Starting phenix.real_space_refine on Tue Sep 15 04:54:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vct_31895/09_2026/7vct_31895.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vct_31895/09_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_31895/09_2026/7vct_31895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vct_31895/09_2026/7vct_31895.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vct_31895/09_2026/7vct_31895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vct_31895/09_2026/7vct_31895.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vct_31895/09_2026/7vct_31895.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vct_31895/09_2026/7vct_31895.cif" } 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): 0.15s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 7.03, 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: 2.88 Conformation dependent library (CDL) restraints added in 1.2 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: 1.20 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: 8.24 Time building geometry restraints manager: 3.87 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: 22090 24.70 - 49.39: 351 49.39 - 74.09: 18 74.09 - 98.78: 6 98.78 - 123.48: 11 Dihedral angle restraints: 22476 sinusoidal: 9498 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 22473 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: 0.12 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 31.950 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 : 9.641 123.478 14064 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/Z covalent geometry : bond 0.00677 / 0.29 (36294) covalent geometry : angle 0.94127 / 0.52 (49086) hydrogen bonds : bond 0.15779 / 10.44 ( 1356) hydrogen bonds : angle 6.08742 / 4.25 ( 3942) Misc. bond : bond 0.46232 / 23.07 ( 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 : 1.409 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: 0.3198 time to fit residues: 305.1526 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 : 1.470 ------------------------------------------------------------------------------- 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... 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 = 0.179073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.115141 restraints weight = 47023.880| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.87 r_work: 0.3186 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2156 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= 0.163 Angle : 0.620 10.028 49086 Z= 0.303 Chirality : 0.046 0.141 5496 Planarity : 0.006 0.061 6474 Dihedral : 8.327 133.058 5028 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.94 % Allowed : 3.91 % Favored : 95.16 % 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: -1.42 (0.11), residues: 4494 helix: -0.34 (0.11), residues: 1794 sheet: 0.07 (0.20), residues: 654 loop : -1.82 (0.12), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 147 TYR 0.018 0.001 TYR C 244 PHE 0.021 0.002 PHE D 674 TRP 0.007 0.001 TRP E 476 HIS 0.004 0.001 HIS B 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 (36294) covalent geometry : angle 0.62003 / 0.30 (49086) hydrogen bonds : bond 0.04696 / 3.15 ( 1356) hydrogen bonds : angle 4.30909 / 3.02 ( 3942) Misc. bond : bond 0.00088 / 0.04 ( 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 385 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 349 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.6579 (mttp) cc_final: 0.6366 (ttpp) REVERT: A 285 ASN cc_start: 0.8238 (m-40) cc_final: 0.8004 (t0) REVERT: A 449 MET cc_start: 0.8078 (tpt) cc_final: 0.7298 (tpp) REVERT: A 457 SER cc_start: 0.9041 (t) cc_final: 0.8601 (p) REVERT: A 561 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8377 (mp0) REVERT: A 611 MET cc_start: 0.8105 (tpp) cc_final: 0.7843 (ttp) REVERT: A 720 MET cc_start: 0.4953 (mpp) cc_final: 0.4414 (mmm) REVERT: A 733 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7935 (mtt-85) REVERT: A 742 PHE cc_start: 0.7430 (m-80) cc_final: 0.6873 (m-10) REVERT: B 285 ASN cc_start: 0.8313 (m-40) cc_final: 0.8003 (t0) REVERT: B 442 MET cc_start: 0.7295 (ppp) cc_final: 0.7014 (ttm) REVERT: B 457 SER cc_start: 0.8881 (t) cc_final: 0.8385 (p) REVERT: B 561 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8419 (mp0) REVERT: C 62 LYS cc_start: 0.6776 (mttp) cc_final: 0.6447 (ttpp) REVERT: C 457 SER cc_start: 0.8919 (t) cc_final: 0.8436 (p) REVERT: C 611 MET cc_start: 0.8045 (tpp) cc_final: 0.7425 (ttp) REVERT: C 678 MET cc_start: 0.6983 (tpt) cc_final: 0.6759 (tpt) REVERT: C 720 MET cc_start: 0.5598 (mpp) cc_final: 0.5078 (mmm) REVERT: D 62 LYS cc_start: 0.6589 (mttp) cc_final: 0.6370 (ttpp) REVERT: D 285 ASN cc_start: 0.8245 (m-40) cc_final: 0.8005 (t0) REVERT: D 449 MET cc_start: 0.8080 (tpt) cc_final: 0.7296 (tpp) REVERT: D 457 SER cc_start: 0.9047 (t) cc_final: 0.8601 (p) REVERT: D 561 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8373 (mp0) REVERT: D 611 MET cc_start: 0.8098 (tpp) cc_final: 0.7837 (ttp) REVERT: D 720 MET cc_start: 0.4953 (mpp) cc_final: 0.4416 (mmm) REVERT: D 733 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7931 (mtt-85) REVERT: D 742 PHE cc_start: 0.7430 (m-80) cc_final: 0.6873 (m-10) REVERT: E 285 ASN cc_start: 0.8313 (m-40) cc_final: 0.7998 (t0) REVERT: E 442 MET cc_start: 0.7287 (ppp) cc_final: 0.7010 (ttm) REVERT: E 457 SER cc_start: 0.8883 (t) cc_final: 0.8385 (p) REVERT: E 561 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8417 (mp0) REVERT: F 62 LYS cc_start: 0.6755 (mttp) cc_final: 0.6431 (ttpp) REVERT: F 457 SER cc_start: 0.8911 (t) cc_final: 0.8424 (p) REVERT: F 611 MET cc_start: 0.8053 (tpp) cc_final: 0.7433 (ttp) REVERT: F 678 MET cc_start: 0.6979 (tpt) cc_final: 0.6754 (tpt) REVERT: F 720 MET cc_start: 0.5600 (mpp) cc_final: 0.5086 (mmm) REVERT: F 742 PHE cc_start: 0.7898 (m-80) cc_final: 0.7533 (m-10) outliers start: 36 outliers final: 24 residues processed: 379 average time/residue: 0.2664 time to fit residues: 157.0123 Evaluate side-chains 313 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 287 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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: 1.9990 chunk 265 optimal weight: 9.9990 chunk 376 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 334 optimal weight: 0.0030 chunk 425 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 96 optimal weight: 0.0670 chunk 178 optimal weight: 1.9990 chunk 372 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.8132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 GLN A 443 ASN B 337 GLN B 443 ASN C 337 GLN C 443 ASN C 568 GLN D 337 GLN D 443 ASN E 337 GLN E 443 ASN F 337 GLN F 443 ASN F 568 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.180373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.116840 restraints weight = 46922.952| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.82 r_work: 0.3223 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 36298 Z= 0.106 Angle : 0.560 8.817 49086 Z= 0.271 Chirality : 0.044 0.136 5496 Planarity : 0.004 0.052 6474 Dihedral : 7.658 120.305 5028 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.83 % Allowed : 4.84 % Favored : 94.32 % 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: -0.62 (0.12), residues: 4494 helix: 0.48 (0.12), residues: 1830 sheet: 0.16 (0.20), residues: 660 loop : -1.44 (0.12), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 753 TYR 0.015 0.001 TYR F 244 PHE 0.011 0.001 PHE E 516 TRP 0.004 0.001 TRP D 551 HIS 0.003 0.001 HIS B 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (36294) covalent geometry : angle 0.55974 / 0.27 (49086) hydrogen bonds : bond 0.03505 / 2.34 ( 1356) hydrogen bonds : angle 3.93448 / 2.77 ( 3942) Misc. bond : bond 0.00120 / 0.06 ( 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: 32 poor density : 312 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.6637 (mttp) cc_final: 0.6418 (ttpp) REVERT: A 285 ASN cc_start: 0.8196 (m-40) cc_final: 0.7959 (t0) REVERT: A 449 MET cc_start: 0.8062 (tpt) cc_final: 0.7789 (tpp) REVERT: A 457 SER cc_start: 0.9134 (t) cc_final: 0.8664 (p) REVERT: A 611 MET cc_start: 0.8123 (tpp) cc_final: 0.7896 (ttp) REVERT: A 711 ARG cc_start: 0.6986 (tmm160) cc_final: 0.6548 (tmm160) REVERT: A 720 MET cc_start: 0.4914 (mpp) cc_final: 0.4193 (mmm) REVERT: A 733 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7939 (mtt-85) REVERT: A 742 PHE cc_start: 0.7527 (m-80) cc_final: 0.6976 (m-10) REVERT: B 69 CYS cc_start: 0.7240 (p) cc_final: 0.6928 (p) REVERT: B 285 ASN cc_start: 0.8209 (m-40) cc_final: 0.7920 (t0) REVERT: B 332 MET cc_start: 0.8744 (mmm) cc_final: 0.8529 (mtp) REVERT: B 457 SER cc_start: 0.8808 (t) cc_final: 0.8342 (p) REVERT: B 561 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8426 (mp0) REVERT: C 62 LYS cc_start: 0.6812 (mttp) cc_final: 0.6480 (ttpp) REVERT: C 449 MET cc_start: 0.7787 (tpt) cc_final: 0.7553 (tpt) REVERT: C 454 TRP cc_start: 0.8472 (t60) cc_final: 0.8268 (t60) REVERT: C 457 SER cc_start: 0.8971 (t) cc_final: 0.8474 (p) REVERT: C 611 MET cc_start: 0.7998 (tpp) cc_final: 0.7628 (ttp) REVERT: C 678 MET cc_start: 0.6901 (tpt) cc_final: 0.6697 (tpt) REVERT: C 720 MET cc_start: 0.5583 (mpp) cc_final: 0.5321 (mmm) REVERT: D 62 LYS cc_start: 0.6629 (mttp) cc_final: 0.6414 (ttpp) REVERT: D 285 ASN cc_start: 0.8192 (m-40) cc_final: 0.7952 (t0) REVERT: D 449 MET cc_start: 0.8068 (tpt) cc_final: 0.7793 (tpp) REVERT: D 457 SER cc_start: 0.9137 (t) cc_final: 0.8667 (p) REVERT: D 611 MET cc_start: 0.8127 (tpp) cc_final: 0.7901 (ttp) REVERT: D 711 ARG cc_start: 0.6984 (tmm160) cc_final: 0.6548 (tmm160) REVERT: D 720 MET cc_start: 0.4918 (mpp) cc_final: 0.4197 (mmm) REVERT: D 733 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7950 (mtt-85) REVERT: D 742 PHE cc_start: 0.7527 (m-80) cc_final: 0.6977 (m-10) REVERT: E 69 CYS cc_start: 0.7241 (p) cc_final: 0.6933 (p) REVERT: E 285 ASN cc_start: 0.8210 (m-40) cc_final: 0.7916 (t0) REVERT: E 332 MET cc_start: 0.8746 (mmm) cc_final: 0.8528 (mtp) REVERT: E 457 SER cc_start: 0.8807 (t) cc_final: 0.8336 (p) REVERT: E 561 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8422 (mp0) REVERT: F 62 LYS cc_start: 0.6801 (mttp) cc_final: 0.6470 (ttpp) REVERT: F 449 MET cc_start: 0.7768 (tpt) cc_final: 0.7536 (tpt) REVERT: F 454 TRP cc_start: 0.8472 (t60) cc_final: 0.8262 (t60) REVERT: F 457 SER cc_start: 0.8962 (t) cc_final: 0.8460 (p) REVERT: F 611 MET cc_start: 0.8013 (tpp) cc_final: 0.7640 (ttp) REVERT: F 678 MET cc_start: 0.6896 (tpt) cc_final: 0.6690 (tpt) REVERT: F 720 MET cc_start: 0.5581 (mpp) cc_final: 0.5318 (mmm) REVERT: F 742 PHE cc_start: 0.7838 (m-80) cc_final: 0.7414 (m-10) outliers start: 32 outliers final: 18 residues processed: 334 average time/residue: 0.2454 time to fit residues: 130.0259 Evaluate side-chains 309 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 289 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 337 GLN 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 337 GLN 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: 9.9990 chunk 121 optimal weight: 7.9990 chunk 435 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 392 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 424 optimal weight: 1.9990 chunk 423 optimal weight: 4.9990 chunk 337 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN A 443 ASN B 337 GLN C 91 ASN C 337 GLN D 91 ASN E 337 GLN F 91 ASN F 337 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.176625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112125 restraints weight = 47393.186| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.81 r_work: 0.3153 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 36298 Z= 0.223 Angle : 0.625 10.752 49086 Z= 0.303 Chirality : 0.047 0.145 5496 Planarity : 0.005 0.056 6474 Dihedral : 7.529 120.453 5028 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.41 % Allowed : 5.52 % Favored : 93.07 % 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 (0.12), residues: 4494 helix: 0.67 (0.12), residues: 1830 sheet: 0.08 (0.20), residues: 654 loop : -1.33 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 599 TYR 0.016 0.002 TYR C 244 PHE 0.017 0.002 PHE E 516 TRP 0.010 0.002 TRP B 551 HIS 0.004 0.001 HIS F 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.22 (36294) covalent geometry : angle 0.62488 / 0.30 (49086) hydrogen bonds : bond 0.04770 / 3.18 ( 1356) hydrogen bonds : angle 4.04129 / 2.83 ( 3942) Misc. bond : bond 0.00149 / 0.07 ( 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 345 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 291 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.6656 (mttp) cc_final: 0.6439 (ttpp) REVERT: A 285 ASN cc_start: 0.8256 (m-40) cc_final: 0.8041 (t0) REVERT: A 449 MET cc_start: 0.8031 (tpt) cc_final: 0.7765 (tpt) REVERT: A 551 TRP cc_start: 0.8637 (t-100) cc_final: 0.8406 (t60) REVERT: A 711 ARG cc_start: 0.7036 (tmm160) cc_final: 0.6666 (tmm160) REVERT: A 720 MET cc_start: 0.4681 (mpp) cc_final: 0.4206 (mmm) REVERT: A 733 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7932 (mtt-85) REVERT: A 742 PHE cc_start: 0.7595 (m-80) cc_final: 0.7100 (m-10) REVERT: B 46 MET cc_start: 0.4633 (tpt) cc_final: 0.4229 (tpt) REVERT: B 69 CYS cc_start: 0.7308 (p) cc_final: 0.7077 (p) REVERT: B 285 ASN cc_start: 0.8339 (m-40) cc_final: 0.8065 (t0) REVERT: B 457 SER cc_start: 0.8936 (t) cc_final: 0.8379 (p) REVERT: C 62 LYS cc_start: 0.6924 (mttp) cc_final: 0.6547 (ttpp) REVERT: C 457 SER cc_start: 0.9042 (t) cc_final: 0.8512 (p) REVERT: C 611 MET cc_start: 0.7933 (tpp) cc_final: 0.7582 (ttp) REVERT: C 678 MET cc_start: 0.6931 (tpt) cc_final: 0.6717 (tpt) REVERT: C 699 ILE cc_start: 0.8897 (mt) cc_final: 0.8691 (mt) REVERT: C 720 MET cc_start: 0.5619 (mpp) cc_final: 0.4989 (mmm) REVERT: D 62 LYS cc_start: 0.6652 (mttp) cc_final: 0.6437 (ttpp) REVERT: D 285 ASN cc_start: 0.8263 (m-40) cc_final: 0.8040 (t0) REVERT: D 449 MET cc_start: 0.8038 (tpt) cc_final: 0.7772 (tpt) REVERT: D 551 TRP cc_start: 0.8633 (t-100) cc_final: 0.8403 (t60) REVERT: D 711 ARG cc_start: 0.7034 (tmm160) cc_final: 0.6663 (tmm160) REVERT: D 720 MET cc_start: 0.4680 (mpp) cc_final: 0.4205 (mmm) REVERT: D 733 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7930 (mtt-85) REVERT: D 742 PHE cc_start: 0.7588 (m-80) cc_final: 0.7092 (m-10) REVERT: E 46 MET cc_start: 0.4627 (tpt) cc_final: 0.4222 (tpt) REVERT: E 69 CYS cc_start: 0.7301 (p) cc_final: 0.7073 (p) REVERT: E 285 ASN cc_start: 0.8337 (m-40) cc_final: 0.8061 (t0) REVERT: E 457 SER cc_start: 0.8931 (t) cc_final: 0.8372 (p) REVERT: F 62 LYS cc_start: 0.6930 (mttp) cc_final: 0.6551 (ttpp) REVERT: F 457 SER cc_start: 0.9038 (t) cc_final: 0.8505 (p) REVERT: F 611 MET cc_start: 0.7933 (tpp) cc_final: 0.7580 (ttp) REVERT: F 678 MET cc_start: 0.6917 (tpt) cc_final: 0.6701 (tpt) REVERT: F 699 ILE cc_start: 0.8896 (mt) cc_final: 0.8691 (mt) REVERT: F 720 MET cc_start: 0.5616 (mpp) cc_final: 0.4984 (mmm) REVERT: F 742 PHE cc_start: 0.7805 (m-80) cc_final: 0.7416 (m-10) outliers start: 54 outliers final: 38 residues processed: 335 average time/residue: 0.2299 time to fit residues: 123.7907 Evaluate side-chains 306 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 266 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 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 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 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 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 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 760 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 100 optimal weight: 0.8980 chunk 437 optimal weight: 0.7980 chunk 383 optimal weight: 0.0010 chunk 267 optimal weight: 0.8980 chunk 355 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 264 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 343 optimal weight: 3.