 0.001 TRP D 748 HIS 0.002 0.000 HIS E 272 Details of bonding type rmsd covalent geometry : bond 0.00173 (34119) covalent geometry : angle 0.45692 (46255) hydrogen bonds : bond 0.02570 ( 1458) hydrogen bonds : angle 4.64909 ( 3990) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 370 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 660 ASN cc_start: 0.8464 (t0) cc_final: 0.7776 (t0) REVERT: B 698 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.7002 (tp30) REVERT: A 287 ASP cc_start: 0.8902 (t0) cc_final: 0.8542 (t0) REVERT: A 329 HIS cc_start: 0.7189 (OUTLIER) cc_final: 0.6499 (p-80) REVERT: A 365 GLU cc_start: 0.6579 (pt0) cc_final: 0.6358 (pt0) REVERT: A 559 LYS cc_start: 0.8550 (ttpp) cc_final: 0.7750 (pmmt) REVERT: A 642 ASN cc_start: 0.8060 (m-40) cc_final: 0.7668 (t0) REVERT: A 714 ASN cc_start: 0.7909 (m-40) cc_final: 0.7585 (p0) REVERT: A 747 TYR cc_start: 0.7232 (OUTLIER) cc_final: 0.6394 (m-80) REVERT: C 225 ASP cc_start: 0.8362 (m-30) cc_final: 0.8105 (p0) REVERT: C 327 GLU cc_start: 0.8381 (tt0) cc_final: 0.7927 (tt0) REVERT: C 329 HIS cc_start: 0.7160 (OUTLIER) cc_final: 0.6712 (p-80) REVERT: C 369 GLN cc_start: 0.7306 (mt0) cc_final: 0.6519 (mt0) REVERT: C 442 LYS cc_start: 0.8316 (tppt) cc_final: 0.8114 (mmtm) REVERT: C 476 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8924 (ttp) REVERT: C 510 LYS cc_start: 0.8960 (tttt) cc_final: 0.8742 (tttm) REVERT: C 523 ARG cc_start: 0.8340 (ptm-80) cc_final: 0.7821 (ptm160) REVERT: C 559 LYS cc_start: 0.7904 (pttm) cc_final: 0.7607 (mptt) REVERT: C 722 ASP cc_start: 0.6939 (m-30) cc_final: 0.6658 (m-30) REVERT: C 734 ASP cc_start: 0.6131 (m-30) cc_final: 0.5898 (m-30) REVERT: D 327 GLU cc_start: 0.8137 (tt0) cc_final: 0.7614 (tm-30) REVERT: D 660 ASN cc_start: 0.8641 (t0) cc_final: 0.8417 (p0) REVERT: D 698 GLU cc_start: 0.8198 (tt0) cc_final: 0.7945 (tt0) REVERT: D 712 LYS cc_start: 0.8525 (mmpt) cc_final: 0.8265 (mmpt) REVERT: D 714 ASN cc_start: 0.8537 (m-40) cc_final: 0.8195 (t160) REVERT: E 329 HIS cc_start: 0.7097 (OUTLIER) cc_final: 0.6638 (p90) REVERT: E 332 THR cc_start: 0.7828 (m) cc_final: 0.7540 (t) REVERT: E 442 LYS cc_start: 0.8197 (tppt) cc_final: 0.7803 (mptt) REVERT: E 559 LYS cc_start: 0.8268 (ptpp) cc_final: 0.7823 (ptpp) REVERT: F 329 HIS cc_start: 0.7066 (t-90) cc_final: 0.6657 (p-80) REVERT: F 369 GLN cc_start: 0.7434 (mt0) cc_final: 0.7204 (mt0) REVERT: F 559 LYS cc_start: 0.8557 (ptpt) cc_final: 0.7837 (pmmt) REVERT: F 735 LYS cc_start: 0.8505 (pttt) cc_final: 0.8162 (mtmm) REVERT: G 510 LYS cc_start: 0.9045 (tttt) cc_final: 0.8775 (tttp) REVERT: G 719 GLN cc_start: 0.8435 (tt0) cc_final: 0.8006 (tt0) REVERT: H 102 ASN cc_start: 0.8847 (m110) cc_final: 0.8248 (t0) REVERT: H 428 GLU cc_start: 0.8222 (pp20) cc_final: 0.7713 (tm-30) outliers start: 46 outliers final: 12 residues processed: 399 average time/residue: 0.6649 time to fit residues: 316.7664 Evaluate side-chains 357 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 339 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain C residue 329 HIS Chi-restraints excluded: chain C residue 476 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain E residue 329 HIS Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 725 VAL Chi-restraints excluded: chain E residue 747 TYR Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 738 ILE Chi-restraints excluded: chain G residue 747 TYR Chi-restraints excluded: chain H residue 163 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 122 optimal weight: 4.9990 chunk 307 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 289 optimal weight: 0.7980 chunk 4 optimal weight: 0.0970 chunk 240 optimal weight: 5.9990 chunk 117 optimal weight: 0.1980 chunk 222 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 285 optimal weight: 1.9990 chunk 274 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 507 GLN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN A 432 ASN A 507 GLN A 584 ASN A 715 ASN C 660 ASN D 369 GLN E 584 ASN E 719 GLN F 362 GLN F 770 GLN H 172 GLN H 295 GLN H 328 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.123306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.069339 restraints weight = 48717.796| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.16 r_work: 0.2704 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34119 Z= 0.128 Angle : 0.489 7.304 46255 Z= 0.268 Chirality : 0.045 0.156 5186 Planarity : 0.003 0.033 5998 Dihedral : 4.244 19.607 4592 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.46 % Allowed : 12.75 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.12), residues: 4293 helix: 0.25 (0.21), residues: 681 sheet: 1.28 (0.13), residues: 1425 loop : -1.03 (0.12), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 180 TYR 0.022 0.001 TYR G 664 PHE 0.023 0.001 PHE A 656 TRP 0.014 0.001 TRP D 748 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00310 (34119) covalent geometry : angle 0.48940 (46255) hydrogen bonds : bond 0.03068 ( 1458) hydrogen bonds : angle 4.61363 ( 3990) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 337 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 365 GLU cc_start: 0.7305 (tt0) cc_final: 0.7081 (tt0) REVERT: B 660 ASN cc_start: 0.8551 (t0) cc_final: 0.7947 (t0) REVERT: B 698 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7076 (tp30) REVERT: B 714 ASN cc_start: 0.8608 (m-40) cc_final: 0.7862 (p0) REVERT: A 287 ASP cc_start: 0.9059 (t0) cc_final: 0.8656 (t0) REVERT: A 365 GLU cc_start: 0.6728 (pt0) cc_final: 0.6508 (pt0) REVERT: A 642 ASN cc_start: 0.7973 (m-40) cc_final: 0.7606 (t0) REVERT: A 714 ASN cc_start: 0.8000 (m-40) cc_final: 0.7694 (p0) REVERT: A 735 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8072 (ptmt) REVERT: A 747 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.6417 (m-80) REVERT: C 225 ASP cc_start: 0.8412 (m-30) cc_final: 0.8210 (p0) REVERT: C 327 GLU cc_start: 0.8488 (tt0) cc_final: 0.8043 (tt0) REVERT: C 369 GLN cc_start: 0.7452 (mt0) cc_final: 0.6682 (mt0) REVERT: C 442 LYS cc_start: 0.8464 (tppt) cc_final: 0.8251 (mmtm) REVERT: C 476 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.8944 (ttp) REVERT: C 559 LYS cc_start: 0.8026 (pttm) cc_final: 0.7711 (pmtt) REVERT: C 722 ASP cc_start: 0.6952 (m-30) cc_final: 0.6661 (m-30) REVERT: D 327 GLU cc_start: 0.8249 (tt0) cc_final: 0.7740 (tm-30) REVERT: D 657 GLN cc_start: 0.7556 (tm-30) cc_final: 0.6978 (tp40) REVERT: D 698 GLU cc_start: 0.8219 (tt0) cc_final: 0.7980 (tt0) REVERT: D 714 ASN cc_start: 0.8551 (m-40) cc_final: 0.8327 (t160) REVERT: E 329 HIS cc_start: 0.7343 (OUTLIER) cc_final: 0.6759 (p90) REVERT: E 442 LYS cc_start: 0.8371 (tppt) cc_final: 0.7949 (mptt) REVERT: E 559 LYS cc_start: 0.8345 (ptpp) cc_final: 0.8001 (ptpp) REVERT: E 656 PHE cc_start: 0.7992 (m-80) cc_final: 0.7686 (m-10) REVERT: E 672 LYS cc_start: 0.8299 (mtmt) cc_final: 0.7879 (mtmm) REVERT: F 329 HIS cc_start: 0.7274 (t-90) cc_final: 0.6823 (p-80) REVERT: F 369 GLN cc_start: 0.7633 (mt0) cc_final: 0.7406 (mt0) REVERT: F 559 LYS cc_start: 0.8620 (ptpt) cc_final: 0.7891 (pmmt) REVERT: F 735 LYS cc_start: 0.8543 (pttt) cc_final: 0.8214 (mtmm) REVERT: G 310 ASN cc_start: 0.8758 (t0) cc_final: 0.8495 (t0) REVERT: G 719 GLN cc_start: 0.8493 (tt0) cc_final: 0.8040 (tt0) REVERT: H 102 ASN cc_start: 0.8857 (m110) cc_final: 0.8243 (t0) REVERT: H 428 GLU cc_start: 0.8323 (pp20) cc_final: 0.7877 (tm-30) outliers start: 55 outliers final: 15 residues processed: 374 average time/residue: 0.6599 time to fit residues: 296.0546 Evaluate side-chains 349 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 329 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain C residue 476 MET Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain D residue 716 GLN Chi-restraints excluded: chain E residue 329 HIS Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 725 VAL Chi-restraints excluded: chain E residue 747 TYR Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 679 VAL Chi-restraints excluded: chain F residue 684 SER Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 738 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 177 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 249 optimal weight: 4.9990 chunk 342 optimal weight: 0.7980 chunk 123 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 349 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 660 ASN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN C 715 ASN D 369 GLN D 445 ASN E 584 ASN E 719 GLN H 172 GLN H 295 GLN H 328 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.120749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.066748 restraints weight = 48899.672| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.14 r_work: 0.2649 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 34119 Z= 0.218 Angle : 0.550 8.281 46255 Z= 0.301 Chirality : 0.047 0.195 5186 Planarity : 0.003 0.036 5998 Dihedral : 4.608 18.739 4592 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.62 % Allowed : 13.04 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.12), residues: 