Starting phenix.real_space_refine on Sat Mar 7 00:24:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vct_31895/03_2026/7vct_31895.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vct_31895/03_2026/7vct_31895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vct_31895/03_2026/7vct_31895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vct_31895/03_2026/7vct_31895.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vct_31895/03_2026/7vct_31895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vct_31895/03_2026/7vct_31895.map" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 6 5.21 5 S 192 5.16 5 C 22296 2.51 5 N 6312 2.21 5 O 6858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35694 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5890 Classifications: {'peptide': 751} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 709} Chain: "B" Number of atoms: 5890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5890 Classifications: {'peptide': 751} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 709} Chain: "C" Number of atoms: 5890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5890 Classifications: {'peptide': 751} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 709} Chain: "D" Number of atoms: 5890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5890 Classifications: {'peptide': 751} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 709} Chain: "E" Number of atoms: 5890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5890 Classifications: {'peptide': 751} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 709} Chain: "F" Number of atoms: 5890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5890 Classifications: {'peptide': 751} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 709} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.30, per 1000 atoms: 0.20 Number of scatterers: 35694 At special positions: 0 Unit cell: (178.2, 176.04, 103.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 30 15.00 Mg 6 11.99 O 6858 8.00 N 6312 7.00 C 22296 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.4 seconds 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8412 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 36 sheets defined 48.7% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 85 through 91 Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.887A pdb=" N LEU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.722A pdb=" N ASP A 205 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 206' Processing helix chain 'A' and resid 209 through 226 removed outlier: 5.153A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.835A pdb=" N ILE A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 296 removed outlier: 4.123A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.935A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 319 through 335 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.854A pdb=" N SER A 352 " --> pdb=" O ARG A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 358 removed outlier: 3.519A pdb=" N ARG A 358 " --> pdb=" O PRO A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.650A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 426 removed outlier: 4.196A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 removed outlier: 3.779A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.739A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 removed outlier: 3.564A pdb=" N ASP A 478 " --> pdb=" O THR A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 494 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 499 through 507 removed outlier: 4.094A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.704A pdb=" N LEU A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.740A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.994A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 610 removed outlier: 3.697A pdb=" N ASN A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 661 removed outlier: 4.173A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.868A pdb=" N THR A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 716 removed outlier: 3.538A pdb=" N LEU A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 removed outlier: 3.837A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 748 through 763 removed outlier: 3.594A pdb=" N GLN A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 85 through 91 Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.886A pdb=" N LEU B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.721A pdb=" N ASP B 205 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 202 through 206' Processing helix chain 'B' and resid 209 through 226 removed outlier: 5.153A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.835A pdb=" N ILE B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 296 removed outlier: 4.123A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.936A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 319 through 335 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.854A pdb=" N SER B 352 " --> pdb=" O ARG B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.518A pdb=" N ARG B 358 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.650A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 426 removed outlier: 4.195A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 removed outlier: 3.779A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.739A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 removed outlier: 3.563A pdb=" N ASP B 478 " --> pdb=" O THR B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 494 Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 499 through 507 removed outlier: 4.094A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.704A pdb=" N LEU B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 553 removed outlier: 3.740A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.995A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 569 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 610 removed outlier: 3.697A pdb=" N ASN B 602 " --> pdb=" O ASP B 598 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 661 removed outlier: 4.173A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.867A pdb=" N THR B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 716 removed outlier: 3.539A pdb=" N LEU B 687 " --> pdb=" O SER B 683 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN B 716 " --> pdb=" O GLU B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 740 removed outlier: 3.837A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 748 through 763 removed outlier: 3.595A pdb=" N GLN B 763 " --> pdb=" O ALA B 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 50 Processing helix chain 'C' and resid 85 through 91 Processing helix chain 'C' and resid 120 through 123 Processing helix chain 'C' and resid 135 through 140 removed outlier: 3.886A pdb=" N LEU C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.722A pdb=" N ASP C 205 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 202 through 206' Processing helix chain 'C' and resid 209 through 226 removed outlier: 5.153A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 232 Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.836A pdb=" N ILE C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 296 removed outlier: 4.122A pdb=" N SER C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.936A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 319 through 335 Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.853A pdb=" N SER C 352 " --> pdb=" O ARG C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 358 removed outlier: 3.519A pdb=" N ARG C 358 " --> pdb=" O PRO C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.650A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 426 removed outlier: 4.196A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 removed outlier: 3.779A pdb=" N MET C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.739A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 removed outlier: 3.564A pdb=" N ASP C 478 " --> pdb=" O THR C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 494 Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 507 removed outlier: 4.093A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.705A pdb=" N LEU C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 553 removed outlier: 3.741A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.995A pdb=" N ARG C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 removed outlier: 3.697A pdb=" N ASN C 602 " --> pdb=" O ASP C 598 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 661 removed outlier: 4.174A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.868A pdb=" N THR C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 716 removed outlier: 3.539A pdb=" N