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN B 337 GLN C 91 ASN C 443 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN E 337 GLN F 91 ASN F 443 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.179399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.115719 restraints weight = 47060.417| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.54 r_work: 0.3232 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 36298 Z= 0.098 Angle : 0.534 8.485 49086 Z= 0.258 Chirality : 0.044 0.135 5496 Planarity : 0.004 0.050 6474 Dihedral : 7.120 117.282 5028 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.99 % Allowed : 6.72 % Favored : 92.29 % 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: 0.16 (0.21), residues: 654 loop : -0.98 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 147 TYR 0.013 0.001 TYR F 244 PHE 0.010 0.001 PHE E 363 TRP 0.004 0.001 TRP A 551 HIS 0.003 0.001 HIS E 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (36294) covalent geometry : angle 0.53415 / 0.26 (49086) hydrogen bonds : bond 0.03257 / 2.18 ( 1356) hydrogen bonds : angle 3.76109 / 2.64 ( 3942) Misc. bond : bond 0.00098 / 0.05 ( 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 324 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 286 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.6661 (mttp) cc_final: 0.6443 (ttpp) REVERT: A 285 ASN cc_start: 0.8176 (m-40) cc_final: 0.7947 (t0) REVERT: A 417 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7583 (tt0) REVERT: A 449 MET cc_start: 0.7949 (tpt) cc_final: 0.7229 (tpt) REVERT: A 561 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: A 711 ARG cc_start: 0.7036 (tmm160) cc_final: 0.6570 (tmm160) REVERT: A 733 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7875 (mtt-85) REVERT: B 46 MET cc_start: 0.4654 (tpt) cc_final: 0.4348 (tpt) REVERT: B 69 CYS cc_start: 0.7237 (p) cc_final: 0.7005 (p) REVERT: B 205 ASP cc_start: 0.8801 (m-30) cc_final: 0.8559 (m-30) REVERT: B 285 ASN cc_start: 0.8216 (m-40) cc_final: 0.7965 (t0) REVERT: B 457 SER cc_start: 0.8883 (t) cc_final: 0.8349 (p) REVERT: C 62 LYS cc_start: 0.6886 (mttp) cc_final: 0.6534 (ttpp) REVERT: C 457 SER cc_start: 0.8993 (t) cc_final: 0.8467 (p) REVERT: C 611 MET cc_start: 0.7911 (tpp) cc_final: 0.7677 (ttp) REVERT: C 720 MET cc_start: 0.5643 (mpp) cc_final: 0.5136 (mmm) REVERT: D 62 LYS cc_start: 0.6662 (mttp) cc_final: 0.6442 (ttpp) REVERT: D 285 ASN cc_start: 0.8169 (m-40) cc_final: 0.7936 (t0) REVERT: D 417 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7579 (tt0) REVERT: D 449 MET cc_start: 0.7962 (tpt) cc_final: 0.7246 (tpt) REVERT: D 561 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: D 711 ARG cc_start: 0.7032 (tmm160) cc_final: 0.6566 (tmm160) REVERT: D 733 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7882 (mtt-85) REVERT: E 46 MET cc_start: 0.4654 (tpt) cc_final: 0.4348 (tpt) REVERT: E 69 CYS cc_start: 0.7230 (p) cc_final: 0.6996 (p) REVERT: E 205 ASP cc_start: 0.8796 (m-30) cc_final: 0.8557 (m-30) REVERT: E 285 ASN cc_start: 0.8208 (m-40) cc_final: 0.7954 (t0) REVERT: E 457 SER cc_start: 0.8886 (t) cc_final: 0.8351 (p) REVERT: F 62 LYS cc_start: 0.6883 (mttp) cc_final: 0.6533 (ttpp) REVERT: F 457 SER cc_start: 0.8988 (t) cc_final: 0.8460 (p) REVERT: F 611 MET cc_start: 0.7909 (tpp) cc_final: 0.7678 (ttp) REVERT: F 720 MET cc_start: 0.5643 (mpp) cc_final: 0.5134 (mmm) REVERT: F 742 PHE cc_start: 0.7761 (m-80) cc_final: 0.7367 (m-10) outliers start: 38 outliers final: 26 residues processed: 310 average time/residue: 0.2461 time to fit residues: 121.6727 Evaluate side-chains 298 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 268 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 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 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 307 ASP Chi-restraints excluded: chain C residue 633 ILE 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 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 