4293 helix: 0.17 (0.21), residues: 681 sheet: 1.27 (0.13), residues: 1404 loop : -1.13 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 180 TYR 0.017 0.002 TYR F 664 PHE 0.027 0.002 PHE A 656 TRP 0.015 0.001 TRP E 640 HIS 0.003 0.001 HIS H 438 Details of bonding type rmsd covalent geometry : bond 0.00540 (34119) covalent geometry : angle 0.55000 (46255) hydrogen bonds : bond 0.03732 ( 1458) hydrogen bonds : angle 4.73890 ( 3990) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 334 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: B 365 GLU cc_start: 0.7154 (tt0) cc_final: 0.6916 (tt0) REVERT: B 660 ASN cc_start: 0.8573 (t0) cc_final: 0.7861 (t0) REVERT: B 737 TYR cc_start: 0.7626 (m-80) cc_final: 0.7412 (m-10) REVERT: A 287 ASP cc_start: 0.8983 (t0) cc_final: 0.8555 (t0) REVERT: A 334 TRP cc_start: 0.6486 (m-10) cc_final: 0.5596 (t60) REVERT: A 365 GLU cc_start: 0.6560 (pt0) cc_final: 0.6342 (pt0) REVERT: A 559 LYS cc_start: 0.8592 (ttpp) cc_final: 0.7618 (pmmt) REVERT: A 642 ASN cc_start: 0.7926 (m-40) cc_final: 0.7519 (t0) REVERT: A 714 ASN cc_start: 0.8077 (m-40) cc_final: 0.7757 (p0) REVERT: A 747 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.6509 (m-80) REVERT: C 225 ASP cc_start: 0.8345 (m-30) cc_final: 0.8051 (p0) REVERT: C 327 GLU cc_start: 0.8341 (tt0) cc_final: 0.7860 (tt0) REVERT: C 369 GLN cc_start: 0.7204 (mt0) cc_final: 0.6481 (mt0) REVERT: C 442 LYS cc_start: 0.8361 (tppt) cc_final: 0.8042 (mmtm) REVERT: C 476 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8799 (ttp) REVERT: C 559 LYS cc_start: 0.7812 (pttm) cc_final: 0.7488 (pmtt) REVERT: C 722 ASP cc_start: 0.6789 (m-30) cc_final: 0.6487 (m-30) REVERT: D 327 GLU cc_start: 0.8044 (tt0) cc_final: 0.7529 (tm-30) REVERT: D 698 GLU cc_start: 0.8189 (tt0) cc_final: 0.7974 (tt0) REVERT: E 329 HIS cc_start: 0.7299 (OUTLIER) cc_final: 0.6648 (p-80) REVERT: E 559 LYS cc_start: 0.8156 (ptpp) cc_final: 0.7797 (ptpp) REVERT: E 665 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8427 (m) REVERT: E 672 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7715 (mtmm) REVERT: F 329 HIS cc_start: 0.7285 (OUTLIER) cc_final: 0.6533 (p-80) REVERT: F 369 GLN cc_start: 0.7424 (mt0) cc_final: 0.7193 (mt0) REVERT: F 559 LYS cc_start: 0.8464 (ptpt) cc_final: 0.7735 (pmmt) REVERT: F 735 LYS cc_start: 0.8440 (pttt) cc_final: 0.8109 (mtmm) REVERT: G 719 GLN cc_start: 0.8374 (tt0) cc_final: 0.7973 (tt0) REVERT: H 428 GLU cc_start: 0.8229 (pp20) cc_final: 0.7804 (tm-30) outliers start: 61 outliers final: 22 residues processed: 368 average time/residue: 0.6672 time to fit residues: 294.0539 Evaluate side-chains 341 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 314 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 685 MET Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain C residue 476 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain E residue 329 HIS Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 725 VAL Chi-restraints excluded: chain E residue 747 TYR Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 329 HIS Chi-restraints excluded: chain F residue 679 VAL Chi-restraints excluded: chain F residue 684 SER Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 651 THR Chi-restraints excluded: chain G residue 738 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 330 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 399 optimal weight: 3.9990 chunk 314 optimal weight: 4.9990 chunk 327 optimal weight: 10.0000 chunk 222 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 417 optimal weight: 7.9990 chunk 353 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 ASN C 660 ASN D 369 GLN D 714 ASN E 584 ASN ** E 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 719 GLN F 362 GLN G 779 GLN H 102 ASN H 172 GLN H 295 GLN H 328 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.119022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.064945 restraints weight = 48867.797| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.14 r_work: 0.2616 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 34119 Z= 0.342 Angle : 0.634 8.720 46255 Z= 0.346 Chirality : 0.052 0.225 5186 Planarity : 0.004 0.041 5998 Dihedral : 5.019 20.554 4592 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.94 % Allowed : 13.28 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.12), residues: 4293 helix: -0.02 (0.21), residues: 674 sheet: 1.23 (0.13), residues: 1411 loop : -1.27 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 180 TYR 0.020 0.002 TYR G 664 PHE 