LEU C 687 " --> pdb=" O SER C 683 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN C 716 " --> pdb=" O GLU C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 removed outlier: 3.836A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 743 No H-bonds generated for 'chain 'C' and resid 741 through 743' Processing helix chain 'C' and resid 748 through 763 removed outlier: 3.595A pdb=" N GLN C 763 " --> pdb=" O ALA C 759 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 85 through 91 Processing helix chain 'D' and resid 120 through 123 Processing helix chain 'D' and resid 135 through 140 removed outlier: 3.887A pdb=" N LEU D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.722A pdb=" N ASP D 205 " --> pdb=" O GLY D 202 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 202 through 206' Processing helix chain 'D' and resid 209 through 226 removed outlier: 5.153A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 232 Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.835A pdb=" N ILE D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 296 removed outlier: 4.123A pdb=" N SER D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.935A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 319 through 335 Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.854A pdb=" N SER D 352 " --> pdb=" O ARG D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 358 removed outlier: 3.519A pdb=" N ARG D 358 " --> pdb=" O PRO D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 403 removed outlier: 3.650A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 426 removed outlier: 4.196A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 removed outlier: 3.779A pdb=" N MET D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 445 " --> pdb=" O VAL D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.739A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 removed outlier: 3.564A pdb=" N ASP D 478 " --> pdb=" O THR D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 494 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 499 through 507 removed outlier: 4.094A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.704A pdb=" N LEU D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 553 removed outlier: 3.740A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.994A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA D 569 " --> pdb=" O LYS D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 removed outlier: 3.697A pdb=" N ASN D 602 " --> pdb=" O ASP D 598 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 661 removed outlier: 4.173A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.868A pdb=" N THR D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 716 removed outlier: 3.538A pdb=" N LEU D 687 " --> pdb=" O SER D 683 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN D 716 " --> pdb=" O GLU D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 removed outlier: 3.837A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 748 through 763 removed outlier: 3.594A pdb=" N GLN D 763 " --> pdb=" O ALA D 759 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 50 Processing helix chain 'E' and resid 85 through 91 Processing helix chain 'E' and resid 120 through 123 Processing helix chain 'E' and resid 135 through 140 removed outlier: 3.886A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.721A pdb=" N ASP E 205 " --> pdb=" O GLY E 202 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 202 through 206' Processing helix chain 'E' and resid 209 through 226 removed outlier: 5.153A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 232 Processing helix chain 'E' and resid 250 through 261 removed outlier: 3.835A pdb=" N ILE E 254 " --> pdb=" O GLY E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 280 through 296 removed outlier: 4.123A pdb=" N SER E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.936A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 319 through 335 Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.854A pdb=" N SER E 352 " --> pdb=" O ARG E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 358 removed outlier: 3.518A pdb=" N ARG E 358 " --> pdb=" O PRO E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.650A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 426 removed outlier: 4.195A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 removed outlier: 3.779A pdb=" N MET E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 445 " --> pdb=" O VAL E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 459 removed outlier: 3.739A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 removed outlier: 3.563A pdb=" N ASP E 478 " --> pdb=" O THR E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 494 Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 499 through 507 removed outlier: 4.094A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.704A pdb=" N LEU E 527 " --> pdb=" O GLY E 523 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 553 removed outlier: 3.740A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 569 removed outlier: 3.995A pdb=" N ARG E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA E 569 " --> pdb=" O LYS E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 610 removed outlier: 3.697A pdb=" N ASN E 602 " --> pdb=" O ASP E 598 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 651 through 661 removed outlier: 4.173A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.867A pdb=" N THR E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 716 removed outlier: 3.539A pdb=" N LEU E 687 " --> pdb=" O SER E 683 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN E 716 " --> pdb=" O GLU E 712 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 740 removed outlier: 3.837A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 743 No H-bonds generated for 'chain 'E' and resid 741 through 743' Processing helix chain 'E' and resid 748 through 763 removed outlier: 3.595A pdb=" N GLN E 763 " --> pdb=" O ALA E 759 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 50 Processing helix chain 'F' and resid 85 through 91 Processing helix chain 'F' and resid 120 through 123 Processing helix chain 'F' and resid 135 through 140 removed outlier: 3.886A pdb=" N LEU F 140 " --> pdb=" O LYS F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 removed outlier: 3.722A pdb=" N ASP F 205 " --> pdb=" O GLY F 202 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE F 206 " --> pdb=" O TYR F 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 202 through 206' Processing helix chain 'F' and resid 209 through 226 removed outlier: 5.153A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 232 Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.836A pdb=" N ILE F 254 " --> pdb=" O GLY F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 280 through 296 removed outlier: 4.122A pdb=" N SER F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.936A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 319 through 335 Processing helix chain 'F' and resid 336 through 338 No H-bonds generated for 'chain 'F' and resid 336 through 338' Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.853A pdb=" N SER F 352 " --> pdb=" O ARG F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 358 removed outlier: 3.519A pdb=" N ARG F 358 " --> pdb=" O PRO F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.650A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 426 removed outlier: 4.196A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 445 removed outlier: 3.779A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU F 445 " --> pdb=" O VAL F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.739A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 removed outlier: 3.564A pdb=" N ASP F 478 " --> pdb=" O THR F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 494 Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'F' and resid 499 through 507 removed outlier: 4.093A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.705A pdb=" N LEU F 527 " --> pdb=" O GLY F 523 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS F 535 " --> pdb=" O ILE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 553 removed outlier: 3.741A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 569 removed outlier: 3.995A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA F 569 " --> pdb=" O LYS F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 610 removed outlier: 3.697A pdb=" N ASN F 602 " --> pdb=" O ASP F 598 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 661 removed outlier: 4.174A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.868A pdb=" N THR F 679 " --> pdb=" O LEU F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 716 removed outlier: 3.539A pdb=" N LEU F 687 " --> pdb=" O SER F 683 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN F 716 " --> pdb=" O GLU F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 740 removed outlier: 3.836A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 743 No H-bonds generated for 'chain 'F' and resid 741 through 743' Processing helix chain 'F' and resid 748 through 763 removed outlier: 3.595A pdb=" N GLN F 763 " --> pdb=" O ALA F 759 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 68 removed outlier: 3.656A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 155 removed outlier: 5.845A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 116 " --> pdb=" O HIS A 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.401A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.515A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLY A 513 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.656A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 38 through 41 Processing sheet with id=AA9, first strand: chain 'B' and resid 151 through 155 removed outlier: 5.845A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 116 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AB2, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.402A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.515A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR B 623 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE B 516 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 66 through 68 removed outlier: 3.656A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 38 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 151 through 155 removed outlier: 5.845A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL C 116 " --> pdb=" O HIS C 183 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB8, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.401A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.515A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR C 623 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE C 516 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLY C 513 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 66 through 68 removed outlier: 3.656A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 38 through 41 Processing sheet with id=AC3, first strand: chain 'D' and resid 151 through 155 removed outlier: 5.845A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL D 116 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AC5, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.401A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.515A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR D 623 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE D 516 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 66 through 68 removed outlier: 3.656A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 38 through 41 Processing sheet with id=AC9, first strand: chain 'E' and resid 151 through 155 removed outlier: 5.845A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL E 116 " --> pdb=" O HIS E 183 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AD2, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.402A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.515A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR E 623 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE E 516 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 66 through 68 removed outlier: 3.656A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 38 through 41 Processing sheet with id=AD6, first strand: chain 'F' and resid 151 through 155 removed outlier: 5.845A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL F 116 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AD8, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.401A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.515A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1356 hydrogen bonds defined for protein. 3942 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: 7.80 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 12410 1.37 - 1.51: 10768 1.51 - 1.66: 12810 1.66 - 1.80: 246 1.80 - 1.95: 60 Bond restraints: 36294 Sorted by residual: bond pdb=" C4 ADP B 903 " pdb=" C5 ADP B 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP C 903 " pdb=" C5 ADP C 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP E 903 " pdb=" C5 ADP E 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP A 903 " pdb=" C5 ADP A 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 ADP D 903 " pdb=" C5 ADP D 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 ... (remaining 36289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 47984 2.58 - 5.16: 925 5.16 - 7.75: 137 7.75 - 10.33: 21 10.33 - 12.91: 19 Bond angle restraints: 49086 Sorted by residual: angle pdb=" N ASP A 592 " pdb=" CA ASP A 592 " pdb=" C ASP A 592 " ideal model delta sigma weight residual 111.03 105.82 5.21 1.11e+00 8.12e-01 2.20e+01 angle pdb=" N ASP D 592 " pdb=" CA ASP D 592 " pdb=" C ASP D 592 " ideal model delta sigma weight residual 111.03 105.82 5.21 1.11e+00 8.12e-01 2.20e+01 angle pdb=" N ASP C 592 " pdb=" CA ASP C 592 " pdb=" C ASP C 592 " ideal model delta sigma weight residual 111.03 105.83 5.20 1.11e+00 8.12e-01 2.19e+01 angle pdb=" N ASP F 592 " pdb=" CA ASP F 592 " pdb=" C ASP F 592 " ideal model delta sigma weight residual 111.03 105.83 5.20 1.11e+00 8.12e-01 2.19e+01 angle pdb=" N ASP B 592 " pdb=" CA ASP B 592 " pdb=" C ASP B 592 " ideal model delta sigma weight residual 111.03 105.85 5.18 1.11e+00 8.12e-01 2.18e+01 ... (remaining 49081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.70: 22138 24.70 - 49.39: 351 49.39 - 74.09: 36 74.09 - 98.78: 6 98.78 - 123.48: 11 Dihedral angle restraints: 22542 sinusoidal: 9564 harmonic: 12978 Sorted by residual: dihedral pdb=" O1B ADP B 903 " pdb=" O3A ADP B 903 " pdb=" PB ADP B 903 " pdb=" PA ADP B 903 " ideal model delta sinusoidal sigma weight residual 300.00 176.52 123.48 1 2.00e+01 2.50e-03 3.72e+01 dihedral pdb=" O1B ADP E 903 " pdb=" O3A ADP E 903 " pdb=" PB ADP E 903 " pdb=" PA ADP E 903 " ideal model delta sinusoidal sigma weight residual 300.00 176.95 123.05 1 2.00e+01 2.50e-03 3.71e+01 dihedral pdb=" C5' ADP C 903 " pdb=" O5' ADP C 903 " pdb=" PA ADP C 903 " pdb=" O2A ADP C 903 " ideal model delta sinusoidal sigma weight residual -60.00 62.18 -122.18 1 2.00e+01 2.50e-03 3.68e+01 ... (remaining 22539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4121 0.058 - 0.116: 1165 0.116 - 0.174: 190 0.174 - 0.232: 14 0.232 - 0.290: 6 Chirality restraints: 5496 Sorted by residual: chirality pdb=" C3' ADP C 903 " pdb=" C2' ADP C 903 " pdb=" C4' ADP C 903 " pdb=" O3' ADP C 903 " both_signs ideal model delta sigma weight residual False -2.51 -2.80 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' ADP E 903 " pdb=" C2' ADP E 903 " pdb=" C4' ADP E 903 " pdb=" O3' ADP E 903 " both_signs ideal model delta sigma weight residual False -2.51 -2.79 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C3' ADP D 903 " pdb=" C2' ADP D 903 " pdb=" C4' ADP D 903 " pdb=" O3' ADP D 903 " both_signs ideal model delta sigma weight residual False -2.51 -2.79 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 5493 not shown) Planarity restraints: 6474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 544 " -0.042 5.00e-02 4.00e+02 6.29e-02 6.34e+00 pdb=" N PRO C 545 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 545 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 545 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 544 " -0.042 5.00e-02 4.00e+02 6.29e-02 6.34e+00 pdb=" N PRO F 545 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 545 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 545 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 544 " -0.042 5.00e-02 4.00e+02 6.28e-02 6.30e+00 pdb=" N PRO D 545 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 545 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 545 " -0.035 5.00e-02 4.00e+02 ... (remaining 6471 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 621 2.69 - 3.24: 31429 3.24 - 3.79: 49579 3.79 - 4.35: 67597 4.35 - 4.90: 112869 Nonbonded interactions: 262095 Sorted by model distance: nonbonded pdb=" O2G AGS E 901 " pdb="MG MG E 902 " model vdw 2.132 2.170 nonbonded pdb=" O2G AGS B 901 " pdb="MG MG B 902 " model vdw 2.132 2.170 nonbonded pdb=" O2G AGS A 901 " pdb="MG MG A 902 " model vdw 2.132 2.170 nonbonded pdb=" O2G AGS D 901 " pdb="MG MG D 902 " model vdw 2.132 2.170 nonbonded pdb=" O2G AGS C 901 " pdb="MG MG C 902 " model vdw 2.132 2.170 ... (remaining 262090 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 30.170 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.100 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.593 36298 Z= 0.567 Angle : 0.941 12.909 49086 Z= 0.518 