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 307 ASP Chi-restraints excluded: chain F residue 633 ILE 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: 6.9990 chunk 104 optimal weight: 4.9990 chunk 391 optimal weight: 50.0000 chunk 74 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 300 optimal weight: 30.0000 chunk 357 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 440 optimal weight: 0.2980 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN A 337 GLN B 337 GLN B 443 ASN C 91 ASN D 91 ASN D 337 GLN E 443 ASN F 91 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.176852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112685 restraints weight = 47121.476| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.84 r_work: 0.3151 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 36298 Z= 0.189 Angle : 0.591 10.022 49086 Z= 0.284 Chirality : 0.046 0.143 5496 Planarity : 0.004 0.055 6474 Dihedral : 7.142 117.124 5028 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.33 % Allowed : 7.16 % Favored : 91.51 % 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: 0.00 (0.13), residues: 4494 helix: 0.94 (0.13), residues: 1866 sheet: 0.10 (0.21), residues: 654 loop : -0.90 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 599 TYR 0.014 0.001 TYR C 244 PHE 0.014 0.002 PHE F 682 TRP 0.009 0.002 TRP E 551 HIS 0.003 0.001 HIS F 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.19 (36294) covalent geometry : angle 0.59087 / 0.28 (49086) hydrogen bonds : bond 0.04244 / 2.84 ( 1356) hydrogen bonds : angle 3.87037 / 2.71 ( 3942) Misc. bond : bond 0.00142 / 0.07 ( 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 320 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 269 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.7329 (p) cc_final: 0.7077 (p) REVERT: A 285 ASN cc_start: 0.8243 (m-40) cc_final: 0.8010 (t0) REVERT: A 449 MET cc_start: 0.7923 (tpt) cc_final: 0.7681 (tpt) REVERT: A 561 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8195 (mm-30) REVERT: A 711 ARG cc_start: 0.7011 (tmm160) cc_final: 0.6629 (tmm160) REVERT: A 733 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7884 (mtt-85) REVERT: A 742 PHE cc_start: 0.7626 (m-80) cc_final: 0.7162 (m-10) REVERT: B 46 MET cc_start: 0.4515 (tpt) cc_final: 0.4165 (tpt) REVERT: B 69 CYS cc_start: 0.7353 (p) cc_final: 0.7146 (p) REVERT: B 205 ASP cc_start: 0.8818 (m-30) cc_final: 0.8599 (m-30) REVERT: B 285 ASN cc_start: 0.8280 (m-40) cc_final: 0.8009 (t0) REVERT: B 633 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8904 (tp) REVERT: C 62 LYS cc_start: 0.6966 (mttp) cc_final: 0.6574 (ttpp) REVERT: C 457 SER cc_start: 0.9025 (t) cc_final: 0.8488 (p) REVERT: C 611 MET cc_start: 0.7962 (tpp) cc_final: 0.7685 (ttp) REVERT: C 720 MET cc_start: 0.5701 (mpp) cc_final: 0.5228 (mmm) REVERT: C 733 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8072 (mtt-85) REVERT: D 69 CYS cc_start: 0.7332 (p) cc_final: 0.7080 (p) REVERT: D 285 ASN cc_start: 0.8245 (m-40) cc_final: 0.8011 (t0) REVERT: D 449 MET cc_start: 0.7930 (tpt) cc_final: 0.7695 (tpt) REVERT: D 561 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8193 (mm-30) REVERT: D 711 ARG cc_start: 0.7006 (tmm160) cc_final: 0.6626 (tmm160) REVERT: D 733 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7880 (mtt-85) REVERT: D 742 PHE cc_start: 0.7624 (m-80) cc_final: 0.7163 (m-10) REVERT: E 46 MET cc_start: 0.4507 (tpt) cc_final: 0.4161 (tpt) REVERT: E 69 CYS cc_start: 0.7348 (p) cc_final: 0.7143 (p) REVERT: E 205 ASP cc_start: 0.8813 (m-30) cc_final: 0.8597 (m-30) REVERT: E 285 ASN cc_start: 0.8273 (m-40) cc_final: 0.8003 (t0) REVERT: E 633 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8900 (tp) REVERT: F 62 LYS cc_start: 0.6959 (mttp) cc_final: 0.6569 (ttpp) REVERT: F 457 SER cc_start: 0.9022 (t) cc_final: 0.8484 (p) REVERT: F 611 MET cc_start: 0.7966 (tpp) cc_final: 0.7692 (ttp) REVERT: F 720 MET cc_start: 0.5698 (mpp) cc_final: 