0.033 0.002 PHE C 656 TRP 0.022 0.002 TRP A 748 HIS 0.005 0.001 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00849 (34119) covalent geometry : angle 0.63386 (46255) hydrogen bonds : bond 0.04462 ( 1458) hydrogen bonds : angle 4.93048 ( 3990) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 317 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 365 GLU cc_start: 0.7282 (tt0) cc_final: 0.7072 (tt0) REVERT: B 660 ASN cc_start: 0.8649 (t0) cc_final: 0.7968 (t0) REVERT: A 334 TRP cc_start: 0.6594 (m-10) cc_final: 0.5645 (t60) REVERT: A 365 GLU cc_start: 0.6715 (pt0) cc_final: 0.6433 (pt0) REVERT: A 559 LYS cc_start: 0.8625 (ttpp) cc_final: 0.8071 (pttm) REVERT: A 642 ASN cc_start: 0.7964 (m-40) cc_final: 0.7496 (t0) REVERT: A 747 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.6658 (m-80) REVERT: C 225 ASP cc_start: 0.8338 (m-30) cc_final: 0.8050 (p0) REVERT: C 327 GLU cc_start: 0.8371 (tt0) cc_final: 0.7941 (tt0) REVERT: C 369 GLN cc_start: 0.7212 (mt0) cc_final: 0.6497 (mt0) REVERT: C 522 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8158 (mp0) REVERT: C 559 LYS cc_start: 0.7871 (pttm) cc_final: 0.7492 (pmmt) REVERT: C 722 ASP cc_start: 0.6835 (m-30) cc_final: 0.6533 (m-30) REVERT: D 327 GLU cc_start: 0.8081 (tt0) cc_final: 0.7563 (tm-30) REVERT: D 698 GLU cc_start: 0.8203 (tt0) cc_final: 0.7991 (tt0) REVERT: E 329 HIS cc_start: 0.7610 (OUTLIER) cc_final: 0.6733 (p-80) REVERT: E 559 LYS cc_start: 0.8185 (ptpp) cc_final: 0.7807 (ptpp) REVERT: E 581 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8836 (mt) REVERT: E 672 LYS cc_start: 0.8173 (mtmt) cc_final: 0.7698 (mtmm) REVERT: F 369 GLN cc_start: 0.7516 (mt0) cc_final: 0.7274 (mt0) REVERT: F 559 LYS cc_start: 0.8566 (ptpt) cc_final: 0.7816 (pmmt) REVERT: G 276 ASP cc_start: 0.9119 (p0) cc_final: 0.8840 (p0) REVERT: H 428 GLU cc_start: 0.8257 (pp20) cc_final: 0.7886 (tm-30) outliers start: 73 outliers final: 37 residues processed: 361 average time/residue: 0.6458 time to fit residues: 279.3123 Evaluate side-chains 353 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 313 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 685 MET Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain C residue 476 MET Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 756 ILE Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 329 HIS Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 699 VAL Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 725 VAL Chi-restraints excluded: chain E residue 747 TYR Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 329 HIS Chi-restraints excluded: chain F residue 476 MET Chi-restraints excluded: chain F residue 569 ASP Chi-restraints excluded: chain F residue 679 VAL Chi-restraints excluded: chain F residue 684 SER Chi-restraints excluded: chain F residue 725 VAL Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain G residue 651 THR Chi-restraints excluded: chain G residue 738 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 182 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 381 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 332 optimal weight: 10.0000 chunk 297 optimal weight: 0.9990 chunk 420 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 384 optimal weight: 0.0470 chunk 180 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 ASN C 660 ASN C 715 ASN D 369 GLN E 584 ASN E 719 GLN F 770 GLN G 481 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.122641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.069322 restraints weight = 48980.000| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.14 r_work: 0.2697 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 34119 Z= 0.102 Angle : 0.489 8.664 46255 Z= 0.267 Chirality : 0.044 0.157 5186 Planarity : 0.003 0.034 5998 Dihedral : 4.293 17.425 4592 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.22 % Allowed : 14.21 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.12), residues: 4293 helix: 0.27 (0.21), residues: 681 sheet: 1.29 (0.13), residues: 1404 loop : -1.10 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 523 TYR 0.019 0.001 TYR F 361 PHE 0.033 0.001 PHE C 656 TRP 0.020 0.001 TRP A 748 HIS 0.002 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00235 (34119) covalent geometry : angle 0.48896 (46255) hydrogen bonds : bond 0.02875 ( 1458) hydrogen bonds : angle 4.62823 ( 3990) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 329 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 365 GLU cc_start: 0.7141 (tt0) cc_final: 0.6907 (tt0) REVERT: B 660 ASN cc_start: 0.8624 (t0) cc_final: 0.7924 (t0) REVERT: A 287 ASP cc_start: 0.8709 (t70) cc_final: 0.8337 (t0) REVERT: A 329 HIS cc_start: 0.7238 (OUTLIER) cc_final: 0.6435 (p-80) REVERT: A 559 LYS cc_start: 0.8542 (ttpp) cc_final: 0.7687 (pmmt) REVERT: A 642 ASN cc_start: 0.7922 (m-40) cc_final: 0.7540 (t0) REVERT: A 714 ASN cc_start: 0.7979 (m-40) cc_final: 0.7762 (p0) REVERT: A 747 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6643 (m-80) REVERT: C 327 GLU cc_start: 0.8309 (tt0) cc_final: 0.7842 (tt0) REVERT: C 329 HIS cc_start: 0.7250 (OUTLIER) cc_final: 0.6485 (p-80) REVERT: C 369 GLN cc_start: 0.7138 (mt0) cc_final: 0.6380 (mt0) REVERT: C 476 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8902 (ttp) REVERT: C 522 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8172 (mp0) REVERT: C 559 LYS cc_start: 0.7794 (pttm) cc_final: 0.7403 (pmtt) REVERT: C 722 ASP cc_start: 0.6755 (OUTLIER) cc_final: 0.6403 (m-30) REVERT: D 327 GLU cc_start: 0.8010 (tt0) cc_final: 0.7473 (tm-30) REVERT: D 698 GLU cc_start: 0.8179 (tt0) cc_final: 0.7944 (tt0) REVERT: E 329 HIS cc_start: 0.7190 (OUTLIER) cc_final: 0.6603 (p-80) REVERT: E 442 LYS cc_start: 0.8182 (tppt) cc_final: 0.7721 (mptt) REVERT: E 559 LYS cc_start: 0.8160 (ptpp) cc_final: 0.7821 (ptpp) REVERT: E 578 MET cc_start: 0.8095 (tpt) cc_final: 0.7831 (tpt) REVERT: F 329 HIS cc_start: 0.7121 (OUTLIER) cc_final: 0.6442 (p-80) REVERT: F 369 GLN cc_start: 0.7313 (mt0) cc_final: 0.7071 (mt0) REVERT: F 559 LYS cc_start: 0.8480 (ptpt) cc_final: 0.7759 (pmmt) REVERT: F 664 TYR cc_start: 0.6316 (p90) cc_final: 0.5976 (p90) REVERT: F 680 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7998 (m-40) REVERT: F 735 LYS cc_start: 0.8290 (pttt) cc_final: 0.8035 (mtmm) REVERT: G 510 LYS cc_start: 0.8964 (tttt) cc_final: 0.8718 (tttp) REVERT: G 683 LEU cc_start: 0.8486 (tp) cc_final: 0.8217 (tp) REVERT: G 719 GLN cc_start: 0.8379 (tt0) cc_final: 0.8043 (tt0) REVERT: H 281 MET cc_start: 0.8009 (mmm) cc_final: 0.7621 (mpm) REVERT: H 428 GLU cc_start: 0.8166 (pp20) cc_final: 0.7780 (tm-30) outliers start: 46 outliers final: 18 residues processed: 360 average time/residue: 0.6666 time to fit residues: 288.0431 Evaluate side-chains 336 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 310 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain C residue 329 HIS Chi-restraints excluded: chain C residue 476 MET Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 722 ASP Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain E residue 329 HIS Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 725 VAL Chi-restraints excluded: chain E residue 747 TYR Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 329 HIS Chi-restraints excluded: chain F residue 476 MET Chi-restraints excluded: chain F residue 679 VAL Chi-restraints excluded: chain F residue 680 ASN Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain G residue 738 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 200 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 0.0270 chunk 115 optimal weight: 0.2980 chunk 231 optimal weight: 1.9990 chunk 261 optimal weight: 0.0870 chunk 181 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 284 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS B 507 GLN B 642 ASN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN A 715 ASN C 660 ASN D 369 GLN E 392 ASN E 584 ASN E 719 GLN F 362 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.125227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.071579 restraints weight = 48840.052| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.19 r_work: 0.2747 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 34119 Z= 0.082 Angle : 0.466 9.923 46255 Z= 0.253 Chirality : 0.043 0.175 5186 Planarity : 0.003 0.033 5998 Dihedral : 3.903 14.964 4592 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.09 % Allowed : 14.40 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.12), residues: 4293 helix: 0.51 (0.21), residues: 681 sheet: 1.52 (0.13), residues: 1376 loop : -1.01 (0.12), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 180 TYR 0.022 0.001 TYR G 664 PHE 0.034 0.001 PHE C 656 TRP 0.023 0.001 TRP A 748 HIS 0.002 0.000 HIS C 493 Details of bonding type rmsd covalent geometry : bond 0.00182 (34119) covalent geometry : angle 0.46607 (46255) hydrogen bonds : bond 0.02445 ( 1458) hydrogen bonds : angle 4.45715 ( 3990) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 335 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 