Chirality : 0.054 0.290 5496 Planarity : 0.008 0.063 6474 Dihedral : 9.934 123.478 14130 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.10), residues: 4494 helix: -2.41 (0.09), residues: 1776 sheet: -0.07 (0.20), residues: 624 loop : -2.29 (0.11), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 599 TYR 0.024 0.003 TYR D 755 PHE 0.041 0.003 PHE C 516 TRP 0.016 0.003 TRP A 454 HIS 0.005 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00677 (36294) covalent geometry : angle 0.94127 (49086) hydrogen bonds : bond 0.15779 ( 1356) hydrogen bonds : angle 6.08742 ( 3942) Misc. bond : bond 0.46232 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 662 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7010 (mttp) cc_final: 0.6753 (ttpp) REVERT: A 443 ASN cc_start: 0.7163 (m-40) cc_final: 0.6863 (m-40) REVERT: A 449 MET cc_start: 0.8007 (tpt) cc_final: 0.7639 (tpt) REVERT: A 457 SER cc_start: 0.8669 (t) cc_final: 0.8306 (p) REVERT: A 678 MET cc_start: 0.6340 (tpt) cc_final: 0.6102 (tpt) REVERT: A 742 PHE cc_start: 0.7442 (m-80) cc_final: 0.6800 (m-10) REVERT: A 752 ILE cc_start: 0.9001 (mt) cc_final: 0.8761 (mm) REVERT: B 443 ASN cc_start: 0.7199 (m-40) cc_final: 0.6723 (m-40) REVERT: B 449 MET cc_start: 0.7920 (tpt) cc_final: 0.7428 (tpp) REVERT: B 457 SER cc_start: 0.8516 (t) cc_final: 0.8209 (p) REVERT: C 62 LYS cc_start: 0.7043 (mttp) cc_final: 0.6757 (ttpp) REVERT: C 443 ASN cc_start: 0.7272 (m-40) cc_final: 0.6940 (m-40) REVERT: C 457 SER cc_start: 0.8585 (t) cc_final: 0.8274 (p) REVERT: C 550 MET cc_start: 0.8766 (mtt) cc_final: 0.8564 (mtm) REVERT: C 678 MET cc_start: 0.6483 (tpt) cc_final: 0.6080 (tpt) REVERT: D 62 LYS cc_start: 0.7011 (mttp) cc_final: 0.6755 (ttpp) REVERT: D 443 ASN cc_start: 0.7163 (m-40) cc_final: 0.6862 (m-40) REVERT: D 449 MET cc_start: 0.8005 (tpt) cc_final: 0.7645 (tpt) REVERT: D 457 SER cc_start: 0.8651 (t) cc_final: 0.8308 (p) REVERT: D 678 MET cc_start: 0.6318 (tpt) cc_final: 0.6086 (tpt) REVERT: D 742 PHE cc_start: 0.7447 (m-80) cc_final: 0.6807 (m-10) REVERT: D 752 ILE cc_start: 0.9001 (mt) cc_final: 0.8756 (mm) REVERT: E 443 ASN cc_start: 0.7198 (m-40) cc_final: 0.6721 (m-40) REVERT: E 449 MET cc_start: 0.7919 (tpt) cc_final: 0.7422 (tpp) REVERT: E 457 SER cc_start: 0.8509 (t) cc_final: 0.8197 (p) REVERT: F 62 LYS cc_start: 0.7043 (mttp) cc_final: 0.6761 (ttpp) REVERT: F 443 ASN cc_start: 0.7274 (m-40) cc_final: 0.6937 (m-40) REVERT: F 457 SER cc_start: 0.8591 (t) cc_final: 0.8272 (p) REVERT: F 678 MET cc_start: 0.6470 (tpt) cc_final: 0.6065 (tpt) REVERT: F 742 PHE cc_start: 0.7510 (m-80) cc_final: 0.7309 (m-10) outliers start: 0 outliers final: 0 residues processed: 662 average time/residue: 0.3030 time to fit residues: 287.4809 Evaluate side-chains 316 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 103 GLN A 443 ASN A 624 ASN B 103 GLN B 443 ASN C 91 ASN C 103 GLN C 443 ASN C 624 ASN D 91 ASN D 103 GLN D 443 ASN D 624 ASN E 103 GLN E 443 ASN F 91 ASN F 103 GLN F 443 ASN F 624 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.179079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115067 restraints weight = 47014.140| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.88 r_work: 0.3182 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 36298 Z= 0.164 Angle : 0.623 10.066 49086 Z= 0.304 Chirality : 0.046 0.147 5496 Planarity : 0.006 0.066 6474 Dihedral : 8.943 133.196 5094 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.99 % Allowed : 3.80 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.11), residues: 4494 helix: -0.32 (0.11), residues: 1788 sheet: 0.06 (0.20), residues: 654 loop : -1.81 (0.12), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 147 TYR 0.018 0.001 TYR C 244 PHE 0.020 0.002 PHE D 674 TRP 0.006 0.001 TRP A 476 HIS 0.004 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00399 (36294) covalent geometry : angle 0.62347 (49086) hydrogen bonds : bond 0.04721 ( 1356) hydrogen bonds : angle 4.32512 ( 3942) Misc. bond : bond 0.00274 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 345 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.6567 (mttp) cc_final: 0.6365 (ttpp) REVERT: A 285 ASN cc_start: 0.8247 (m-40) cc_final: 0.8006 (t0) REVERT: A 449 MET cc_start: 0.8083 (tpt) cc_final: 0.7306 (tpp) REVERT: A 457 SER cc_start: 0.9033 (t) cc_final: 0.8591 (p) REVERT: A 561 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8382 (mp0) REVERT: A 611 MET cc_start: 0.8125 (tpp) cc_final: 0.7890 (ttp) REVERT: A 678 MET cc_start: 0.6784 (tpt) cc_final: 0.6555 (tpt) REVERT: A 720 MET cc_start: 0.4951 (mpp) cc_final: 0.4412 (mmm) REVERT: A 733 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7853 (mtt-85) REVERT: A 742 PHE cc_start: 0.7439 (m-80) cc_final: 0.6863 (m-10) REVERT: B 285 ASN cc_start: 0.8321 (m-40) cc_final: 0.8004 (t0) REVERT: B 442 MET cc_start: 0.7285 (ppp) cc_final: 0.7007 (ttm) REVERT: B 457 SER cc_start: 0.8877 (t) cc_final: 0.8384 (p) REVERT: C 62 LYS cc_start: 0.6799 (mttp) cc_final: 0.6477 (ttpp) REVERT: C 457 SER cc_start: 0.8925 (t) cc_final: 0.8446 (p) REVERT: C 611 MET cc_start: 0.8058 (tpp) cc_final: 0.7389 (ttp) REVERT: C 678 MET cc_start: 0.6968 (tpt) cc_final: 0.6686 (tpt) REVERT: C 720 MET cc_start: 0.5477 (mpp) cc_final: 0.4918 (mmm) REVERT: D 62 LYS cc_start: 0.6572 (mttp) cc_final: 0.6366 (ttpp) REVERT: D 285 ASN cc_start: 0.8250 (m-40) cc_final: 0.8004 (t0) REVERT: D 449 MET cc_start: 0.8088 (tpt) cc_final: 0.7308 (tpp) REVERT: D 457 SER cc_start: 0.9042 (t) cc_final: 0.8595 (p) REVERT: D 561 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8380 (mp0) REVERT: D 611 MET cc_start: 0.8119 (tpp) cc_final: 0.7886 (ttp) REVERT: D 678 MET cc_start: 0.6789 (tpt) cc_final: 0.6558 (tpt) REVERT: D 720 MET cc_start: 0.4955 (mpp) cc_final: 0.4417 (mmm) REVERT: D 733 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7851 (mtt-85) REVERT: D 742 PHE cc_start: 0.7439 (m-80) cc_final: 0.6861 (m-10) REVERT: E 285 ASN cc_start: 0.8323 (m-40) cc_final: 0.7999 (t0) REVERT: E 442 MET cc_start: 0.7277 (ppp) cc_final: 0.7002 (ttm) REVERT: E 457 SER cc_start: 0.8880 (t) cc_final: 0.8385 (p) REVERT: E 561 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8463 (mp0) REVERT: F 62 LYS cc_start: 0.6781 (mttp) cc_final: 0.6462 (ttpp) REVERT: F 457 SER cc_start: 0.8915 (t) cc_final: 0.8432 (p) REVERT: F 611 MET cc_start: 0.8066 (tpp) cc_final: 0.7400 (ttp) REVERT: F 678 MET cc_start: 0.6967 (tpt) cc_final: 0.6686 (tpt) REVERT: F 720 MET cc_start: 0.5482 (mpp) cc_final: 0.4926 (mmm) REVERT: F 742 PHE cc_start: 0.7900 (m-80) cc_final: 0.7530 (m-10) outliers start: 38 outliers final: 24 residues processed: 375 average time/residue: 0.2415 time to fit residues: 140.2923 Evaluate side-chains 306 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 280 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 662 ARG Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 662 ARG Chi-restraints excluded: chain D residue 733 ARG Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 662 ARG Chi-restraints excluded: chain E residue 752 ILE Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 760 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 382 optimal weight: 6.9990 chunk 265 optimal weight: 10.0000 chunk 376 optimal weight: 3.9990 chunk 112 optimal weight: 0.4980 chunk 334 optimal weight: 0.0170 chunk 425 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 372 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.0620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN A 443 ASN B 337 GLN C 91 ASN C 443 ASN D 337 GLN D 443 ASN E 337 GLN F 91 ASN F 443 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.179787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116146 restraints weight = 46994.569| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.82 r_work: 0.3213 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36298 Z= 0.114 Angle : 0.562 9.000 49086 Z= 0.272 Chirality : 0.044 0.133 5496 Planarity : 0.004 0.053 6474 Dihedral : 8.195 120.750 5094 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.89 % Allowed : 4.77 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.65 (0.12), residues: 4494 helix: 0.47 (0.12), residues: 1830 sheet: 0.16 (0.20), residues: 654 loop : -1.47 (0.12), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 711 TYR 0.015 0.001 TYR F 244 PHE 0.012 0.001 PHE E 516 TRP 0.004 0.001 TRP A 551 HIS 0.003 0.001 HIS E 499 Details of bonding type rmsd covalent geometry : bond 0.00268 (36294) covalent geometry : angle 0.56245 (49086) hydrogen bonds : bond 0.03676 ( 1356) hydrogen bonds : angle 3.96585 ( 3942) Misc. bond : bond 0.00077 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 310 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.6634 (mttp) cc_final: 0.6417 (ttpp) REVERT: A 285 ASN cc_start: 0.8211 (m-40) cc_final: 0.7987 (t0) REVERT: A 449 MET cc_start: 0.8055 (tpt) cc_final: 0.7778 (tpp) REVERT: A 457 SER cc_start: 0.9114 (t) cc_final: 0.8674 (p) REVERT: A 611 MET cc_start: 0.8089 (tpp) cc_final: 0.7833 (ttp) REVERT: A 711 ARG cc_start: 0.6996 (tmm160) cc_final: 0.6599 (tmm160) REVERT: A 720 MET cc_start: 0.4919 (mpp) cc_final: 0.4204 (mmm) REVERT: A 733 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8031 (mtt-85) REVERT: A 742 PHE cc_start: 0.7519 (m-80) cc_final: 0.6930 (m-10) REVERT: B 285 ASN cc_start: 0.8213 (m-40) cc_final: 0.7912 (t0) REVERT: B 332 MET cc_start: 0.8740 (mmm) cc_final: 0.8531 (mtp) REVERT: B 457 SER cc_start: 0.8819 (t) cc_final: 0.8350 (p) REVERT: C 62 LYS cc_start: 0.6803 (mttp) cc_final: 0.6475 (ttpp) REVERT: C 454 TRP cc_start: 0.8490 (t60) cc_final: 0.8279 (t60) REVERT: C 457 SER cc_start: 0.8972 (t) cc_final: 0.8474 (p) REVERT: C 611 MET cc_start: 0.7989 (tpp) cc_final: 0.7570 (ttp) REVERT: C 678 MET cc_start: 0.6955 (tpt) cc_final: 0.6725 (tpt) REVERT: C 720 MET cc_start: 0.5643 (mpp) cc_final: 0.5374 (mmm) REVERT: D 62 LYS cc_start: 0.6628 (mttp) cc_final: 0.6413 (ttpp) REVERT: D 285 ASN cc_start: 0.8207 (m-40) cc_final: 0.7981 (t0) REVERT: D 449 MET cc_start: 0.8077 (tpt) cc_final: 0.7801 (tpp) REVERT: D 457 SER cc_start: 0.9119 (t) cc_final: 0.8678 (p) REVERT: D 611 MET cc_start: 0.8090 (tpp) cc_final: 0.7835 (ttp) REVERT: D 711 ARG cc_start: 0.6991 (tmm160) cc_final: 0.6594 (tmm160) REVERT: D 720 MET cc_start: 0.4919 (mpp) cc_final: 0.4201 (mmm) REVERT: D 733 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8030 (mtt-85) REVERT: D 742 PHE cc_start: 0.7520 (m-80) cc_final: 0.6934 (m-10) REVERT: E 285 ASN cc_start: 0.8223 (m-40) cc_final: 0.7915 (t0) REVERT: E 332 MET cc_start: 0.8742 (mmm) cc_final: 0.8533 (mtp) REVERT: E 457 SER cc_start: 0.8819 (t) cc_final: 0.8349 (p) REVERT: E 561 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8407 (mp0) REVERT: F 62 LYS cc_start: 0.6794 (mttp) cc_final: 0.6467 (ttpp) REVERT: F 454 TRP cc_start: 0.8486 (t60) cc_final: 0.8277 (t60) REVERT: F 457 SER cc_start: 0.8960 (t) cc_final: 0.8457 (p) REVERT: F 611 MET cc_start: 0.7993 (tpp) cc_final: 0.7574 (ttp) REVERT: F 678 MET cc_start: 0.6934 (tpt) cc_final: 0.6702 (tpt) REVERT: F 720 MET cc_start: 0.5641 (mpp) cc_final: 0.5371 (mmm) REVERT: F 742 PHE cc_start: 0.7844 (m-80) cc_final: 0.7415 (m-10) outliers start: 34 outliers final: 16 residues processed: 334 average time/residue: 0.2453 time to fit residues: 129.7158 Evaluate side-chains 314 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 296 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 662 ARG Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 662 ARG Chi-restraints excluded: chain D residue 733 ARG Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 662 ARG Chi-restraints excluded: chain E residue 752 ILE Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 760 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 340 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 435 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 392 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 424 optimal weight: 1.9990 chunk 423 optimal weight: 4.9990 chunk 337 optimal weight: 0.0170 chunk 111 optimal weight: 7.9990 overall best weight: 2.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN B 337 GLN B 443 ASN C 91 ASN C 337 GLN D 91 ASN E 337 GLN E 443 ASN F 91 ASN F 337 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.177709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113526 restraints weight = 47380.044| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.54 r_work: 0.3199 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 36298 Z= 0.161 Angle : 0.583 9.596 49086 Z= 0.281 Chirality : 0.046 0.138 5496 Planarity : 0.004 0.054 6474 Dihedral : 7.774 118.476 5094 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.43 % Allowed : 5.44 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.24 (0.12), residues: 4494 helix: 0.85 (0.12), residues: 1830 sheet: 0.15 (0.21), residues: 654 loop : -1.21 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 599 TYR 0.016 0.001 TYR C 244 PHE 0.016 0.002 PHE D 674 TRP 0.008 0.002 TRP A 551 HIS 0.003 0.001 HIS F 183 Details of bonding type rmsd covalent geometry : bond 0.00401 (36294) covalent geometry : angle 0.58344 (49086) hydrogen bonds : bond 0.04179 ( 1356) hydrogen bonds : angle 3.91200 ( 3942) Misc. bond : bond 0.00132 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 300 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.6664 (mttp) cc_final: 0.6439 (ttpp) REVERT: A 285 ASN cc_start: 0.8210 (m-40) cc_final: 0.7996 (t0) REVERT: A 449 MET cc_start: 0.7991 (tpt) cc_final: 0.7723 (tpt) REVERT: A 561 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: A 711 ARG cc_start: 0.6977 (tmm160) cc_final: 0.6617 (tmm160) REVERT: A 720 MET cc_start: 0.4957 (mpp) cc_final: 0.4385 (mmm) REVERT: A 733 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8010 (mtt-85) REVERT: A 742 PHE cc_start: 0.7532 (m-80) cc_final: 0.7049 (m-10) REVERT: B 46 MET cc_start: 0.4488 (tpt) cc_final: 0.4281 (tpt) REVERT: B 205 ASP cc_start: 0.8806 (m-30) cc_final: 0.8559 (m-30) REVERT: B 285 ASN cc_start: 0.8272 (m-40) cc_final: 0.8003 (t0) REVERT: B 457 SER cc_start: 0.8899 (t) cc_final: 0.8334 (p) REVERT: C 62 LYS cc_start: 0.6866 (mttp) cc_final: 0.6493 (ttpp) REVERT: C 457 SER cc_start: 0.9016 (t) cc_final: 0.8484 (p) REVERT: C 611 MET cc_start: 0.7916 (tpp) cc_final: 0.7595 (ttp) REVERT: C 678 MET cc_start: 0.6896 (tpt) cc_final: 0.6685 (tpt) REVERT: C 720 MET cc_start: 0.5580 (mpp) cc_final: 0.4954 (mmm) REVERT: D 62 LYS cc_start: 0.6657 (mttp) cc_final: 0.6436 (ttpp) REVERT: D 285 ASN cc_start: 0.8211 (m-40) cc_final: 0.7985 (t0) REVERT: D 449 MET cc_start: 0.7993 (tpt) cc_final: 0.7728 (tpt) REVERT: D 561 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: D 711 ARG cc_start: 0.6975 (tmm160) cc_final: 0.6615 (tmm160) REVERT: D 720 MET cc_start: 0.4956 (mpp) cc_final: 0.4384 (mmm) REVERT: D 733 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8010 (mtt-85) REVERT: D 742 PHE cc_start: 0.7527 (m-80) cc_final: 0.7043 (m-10) REVERT: E 46 MET cc_start: 0.4480 (tpt) cc_final: 0.4277 (tpt) REVERT: E 205 ASP cc_start: 0.8804 (m-30) cc_final: 0.8558 (m-30) REVERT: E 285 ASN cc_start: 0.8276 (m-40) cc_final: 0.8000 (t0) REVERT: E 457 SER cc_start: 0.8898 (t) cc_final: 0.8332 (p) REVERT: F 62 LYS cc_start: 0.6868 (mttp) cc_final: 0.6495 (ttpp) REVERT: F 457 SER cc_start: 0.9019 (t) cc_final: 0.8482 (p) REVERT: F 611 MET cc_start: 0.7899 (tpp) cc_final: 0.7574 (ttp) REVERT: F 678 MET cc_start: 0.6873 (tpt) cc_final: 0.6659 (tpt) REVERT: F 720 MET cc_start: 0.5578 (mpp) cc_final: 0.4950 (mmm) REVERT: F 742 PHE cc_start: 0.7785 (m-80) cc_final: 0.7382 (m-10) outliers start: 55 outliers final: 34 residues processed: 338 average time/residue: 0.2322 time to fit residues: 124.3082 Evaluate side-chains 312 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 274 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 662 ARG Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain B residue 337 GLN Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 760 GLN Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 337 GLN Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 662 ARG Chi-restraints excluded: chain D residue 733 ARG Chi-restraints excluded: chain E residue 337 GLN Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 662 ARG Chi-restraints excluded: chain E residue 752 ILE Chi-restraints excluded: chain E residue 760 GLN Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 337 GLN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 760 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 100 optimal weight: 0.9990 chunk 437 optimal weight: 0.3980 chunk 383 optimal weight: 7.9990 chunk 267 optimal weight: 8.9990 chunk 355 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 264 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 343 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 337 GLN A 443 ASN C 91 ASN C 443 ASN D 91 ASN D 337 GLN D 443 ASN F 91 ASN F 443 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.178573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114523 restraints weight = 47233.035| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.53 r_work: 0.3215 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 36298 Z= 0.122 Angle : 0.547 8.940 49086 Z= 0.263 Chirality : 0.044 0.138 5496 Planarity : 0.004 0.052 6474 Dihedral : 7.531 116.811 5094 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.41 % Allowed : 6.12 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.01 (0.13), residues: 4494 helix: 0.97 (0.13), residues: 1866 sheet: 0.18 (0.21), residues: 654 loop : -0.96 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 