276 ASP cc_start: 0.8482 (p0) cc_final: 0.8203 (p0) REVERT: B 416 LYS cc_start: 0.8755 (mtpt) cc_final: 0.8449 (mmpt) REVERT: B 660 ASN cc_start: 0.8679 (t0) cc_final: 0.8042 (t0) REVERT: B 698 GLU cc_start: 0.6905 (tp30) cc_final: 0.6164 (mm-30) REVERT: B 714 ASN cc_start: 0.8447 (m-40) cc_final: 0.7780 (p0) REVERT: A 287 ASP cc_start: 0.8720 (t70) cc_final: 0.8439 (OUTLIER) REVERT: A 329 HIS cc_start: 0.7015 (OUTLIER) cc_final: 0.6436 (p-80) REVERT: A 559 LYS cc_start: 0.8477 (ttpp) cc_final: 0.7654 (pmmt) REVERT: A 642 ASN cc_start: 0.7881 (m-40) cc_final: 0.7465 (t0) REVERT: A 714 ASN cc_start: 0.7981 (m-40) cc_final: 0.7685 (p0) REVERT: A 747 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.6558 (m-80) REVERT: C 327 GLU cc_start: 0.8270 (tt0) cc_final: 0.7777 (tt0) REVERT: C 329 HIS cc_start: 0.7033 (OUTLIER) cc_final: 0.6561 (p-80) REVERT: C 369 GLN cc_start: 0.7129 (mt0) cc_final: 0.6307 (mt0) REVERT: C 377 ASN cc_start: 0.7684 (p0) cc_final: 0.7402 (p0) REVERT: C 442 LYS cc_start: 0.8267 (tppt) cc_final: 0.8059 (mmtm) REVERT: C 559 LYS cc_start: 0.7786 (pttm) cc_final: 0.7395 (pmtt) REVERT: C 722 ASP cc_start: 0.6596 (OUTLIER) cc_final: 0.6271 (m-30) REVERT: D 327 GLU cc_start: 0.8025 (tt0) cc_final: 0.7473 (tm-30) REVERT: D 657 GLN cc_start: 0.7470 (tm-30) cc_final: 0.6769 (tp40) REVERT: D 698 GLU cc_start: 0.8151 (tt0) cc_final: 0.7942 (tt0) REVERT: E 287 ASP cc_start: 0.8750 (t70) cc_final: 0.8254 (t0) REVERT: E 329 HIS cc_start: 0.7001 (OUTLIER) cc_final: 0.6498 (p90) REVERT: E 332 THR cc_start: 0.7581 (m) cc_final: 0.7298 (t) REVERT: E 441 LYS cc_start: 0.8306 (ptpp) cc_final: 0.7603 (mmmm) REVERT: E 442 LYS cc_start: 0.8177 (tppt) cc_final: 0.7756 (mptt) REVERT: E 559 LYS cc_start: 0.8154 (ptpp) cc_final: 0.7728 (ptpp) REVERT: E 672 LYS cc_start: 0.8114 (mtmt) cc_final: 0.7688 (mtmm) REVERT: F 329 HIS cc_start: 0.6969 (OUTLIER) cc_final: 0.6495 (p-80) REVERT: F 369 GLN cc_start: 0.7205 (mt0) cc_final: 0.6991 (mt0) REVERT: F 559 LYS cc_start: 0.8439 (ptpt) cc_final: 0.7713 (pmmt) REVERT: F 664 TYR cc_start: 0.6380 (p90) cc_final: 0.6054 (p90) REVERT: F 735 LYS cc_start: 0.8258 (pttt) cc_final: 0.8024 (mtmm) REVERT: G 310 ASN cc_start: 0.8505 (t0) cc_final: 0.8223 (t0) REVERT: G 510 LYS cc_start: 0.8943 (tttt) cc_final: 0.8726 (tttp) REVERT: G 719 GLN cc_start: 0.8288 (tt0) cc_final: 0.7989 (tt0) REVERT: G 756 ILE cc_start: 0.8447 (tt) cc_final: 0.8181 (mt) REVERT: H 428 GLU cc_start: 0.8163 (pp20) cc_final: 0.7771 (tm-30) outliers start: 41 outliers final: 14 residues processed: 358 average time/residue: 0.6544 time to fit residues: 280.0538 Evaluate side-chains 336 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 317 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain C residue 329 HIS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 722 ASP Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain E residue 329 HIS Chi-restraints excluded: chain E residue 725 VAL Chi-restraints excluded: chain E residue 747 TYR Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 329 HIS Chi-restraints excluded: chain F residue 679 VAL Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain G residue 738 ILE Chi-restraints excluded: chain H residue 163 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 321 optimal weight: 0.3980 chunk 167 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 331 optimal weight: 10.0000 chunk 269 optimal weight: 0.9990 chunk 312 optimal weight: 0.8980 chunk 393 optimal weight: 4.9990 chunk 267 optimal weight: 10.0000 chunk 63 optimal weight: 0.0010 chunk 166 optimal weight: 6.9990 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 507 GLN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 ASN C 660 ASN D 369 GLN E 392 ASN E 584 ASN E 719 GLN F 362 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.122434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.068916 restraints weight = 48500.614| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.14 r_work: 0.2689 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34119 Z= 0.131 Angle : 0.503 8.695 46255 Z= 0.274 Chirality : 0.045 0.160 5186 Planarity : 0.003 0.036 5998 Dihedral : 4.209 18.287 4592 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.01 % Allowed : 14.69 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.12), residues: 4293 helix: 0.45 (0.21), residues: 680 sheet: 1.51 (0.13), residues: 1376 loop : -1.03 (0.12), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 523 TYR 0.017 0.001 TYR D 641 PHE 0.040 0.001 PHE C 