147 TYR 0.013 0.001 TYR C 244 PHE 0.011 0.001 PHE E 516 TRP 0.006 0.001 TRP B 551 HIS 0.003 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00297 (36294) covalent geometry : angle 0.54666 (49086) hydrogen bonds : bond 0.03620 ( 1356) hydrogen bonds : angle 3.79573 ( 3942) Misc. bond : bond 0.00121 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 284 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.6638 (mttp) cc_final: 0.6412 (ttpp) REVERT: A 69 CYS cc_start: 0.7321 (p) cc_final: 0.7061 (p) REVERT: A 285 ASN cc_start: 0.8337 (m-40) cc_final: 0.8056 (t0) REVERT: A 449 MET cc_start: 0.8038 (tpt) cc_final: 0.7325 (tpt) REVERT: A 711 ARG cc_start: 0.7011 (tmm160) cc_final: 0.6560 (tmm160) REVERT: A 733 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8095 (mtt-85) REVERT: B 46 MET cc_start: 0.4350 (tpt) cc_final: 0.4060 (tpt) REVERT: B 204 ASP cc_start: 0.8504 (p0) cc_final: 0.8230 (p0) REVERT: B 205 ASP cc_start: 0.8915 (m-30) cc_final: 0.8596 (m-30) REVERT: B 285 ASN cc_start: 0.8343 (m-40) cc_final: 0.8048 (t0) REVERT: B 457 SER cc_start: 0.8950 (t) cc_final: 0.8439 (p) REVERT: C 62 LYS cc_start: 0.6937 (mttp) cc_final: 0.6535 (ttpp) REVERT: C 457 SER cc_start: 0.9084 (t) cc_final: 0.8577 (p) REVERT: C 611 MET cc_start: 0.8053 (tpp) cc_final: 0.7781 (ttp) REVERT: C 720 MET cc_start: 0.5656 (mpp) cc_final: 0.5158 (mmm) REVERT: C 733 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8093 (mtt-85) REVERT: D 62 LYS cc_start: 0.6628 (mttp) cc_final: 0.6410 (ttpp) REVERT: D 69 CYS cc_start: 0.7295 (p) cc_final: 0.7041 (p) REVERT: D 285 ASN cc_start: 0.8335 (m-40) cc_final: 0.8056 (t0) REVERT: D 449 MET cc_start: 0.8059 (tpt) cc_final: 0.7351 (tpt) REVERT: D 711 ARG cc_start: 0.7009 (tmm160) cc_final: 0.6558 (tmm160) REVERT: D 733 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8095 (mtt-85) REVERT: E 46 MET cc_start: 0.4344 (tpt) cc_final: 0.4062 (tpt) REVERT: E 204 ASP cc_start: 0.8505 (p0) cc_final: 0.8238 (p0) REVERT: E 205 ASP cc_start: 0.8915 (m-30) cc_final: 0.8597 (m-30) REVERT: E 285 ASN cc_start: 0.8335 (m-40) cc_final: 0.8031 (t0) REVERT: E 457 SER cc_start: 0.8949 (t) cc_final: 0.8438 (p) REVERT: F 62 LYS cc_start: 0.6930 (mttp) cc_final: 0.6528 (ttpp) REVERT: F 457 SER cc_start: 0.9080 (t) cc_final: 0.8568 (p) REVERT: F 611 MET cc_start: 0.8062 (tpp) cc_final: 0.7790 (ttp) REVERT: F 720 MET cc_start: 0.5658 (mpp) cc_final: 0.5158 (mmm) REVERT: F 733 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8073 (mtt-85) REVERT: F 742 PHE cc_start: 0.7820 (m-80) cc_final: 0.7422 (m-10) outliers start: 54 outliers final: 36 residues processed: 326 average time/residue: 0.2230 time to fit residues: 115.7641 Evaluate side-chains 315 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 275 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 662 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 733 ARG Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 337 GLN Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 662 ARG Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 733 ARG Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 662 ARG Chi-restraints excluded: chain E residue 752 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 733 ARG Chi-restraints excluded: chain F residue 760 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 376 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 391 optimal weight: 50.0000 chunk 74 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 208 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 300 optimal weight: 30.0000 chunk 357 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 440 optimal weight: 2.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 337 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN D 91 ASN D 337 GLN ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.174985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110119 restraints weight = 47295.968| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.69 r_work: 0.3132 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 36298 Z= 0.276 Angle : 0.664 11.078 49086 Z= 0.323 Chirality : 0.049 0.152 5496 Planarity : 0.005 0.060 6474 Dihedral : 7.833 119.371 5094 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.67 % Allowed : 6.95 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.20 (0.12), residues: 4494 helix: 0.70 (0.12), residues: 1866 sheet: 0.22 (0.21), residues: 612 loop : -1.00 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 599 TYR 0.016 0.002 TYR D 244 PHE 0.021 0.002 PHE F 682 TRP 0.013 0.003 TRP E 551 HIS 0.005 0.001 HIS F 183 Details of bonding type rmsd covalent geometry : bond 0.00691 (36294) covalent geometry : angle 0.66416 (49086) hydrogen bonds : bond 0.05272 ( 1356) hydrogen bonds : angle 4.08590 ( 3942) Misc. bond : bond 0.00188 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 279 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.6747 (mttp) cc_final: 0.6529 (ttpp) REVERT: A 69 CYS cc_start: 0.7416 (p) cc_final: 0.7140 (p) REVERT: A 285 ASN cc_start: 0.8282 (m-40) cc_final: 0.8076 (t0) REVERT: A 449 MET cc_start: 0.8009 (tpt) cc_final: 0.7766 (tpt) REVERT: A 711 ARG cc_start: 0.7077 (tmm160) cc_final: 0.6741 (tmm160) REVERT: A 733 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8062 (mtt-85) REVERT: A 742 PHE cc_start: 0.7630 (m-80) cc_final: 0.7180 (m-10) REVERT: B 46 MET cc_start: 0.4218 (tpt) cc_final: 0.3906 (tpt) REVERT: B 285 ASN cc_start: 0.8371 (m-40) cc_final: 0.8115 (t0) REVERT: C 62 LYS cc_start: 0.6998 (mttp) cc_final: 0.6589 (ttpp) REVERT: C 457 SER cc_start: 0.9026 (t) cc_final: 0.8467 (p) REVERT: C 611 MET cc_start: 0.7895 (tpp) cc_final: 0.7624 (ttp) REVERT: C 699 ILE cc_start: 0.8932 (mt) cc_final: 0.8728 (mt) REVERT: C 720 MET cc_start: 0.5607 (mpp) cc_final: 0.5075 (mmm) REVERT: C 733 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8099 (mtt-85) REVERT: D 62 LYS cc_start: 0.6747 (mttp) cc_final: 0.6531 (ttpp) REVERT: D 69 CYS cc_start: 0.7405 (p) cc_final: 0.7128 (p) REVERT: D 285 ASN cc_start: 0.8284 (m-40) cc_final: 0.8072 (t0) REVERT: D 449 MET cc_start: 0.8022 (tpt) cc_final: 0.7784 (tpt) REVERT: D 711 ARG cc_start: 0.7077 (tmm160) cc_final: 0.6741 (tmm160) REVERT: D 733 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8074 (mtt-85) REVERT: D 742 PHE cc_start: 0.7632 (m-80) cc_final: 0.7182 (m-10) REVERT: E 46 MET cc_start: 0.4217 (tpt) cc_final: 0.3903 (tpt) REVERT: E 285 ASN cc_start: 0.8371 (m-40) cc_final: 0.8114 (t0) REVERT: F 62 LYS cc_start: 0.6991 (mttp) cc_final: 0.6581 (ttpp) REVERT: F 457 SER cc_start: 0.9027 (t) cc_final: 0.8468 (p) REVERT: F 611 MET cc_start: 0.7915 (tpp) cc_final: 0.7644 (ttp) REVERT: F 699 ILE cc_start: 0.8922 (mt) cc_final: 0.8716 (mt) REVERT: F 720 MET cc_start: 0.5604 (mpp) cc_final: 0.5072 (mmm) REVERT: F 733 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.8073 (mtt-85) REVERT: F 742 PHE cc_start: 0.7788 (m-80) cc_final: 0.7350 (m-10) outliers start: 64 outliers final: 40 residues processed: 329 average time/residue: 0.2288 time to fit residues: 119.4313 Evaluate side-chains 309 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 265 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 662 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 760 GLN Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 337 GLN Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 733 ARG Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 662 ARG Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 733 ARG Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 662 ARG Chi-restraints excluded: chain E residue 752 ILE Chi-restraints excluded: chain E residue 760 GLN Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 337 GLN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 733 ARG Chi-restraints excluded: chain F residue 760 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 401 optimal weight: 0.9980 chunk 191 optimal weight: 30.0000 chunk 436 optimal weight: 0.0060 chunk 279 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 chunk 175 optimal weight: 0.0980 chunk 199 optimal weight: 2.9990 chunk 354 optimal weight: 2.9990 chunk 254 optimal weight: 10.0000 chunk 444 optimal weight: 5.