656 TRP 0.036 0.001 TRP A 748 HIS 0.003 0.001 HIS C 272 Details of bonding type rmsd covalent geometry : bond 0.00318 (34119) covalent geometry : angle 0.50272 (46255) hydrogen bonds : bond 0.03051 ( 1458) hydrogen bonds : angle 4.48859 ( 3990) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 321 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 365 GLU cc_start: 0.7150 (tt0) cc_final: 0.6900 (tt0) REVERT: B 416 LYS cc_start: 0.8711 (mtpt) cc_final: 0.8388 (mmpt) REVERT: B 660 ASN cc_start: 0.8656 (t0) cc_final: 0.8020 (t0) REVERT: B 698 GLU cc_start: 0.6874 (tp30) cc_final: 0.6071 (mm-30) REVERT: B 714 ASN cc_start: 0.8535 (m-40) cc_final: 0.7899 (p0) REVERT: A 287 ASP cc_start: 0.8767 (t70) cc_final: 0.8404 (t0) REVERT: A 329 HIS cc_start: 0.7159 (OUTLIER) cc_final: 0.6480 (p-80) REVERT: A 559 LYS cc_start: 0.8497 (ttpp) cc_final: 0.7647 (pmmt) REVERT: A 642 ASN cc_start: 0.8000 (m-40) cc_final: 0.7631 (t0) REVERT: A 747 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.6749 (m-80) REVERT: C 327 GLU cc_start: 0.8295 (tt0) cc_final: 0.7828 (tt0) REVERT: C 329 HIS cc_start: 0.7180 (OUTLIER) cc_final: 0.6561 (p-80) REVERT: C 369 GLN cc_start: 0.7154 (mt0) cc_final: 0.6380 (mt0) REVERT: C 442 LYS cc_start: 0.8315 (tppt) cc_final: 0.8073 (mmtm) REVERT: C 559 LYS cc_start: 0.7799 (pttm) cc_final: 0.7473 (pmtt) REVERT: C 722 ASP cc_start: 0.6706 (OUTLIER) cc_final: 0.6380 (m-30) REVERT: C 734 ASP cc_start: 0.6723 (m-30) cc_final: 0.6165 (m-30) REVERT: D 327 GLU cc_start: 0.8072 (tt0) cc_final: 0.7551 (tm-30) REVERT: D 657 GLN cc_start: 0.7498 (tm-30) cc_final: 0.6840 (tp40) REVERT: D 714 ASN cc_start: 0.8625 (t0) cc_final: 0.8235 (t0) REVERT: E 329 HIS cc_start: 0.7099 (OUTLIER) cc_final: 0.6515 (p90) REVERT: E 442 LYS cc_start: 0.8272 (tppt) cc_final: 0.7792 (mptt) REVERT: E 559 LYS cc_start: 0.8120 (ptpp) cc_final: 0.7668 (ptpp) REVERT: E 578 MET cc_start: 0.8089 (tpt) cc_final: 0.7828 (tpt) REVERT: E 672 LYS cc_start: 0.8050 (mtmt) cc_final: 0.7646 (mtmm) REVERT: F 329 HIS cc_start: 0.7107 (OUTLIER) cc_final: 0.6468 (p-80) REVERT: F 369 GLN cc_start: 0.7323 (mt0) cc_final: 0.7105 (mt0) REVERT: F 559 LYS cc_start: 0.8451 (ptpt) cc_final: 0.7715 (pmmt) REVERT: F 664 TYR cc_start: 0.6344 (p90) cc_final: 0.5922 (p90) REVERT: F 735 LYS cc_start: 0.8307 (pttt) cc_final: 0.8082 (mtmm) REVERT: G 510 LYS cc_start: 0.8967 (tttt) cc_final: 0.8703 (tttp) REVERT: G 719 GLN cc_start: 0.8304 (tt0) cc_final: 0.7925 (tt0) REVERT: G 756 ILE cc_start: 0.8503 (tt) cc_final: 0.8239 (mt) REVERT: H 428 GLU cc_start: 0.8210 (pp20) cc_final: 0.7846 (tm-30) outliers start: 38 outliers final: 14 residues processed: 340 average time/residue: 0.6662 time to fit residues: 270.5505 Evaluate side-chains 335 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 315 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain C residue 329 HIS Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 722 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain E residue 329 HIS Chi-restraints excluded: chain E residue 725 VAL Chi-restraints excluded: chain E residue 747 TYR Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 329 HIS Chi-restraints excluded: chain G residue 651 THR Chi-restraints excluded: chain G residue 723 ILE Chi-restraints excluded: chain G residue 738 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 106 optimal weight: 8.9990 chunk 93 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 chunk 236 optimal weight: 6.9990 chunk 380 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 246 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 285 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 662 ASN A 715 ASN C 660 ASN C 715 ASN D 369 GLN E 584 ASN E 719 GLN F 362 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.121082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.067067 restraints weight = 49080.981| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.15 r_work: 0.2652 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 34119 Z= 0.200 Angle : 0.554 9.617 46255 Z= 0.302 Chirality : 0.047 0.176 5186 Planarity : 0.004 0.037 5998 Dihedral : 4.528 18.956 4592 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.93 % Allowed : 15.01 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.12), residues: 4293 helix: 0.31 (0.21), residues: 680 sheet: 1.49 (0.13), residues: 1348 loop : -1.08 (0.12), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 180 TYR 0.025 0.002 TYR G 664 PHE 0.046 0.002 PHE C 656 TRP 0.048 0.002 TRP A 748 HIS 0.003 0.001 