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN C 443 ASN D 91 ASN F 91 ASN F 337 GLN F 443 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.177847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.113791 restraints weight = 47210.413| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.54 r_work: 0.3204 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 36298 Z= 0.115 Angle : 0.546 8.723 49086 Z= 0.264 Chirality : 0.044 0.138 5496 Planarity : 0.004 0.054 6474 Dihedral : 7.408 117.723 5094 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.17 % Allowed : 7.86 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 (0.13), residues: 4494 helix: 1.03 (0.13), residues: 1872 sheet: 0.08 (0.21), residues: 654 loop : -0.76 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 239 TYR 0.017 0.001 TYR E 244 PHE 0.009 0.001 PHE C 516 TRP 0.006 0.001 TRP E 551 HIS 0.003 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00272 (36294) covalent geometry : angle 0.54568 (49086) hydrogen bonds : bond 0.03527 ( 1356) hydrogen bonds : angle 3.79066 ( 3942) Misc. bond : bond 0.00093 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 279 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.6662 (mttp) cc_final: 0.6458 (ttpp) REVERT: A 69 CYS cc_start: 0.7348 (p) cc_final: 0.7027 (p) REVERT: A 152 PHE cc_start: 0.5586 (p90) cc_final: 0.5162 (p90) REVERT: A 285 ASN cc_start: 0.8204 (m-40) cc_final: 0.7970 (t0) REVERT: A 417 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7597 (tt0) REVERT: A 449 MET cc_start: 0.7934 (tpt) cc_final: 0.7714 (tpt) REVERT: A 711 ARG cc_start: 0.6996 (tmm160) cc_final: 0.6543 (tmm160) REVERT: A 733 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8030 (mtt-85) REVERT: B 46 MET cc_start: 0.4384 (tpt) cc_final: 0.4120 (tpt) REVERT: B 205 ASP cc_start: 0.8775 (m-30) cc_final: 0.8572 (m-30) REVERT: B 285 ASN cc_start: 0.8243 (m-40) cc_final: 0.7978 (t0) REVERT: B 733 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7977 (mtt-85) REVERT: C 62 LYS cc_start: 0.6979 (mttp) cc_final: 0.6592 (ttpp) REVERT: C 236 LYS cc_start: 0.8264 (tttt) cc_final: 0.8002 (tttm) REVERT: C 457 SER cc_start: 0.8980 (t) cc_final: 0.8411 (p) REVERT: C 720 MET cc_start: 0.5678 (mpp) cc_final: 0.5228 (mmm) REVERT: D 62 LYS cc_start: 0.6659 (mttp) cc_final: 0.6457 (ttpp) REVERT: D 69 CYS cc_start: 0.7350 (p) cc_final: 0.7032 (p) REVERT: D 152 PHE cc_start: 0.5561 (p90) cc_final: 0.5140 (p90) REVERT: D 285 ASN cc_start: 0.8207 (m-40) cc_final: 0.7962 (t0) REVERT: D 417 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7593 (tt0) REVERT: D 449 MET cc_start: 0.7958 (tpt) cc_final: 0.7741 (tpt) REVERT: D 711 ARG cc_start: 0.6990 (tmm160) cc_final: 0.6538 (tmm160) REVERT: D 733 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8031 (mtt-85) REVERT: E 46 MET cc_start: 0.4375 (tpt) cc_final: 0.4112 (tpt) REVERT: E 205 ASP cc_start: 0.8769 (m-30) cc_final: 0.8567 (m-30) REVERT: E 285 ASN cc_start: 0.8243 (m-40) cc_final: 0.7976 (t0) REVERT: E 733 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7977 (mtt-85) REVERT: F 62 LYS cc_start: 0.6978 (mttp) cc_final: 0.6590 (ttpp) REVERT: F 236 LYS cc_start: 0.8259 (tttt) cc_final: 0.7999 (tttm) REVERT: F 457 SER cc_start: 0.8980 (t) cc_final: 0.8409 (p) REVERT: F 720 MET cc_start: 0.5675 (mpp) cc_final: 0.5227 (mmm) REVERT: F 742 PHE cc_start: 0.7770 (m-80) cc_final: 0.7295 (m-10) outliers start: 45 outliers final: 34 residues processed: 315 average time/residue: 0.2453 time to fit residues: 121.7608 Evaluate side-chains 295 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 662 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain B residue 733 ARG Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 662 ARG Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 733 ARG Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 662 ARG Chi-restraints excluded: chain E residue 733 ARG Chi-restraints excluded: chain E residue 752 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 760 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 297 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 329 optimal weight: 0.9990 chunk 444 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 chunk 335 optimal weight: 0.0670 chunk 168 optimal weight: 0.6980 chunk 439 optimal weight: 6.9990 chunk 325 optimal weight: 5.9990 chunk 170 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN B 337 GLN C 91 ASN D 91 ASN E 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.178549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115084 restraints weight = 47117.775| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.77 r_work: 0.3199 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 36298 Z= 0.102 Angle : 0.527 8.359 49086 Z= 0.254 Chirality : 0.044 0.137 5496 Planarity : 0.004 0.053 6474 Dihedral : 7.175 114.609 5094 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.35 % Allowed : 7.94 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.43 (0.13), residues: 4494 helix: 1.23 (0.13), residues: 1872 sheet: 0.28 (0.21), residues: 648 loop : -0.59 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 89 TYR 0.019 0.001 TYR B 244 PHE 0.018 0.001 PHE D 674 TRP 0.005 0.001 TRP D 551 HIS 0.003 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00241 (36294) covalent geometry : angle 0.52713 (49086) hydrogen bonds : bond 0.03179 ( 1356) hydrogen bonds : angle 3.66380 ( 3942) Misc. bond : bond 0.00095 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 272 time to evaluate : 1.294 Fit side-chains REVERT: A 62 LYS cc_start: 0.6666 (mttp) cc_final: 0.6462 (ttpp) REVERT: A 69 CYS cc_start: 0.7345 (p) cc_final: 0.7023 (p) REVERT: A 152 PHE cc_start: 0.5538 (p90) cc_final: 0.5138 (p90) REVERT: A 285 ASN cc_start: 0.8200 (m-40) cc_final: 0.7983 (t0) REVERT: A 449 MET cc_start: 0.7921 (tpt) cc_final: 0.7265 (tpt) REVERT: B 46 MET cc_start: 0.4358 (tpt) cc_final: 0.4094 (tpt) REVERT: B 205 ASP cc_start: 0.8786 (m-30) cc_final: 0.8586 (m-30) REVERT: B 285 ASN cc_start: 0.8254 (m-40) cc_final: 0.8013 (t0) REVERT: B 633 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8904 (tp) REVERT: B 733 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.8002 (mtt-85) REVERT: C 62 LYS cc_start: 0.7008 (mttp) cc_final: 0.6607 (ttpp) REVERT: C 69 CYS cc_start: 0.7735 (p) cc_final: 0.7445 (p) REVERT: C 236 LYS cc_start: 0.8262 (tttt) cc_final: 0.7983 (tttm) REVERT: C 457 SER cc_start: 0.8962 (t) cc_final: 0.8409 (p) REVERT: C 720 MET cc_start: 0.5652 (mpp) cc_final: 0.5213 (mmm) REVERT: D 69 CYS cc_start: 0.7341 (p) cc_final: 0.7018 (p) REVERT: D 152 PHE cc_start: 0.5533 (p90) cc_final: 0.5132 (p90) REVERT: D 285 ASN cc_start: 0.8206 (m-40) cc_final: 0.7978 (t0) REVERT: D 449 MET cc_start: 0.7942 (tpt) cc_final: 0.7287 (tpt) REVERT: E 46 MET cc_start: 0.4337 (tpt) cc_final: 0.4080 (tpt) REVERT: E 285 ASN cc_start: 0.8250 (m-40) cc_final: 0.8008 (t0) REVERT: E 633 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8903 (tp) REVERT: E 733 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7994 (mtt-85) REVERT: F 62 LYS cc_start: 0.7002 (mttp) cc_final: 0.6600 (ttpp) REVERT: F 69 CYS cc_start: 0.7748 (p) cc_final: 0.7459 (p) REVERT: F 236 LYS cc_start: 0.8260 (tttt) cc_final: 0.7976 (tttm) REVERT: F 457 SER cc_start: 0.8962 (t) cc_final: 0.8408 (p) REVERT: F 720 MET cc_start: 0.5653 (mpp) cc_final: 0.5213 (mmm) REVERT: F 742 PHE cc_start: 0.7771 (m-80) cc_final: 0.7312 (m-10) outliers start: 52 outliers final: 36 residues processed: 312 average time/residue: 0.2326 time to fit residues: 115.8697 Evaluate side-chains 297 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 257 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 662 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 337 GLN Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain B residue 733 ARG Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 662 ARG Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain E residue 337 GLN Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 662 ARG Chi-restraints excluded: chain E residue 733 ARG Chi-restraints excluded: chain E residue 752 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 760 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 17 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 140 optimal weight: 0.0370 chunk 146 optimal weight: 7.9990 chunk 402 optimal weight: 1.9990 chunk 235 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 252 optimal weight: 0.7980 chunk 296 optimal weight: 0.9980 overall best weight: 1.