HIS H 438 Details of bonding type rmsd covalent geometry : bond 0.00496 (34119) covalent geometry : angle 0.55362 (46255) hydrogen bonds : bond 0.03609 ( 1458) hydrogen bonds : angle 4.62792 ( 3990) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 314 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 365 GLU cc_start: 0.7198 (tt0) cc_final: 0.6957 (tt0) REVERT: B 416 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8398 (mmpt) REVERT: B 660 ASN cc_start: 0.8695 (t0) cc_final: 0.8059 (t0) REVERT: B 698 GLU cc_start: 0.6836 (tp30) cc_final: 0.6060 (mm-30) REVERT: A 287 ASP cc_start: 0.8815 (t70) cc_final: 0.8424 (t0) REVERT: A 642 ASN cc_start: 0.7863 (m-40) cc_final: 0.7480 (t0) REVERT: A 747 TYR cc_start: 0.7533 (OUTLIER) cc_final: 0.6890 (m-80) REVERT: C 327 GLU cc_start: 0.8349 (tt0) cc_final: 0.7861 (tt0) REVERT: C 329 HIS cc_start: 0.7423 (OUTLIER) cc_final: 0.6522 (p-80) REVERT: C 369 GLN cc_start: 0.7175 (mt0) cc_final: 0.6447 (mt0) REVERT: C 442 LYS cc_start: 0.8416 (tppt) cc_final: 0.8067 (mmtm) REVERT: C 476 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8891 (ttp) REVERT: C 559 LYS cc_start: 0.7821 (pttm) cc_final: 0.7496 (pmtt) REVERT: C 722 ASP cc_start: 0.6746 (OUTLIER) cc_final: 0.6430 (m-30) REVERT: C 734 ASP cc_start: 0.6751 (m-30) cc_final: 0.6329 (m-30) REVERT: D 327 GLU cc_start: 0.7997 (tt0) cc_final: 0.7488 (tm-30) REVERT: D 714 ASN cc_start: 0.8685 (t0) cc_final: 0.8297 (t0) REVERT: E 329 HIS cc_start: 0.7190 (OUTLIER) cc_final: 0.6515 (p-80) REVERT: E 559 LYS cc_start: 0.8139 (ptpp) cc_final: 0.7790 (ptpp) REVERT: E 656 PHE cc_start: 0.7928 (m-80) cc_final: 0.7493 (m-10) REVERT: E 672 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7626 (mtmm) REVERT: F 329 HIS cc_start: 0.7270 (OUTLIER) cc_final: 0.6486 (p-80) REVERT: F 369 GLN cc_start: 0.7385 (mt0) cc_final: 0.7171 (mt0) REVERT: F 559 LYS cc_start: 0.8481 (ptpt) cc_final: 0.7752 (pmmt) REVERT: F 664 TYR cc_start: 0.6373 (p90) cc_final: 0.5971 (p90) REVERT: F 735 LYS cc_start: 0.8326 (pttt) cc_final: 0.8110 (mtmm) REVERT: G 719 GLN cc_start: 0.8310 (tt0) cc_final: 0.7936 (tt0) REVERT: H 428 GLU cc_start: 0.8166 (pp20) cc_final: 0.7832 (tm-30) outliers start: 35 outliers final: 17 residues processed: 335 average time/residue: 0.6523 time to fit residues: 261.8518 Evaluate side-chains 331 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 308 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain C residue 329 HIS Chi-restraints excluded: chain C residue 476 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 722 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain E residue 329 HIS Chi-restraints excluded: chain E residue 725 VAL Chi-restraints excluded: chain E residue 747 TYR Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 329 HIS Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 651 THR Chi-restraints excluded: chain G residue 723 ILE Chi-restraints excluded: chain G residue 738 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 72 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 254 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 chunk 318 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 299 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 223 optimal weight: 0.0070 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 ASN C 660 ASN C 715 ASN D 362 GLN D 369 GLN E 584 ASN E 719 GLN F 362 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.124251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.070251 restraints weight = 48454.543| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.19 r_work: 0.2717 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34119 Z= 0.093 Angle : 0.479 9.550 46255 Z= 0.261 Chirality : 0.044 0.157 5186 Planarity : 0.003 0.033 5998 Dihedral : 4.036 15.942 4592 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.74 % Allowed : 15.20 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.12), residues: 4293 helix: 0.48 (0.21), residues: 680 sheet: 1.52 (0.13), residues: 1376 loop : -1.00 (0.12), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 180 TYR 0.019 0.001 TYR F 361 PHE 0.037 0.001 PHE C 656 TRP 0.033 0.001 TRP A 748 HIS 0.002 0.001 HIS C 493 Details of bonding type rmsd covalent geometry : bond 0.00212 (34119) covalent geometry : angle 0.47905 (46255) hydrogen bonds : bond 0.02645 ( 1458) hydrogen bonds : angle 4.46061 ( 3990) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18405.28 seconds wall clock time: 312 minutes 24.45 seconds (18744.45 seconds total)