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN D 337 GLN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.177669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113276 restraints weight = 47206.081| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.55 r_work: 0.3196 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 36298 Z= 0.149 Angle : 0.562 9.095 49086 Z= 0.270 Chirality : 0.045 0.141 5496 Planarity : 0.004 0.054 6474 Dihedral : 7.197 114.138 5094 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.20 % Allowed : 8.31 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.45 (0.13), residues: 4494 helix: 1.17 (0.13), residues: 1872 sheet: 0.57 (0.22), residues: 606 loop : -0.57 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 753 TYR 0.020 0.001 TYR E 244 PHE 0.011 0.001 PHE C 516 TRP 0.008 0.002 TRP E 551 HIS 0.003 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00371 (36294) covalent geometry : angle 0.56239 (49086) hydrogen bonds : bond 0.03680 ( 1356) hydrogen bonds : angle 3.72313 ( 3942) Misc. bond : bond 0.00120 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 265 time to evaluate : 1.386 Fit side-chains REVERT: A 69 CYS cc_start: 0.7393 (p) cc_final: 0.7051 (p) REVERT: A 152 PHE cc_start: 0.5582 (p90) cc_final: 0.5175 (p90) REVERT: A 285 ASN cc_start: 0.8207 (m-40) cc_final: 0.8005 (t0) REVERT: A 449 MET cc_start: 0.7932 (tpt) cc_final: 0.7726 (tpt) REVERT: A 742 PHE cc_start: 0.7618 (m-80) cc_final: 0.7200 (m-10) REVERT: B 46 MET cc_start: 0.4362 (tpt) cc_final: 0.4070 (tpt) REVERT: B 285 ASN cc_start: 0.8242 (m-40) cc_final: 0.7991 (t0) REVERT: B 633 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8909 (tp) REVERT: B 733 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7977 (mtt-85) REVERT: C 62 LYS cc_start: 0.7022 (mttp) cc_final: 0.6612 (ttpp) REVERT: C 69 CYS cc_start: 0.7764 (p) cc_final: 0.7526 (p) REVERT: C 236 LYS cc_start: 0.8288 (tttt) cc_final: 0.8046 (tttm) REVERT: C 457 SER cc_start: 0.9001 (t) cc_final: 0.8434 (p) REVERT: C 720 MET cc_start: 0.5650 (mpp) cc_final: 0.5216 (mmm) REVERT: D 69 CYS cc_start: 0.7394 (p) cc_final: 0.7056 (p) REVERT: D 152 PHE cc_start: 0.5579 (p90) cc_final: 0.5170 (p90) REVERT: D 285 ASN cc_start: 0.8214 (m-40) cc_final: 0.7999 (t0) REVERT: D 449 MET cc_start: 0.7944 (tpt) cc_final: 0.7740 (tpt) REVERT: D 742 PHE cc_start: 0.7612 (m-80) cc_final: 0.7199 (m-10) REVERT: E 46 MET cc_start: 0.4351 (tpt) cc_final: 0.4067 (tpt) REVERT: E 285 ASN cc_start: 0.8239 (m-40) cc_final: 0.7988 (t0) REVERT: E 633 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8907 (tp) REVERT: E 733 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7986 (mtt-85) REVERT: F 62 LYS cc_start: 0.7014 (mttp) cc_final: 0.6604 (ttpp) REVERT: F 69 CYS cc_start: 0.7755 (p) cc_final: 0.7516 (p) REVERT: F 236 LYS cc_start: 0.8283 (tttt) cc_final: 0.8041 (tttm) REVERT: F 457 SER cc_start: 0.9000 (t) cc_final: 0.8434 (p) REVERT: F 720 MET cc_start: 0.5647 (mpp) cc_final: 0.5214 (mmm) REVERT: F 742 PHE cc_start: 0.7823 (m-80) cc_final: 0.7392 (m-10) outliers start: 46 outliers final: 36 residues processed: 299 average time/residue: 0.2274 time to fit residues: 108.7281 Evaluate side-chains 291 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 251 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 662 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain B residue 733 ARG Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 337 GLN Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 662 ARG Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 662 ARG Chi-restraints excluded: chain E residue 733 ARG Chi-restraints excluded: chain E residue 752 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 760 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 125 optimal weight: 0.9990 chunk 366 optimal weight: 0.9990 chunk 274 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 310 optimal weight: 9.9990 chunk 246 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 150 optimal weight: 30.0000 chunk 406 optimal weight: 5.9990 chunk 320 optimal weight: 0.0170 chunk 255 optimal weight: 3.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 ASN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.177844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113775 restraints weight = 47197.813| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.66 r_work: 0.3187 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 36298 Z= 0.152 Angle : 0.743 59.148 49086 Z= 0.400 Chirality : 0.045 0.459 5496 Planarity : 0.004 0.054 6474 Dihedral : 7.191 114.140 5094 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.15 % Allowed : 8.44 % Favored : 90.42 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 7.32 % 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: 0.47 (0.13), residues: 4494 helix: 1.20 (0.13), residues: 1872 sheet: 0.57 (0.22), residues: 606 loop : -0.57 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 753 TYR 0.018 0.001 TYR E 244 PHE 0.010 0.001 PHE E 516 TRP 0.007 0.001 TRP E 551 HIS 0.003 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00350 (36294) covalent geometry : angle 0.74279 (49086) hydrogen bonds : bond 0.03586 ( 1356) hydrogen bonds : angle 3.72458 ( 3942) Misc. bond : bond 0.00100 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8988 Ramachandran restraints generated. 4494 Oldfield, 0 Emsley, 4494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 1.290 Fit side-chains REVERT: A 69 CYS cc_start: 0.7340 (p) cc_final: 0.6995 (p) REVERT: A 152 PHE cc_start: 0.5490 (p90) cc_final: 0.5090 (p90) REVERT: A 285 ASN cc_start: 0.8213 (m-40) cc_final: 0.7997 (t0) REVERT: A 449 MET cc_start: 0.7915 (tpt) cc_final: 0.7254 (tpt) REVERT: A 742 PHE cc_start: 0.7612 (m-80) cc_final: 0.7188 (m-10) REVERT: B 46 MET cc_start: 0.4337 (tpt) cc_final: 0.4056 (tpt) REVERT: B 285 ASN cc_start: 0.8239 (m-40) cc_final: 0.7985 (t0) REVERT: B 633 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8904 (tp) REVERT: B 733 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7971 (mtt-85) REVERT: C 62 LYS cc_start: 0.6979 (mttp) cc_final: 0.6578 (ttpp) REVERT: C 69 CYS cc_start: 0.7721 (p) cc_final: 0.7474 (p) REVERT: C 236 LYS cc_start: 0.8297 (tttt) cc_final: 0.8050 (tttm) REVERT: C 457 SER cc_start: 0.9003 (t) cc_final: 0.8432 (p) REVERT: C 720 MET cc_start: 0.5655 (mpp) cc_final: 0.5223 (mmm) REVERT: D 69 CYS cc_start: 0.7334 (p) cc_final: 0.6990 (p) REVERT: D 152 PHE cc_start: 0.5486 (p90) cc_final: 0.5087 (p90) REVERT: D 285 ASN cc_start: 0.8215 (m-40) cc_final: 0.7992 (t0) REVERT: D 449 MET cc_start: 0.7933 (tpt) cc_final: 0.7272 (tpt) REVERT: D 742 PHE cc_start: 0.7607 (m-80) cc_final: 0.7187 (m-10) REVERT: E 46 MET cc_start: 0.4326 (tpt) cc_final: 0.4049 (tpt) REVERT: E 285 ASN cc_start: 0.8235 (m-40) cc_final: 0.7979 (t0) REVERT: E 633 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8901 (tp) REVERT: E 733 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7978 (mtt-85) REVERT: F 62 LYS cc_start: 0.6967 (mttp) cc_final: 0.6569 (ttpp) REVERT: F 69 CYS cc_start: 0.7713 (p) cc_final: 0.7475 (p) REVERT: F 236 LYS cc_start: 0.8292 (tttt) cc_final: 0.8046 (tttm) REVERT: F 457 SER cc_start: 0.9003 (t) cc_final: 0.8431 (p) REVERT: F 720 MET cc_start: 0.5654 (mpp) cc_final: 0.5221 (mmm) REVERT: F 742 PHE cc_start: 0.7827 (m-80) cc_final: 0.7391 (m-10) outliers start: 44 outliers final: 36 residues processed: 284 average time/residue: 0.2280 time to fit residues: 103.5818 Evaluate side-chains 288 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 248 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 662 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain B residue 733 ARG Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 662 ARG Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 662 ARG Chi-restraints excluded: chain E residue 733 ARG Chi-restraints excluded: chain E residue 752 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 760 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 241 optimal weight: 0.1980 chunk 128 optimal weight: 2.9990 chunk 167 optimal weight: 20.0000 chunk 256 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 382 optimal weight: 9.9990 chunk 381 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 282 optimal weight: 9.9990 chunk 193 optimal weight: 8.9990 chunk 410 optimal weight: 0.7980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN D 568 GLN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 ASN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.177836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.113642 restraints weight = 47041.511| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.53 r_work: 0.3200 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 36298 Z= 0.152 Angle : 0.743 59.148 49086 Z= 0.400 Chirality : 0.045 0.459 5496 Planarity : 0.004 0.054 6474 Dihedral : 7.191 114.140 5094 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.15 % Allowed : 8.44 % Favored : 90.42 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 7.32 % 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: 0.47 (0.13), residues: 4494 helix: 1.20 (0.13), residues: 1872 sheet: 0.57 (0.22), residues: 606 loop : -0.57 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 753 TYR 0.018 0.001 TYR E 244 PHE 0.010 0.001 PHE E 516 TRP 0.007 0.001 TRP E 551 HIS 0.003 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00350 (36294) covalent geometry : angle 0.74279 (49086) hydrogen bonds : bond 0.03586 ( 1356) hydrogen bonds : angle 3.72458 ( 3942) Misc. bond : bond 0.00100 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9151.68 seconds wall clock time: 156 minutes 32.44 seconds (9392.44 seconds total)