0.5225 (mmm) REVERT: F 733 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.8047 (mtt-85) REVERT: F 742 PHE cc_start: 0.7754 (m-80) cc_final: 0.7362 (m-10) outliers start: 51 outliers final: 24 residues processed: 308 average time/residue: 0.2393 time to fit residues: 118.0858 Evaluate side-chains 284 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 252 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 307 ASP 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 561 GLU Chi-restraints excluded: chain D residue 662 ARG 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 307 ASP 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: 0.8980 chunk 191 optimal weight: 2.9990 chunk 436 optimal weight: 0.7980 chunk 279 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 175 optimal weight: 0.0870 chunk 199 optimal weight: 1.9990 chunk 354 optimal weight: 0.5980 chunk 254 optimal weight: 10.0000 chunk 444 optimal weight: 6.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN C 443 ASN C 558 ASN D 91 ASN F 443 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.179287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.115583 restraints weight = 47243.388| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.83 r_work: 0.3207 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 : 0.002 0.033 36298 Z= 0.098 Angle : 0.519 8.430 49086 Z= 0.250 Chirality : 0.044 0.141 5496 Planarity : 0.004 0.051 6474 Dihedral : 6.827 114.142 5028 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.09 % Allowed : 7.42 % Favored : 91.48 % 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: 0.36 (0.13), residues: 4494 helix: 1.20 (0.13), residues: 1872 sheet: 0.26 (0.21), residues: 654 loop : -0.65 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 733 TYR 0.011 0.001 TYR F 244 PHE 0.009 0.001 PHE E 152 TRP 0.004 0.001 TRP B 551 HIS 0.003 0.001 HIS B 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (36294) covalent geometry : angle 0.51944 / 0.25 (49086) hydrogen bonds : bond 0.03053 / 2.04 ( 1356) hydrogen bonds : angle 3.65377 / 2.57 ( 3942) Misc. bond : bond 0.00069 / 0.03 ( 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 322 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 280 time to evaluate : 1.431 Fit side-chains REVERT: A 69 CYS cc_start: 0.7383 (p) cc_final: 0.7099 (p) REVERT: A 152 PHE cc_start: 0.5574 (p90) cc_final: 0.5113 (p90) REVERT: A 285 ASN cc_start: 0.8198 (m-40) cc_final: 0.7961 (t0) REVERT: A 417 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7628 (tt0) REVERT: A 449 MET cc_start: 0.7916 (tpt) cc_final: 0.7242 (tpt) REVERT: A 711 ARG cc_start: 0.7111 (tmm160) cc_final: 0.6637 (tmm160) REVERT: A 733 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7871 (mtt-85) REVERT: B 46 MET cc_start: 0.4277 (tpt) cc_final: 0.3959 (tpt) REVERT: B 69 CYS cc_start: 0.7341 (p) cc_final: 0.7071 (p) REVERT: B 205 ASP cc_start: 0.8785 (m-30) cc_final: 0.8581 (m-30) REVERT: B 236 LYS cc_start: 0.8338 (tttt) cc_final: 0.8046 (tptm) REVERT: B 285 ASN cc_start: 0.8214 (m-40) cc_final: 0.7967 (t0) REVERT: B 633 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8878 (tp) REVERT: C 62 LYS cc_start: 0.6938 (mttp) cc_final: 0.6541 (ttpp) REVERT: C 69 CYS cc_start: 0.7788 (p) cc_final: 0.7517 (p) REVERT: C 457 SER cc_start: 0.8998 (t) cc_final: 0.8462 (p) REVERT: C 720 MET cc_start: 0.5648 (mpp) cc_final: 0.5188 (mmm) REVERT: D 69 CYS cc_start: 0.7390 (p) cc_final: 0.7106 (p) REVERT: D 152 PHE cc_start: 0.5571 (p90) cc_final: 0.5109 (p90) REVERT: D 285 ASN cc_start: 0.8199 (m-40) cc_final: 0.7957 (t0) REVERT: D 417 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7625 (tt0) REVERT: D 449 MET cc_start: 0.7925 (tpt) cc_final: 0.7254 (tpt) REVERT: D 711 ARG cc_start: 0.7109 (tmm160) cc_final: 0.6634 (tmm160) REVERT: D 733 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7864 (mtt-85) REVERT: E 46 MET cc_start: 0.4265 (tpt) cc_final: 0.3951 (tpt) REVERT: E 69 CYS cc_start: 0.7336 (p) cc_final: 0.7067 (p) REVERT: E 205 ASP cc_start: 0.8779 (m-30) cc_final: 0.8576 (m-30) REVERT: E 236 LYS cc_start: 0.8324 (tttt) cc_final: 0.8033 (tptm) REVERT: E 285 ASN cc_start: 0.8208 (m-40) cc_final: 0.7959 (t0) REVERT: E 633 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8880 (tp) REVERT: F 62 LYS cc_start: 0.6926 (mttp) cc_final: 0.6533 (ttpp) REVERT: F 69 CYS cc_start: 0.7796 (p) cc_final: 0.7527 (p) REVERT: F 457 SER cc_start: 0.8998 (t) cc_final: 0.8462 (p) REVERT: F 720 MET cc_start: 0.5647 (mpp) cc_final: 0.5186 (mmm) REVERT: F 742 PHE cc_start: 0.7726 (m-80) cc_final: 0.7358 (m-10) outliers start: 42 outliers final: 22 residues processed: 312 average time/residue: 0.2576 time to fit residues: 127.4271 Evaluate side-chains 288 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 262 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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 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 46 MET Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 633 ILE 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 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 46 MET Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 633 ILE 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: 3.9990 chunk 11 optimal weight: 7.9990 chunk 329 optimal weight: 6.9990 chunk 444 optimal weight: 0.8980 chunk 254 optimal weight: 8.9990 chunk 335 optimal weight: 0.9990 chunk 168 optimal weight: 0.0370 chunk 439 optimal weight: 7.9990 chunk 325 optimal weight: 0.2980 chunk 170 optimal weight: 0.0770 chunk 169 optimal weight: 0.3980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN A 337 GLN D 91 ASN D 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.180615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.117095 restraints weight = 47104.584| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.63 r_work: 0.3242 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 36298 Z= 0.088 Angle : 0.515 7.718 49086 Z= 0.247 Chirality : 0.043 0.134 5496 Planarity : 0.004 0.050 6474 Dihedral : 6.658 110.287 5028 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.89 % Allowed : 7.89 % Favored : 91.22 % 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: 0.62 (0.13), residues: 4494 helix: 1.38 (0.13), residues: 1872 sheet: 0.46 (0.21), residues: 654 loop : -0.50 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 753 TYR 0.011 0.001 TYR C 244 PHE 0.018 0.001 PHE A 674 TRP 0.004 0.001 TRP D 551 HIS 0.003 0.000 HIS B 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (36294) covalent geometry : angle 0.51494 / 0.25 (49086) hydrogen bonds : bond 0.02708 / 1.80 ( 1356) hydrogen bonds : angle 3.53750 / 2.49 ( 3942) Misc. bond : bond 0.00067 / 0.03 ( 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 319 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 285 time to evaluate : 1.312 Fit side-chains REVERT: A 69 CYS cc_start: 0.7291 (p) cc_final: 0.6988 (p) REVERT: A 152 PHE cc_start: 0.5510 (p90) cc_final: 0.5169 (p90) REVERT: A 285 ASN cc_start: 0.8154 (m-40) cc_final: 0.7932 (t0) REVERT: A 417 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7601 (tt0) REVERT: A 449 MET cc_start: 0.7904 (tpt) cc_final: 0.7269 (tpt) REVERT: A 674 PHE cc_start: 0.7284 (t80) cc_final: 0.7082 (t80) REVERT: A 711 ARG cc_start: 0.7140 (tmm160) cc_final: 0.6659 (tmm160) REVERT: A 733 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7849 (mtt-85) REVERT: B 46 MET cc_start: 0.4258 (tpt) cc_final: 0.3943 (tpt) REVERT: B 69 CYS cc_start: 0.7363 (p) cc_final: 0.7059 (p) REVERT: B 285 ASN cc_start: 0.8176 (m-40) cc_final: 0.7947 (t0) REVERT: B 633 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8914 (tp) REVERT: C 62 LYS cc_start: 0.6909 (mttp) cc_final: 0.6532 (ttpp) REVERT: C 69 CYS cc_start: 0.7634 (p) cc_final: 0.7365 (p) REVERT: C 236 LYS cc_start: 0.8413 (tttt) cc_final: 0.8201 (tttm) REVERT: C 457 SER cc_start: 0.9002 (t) cc_final: 0.8477 (p) REVERT: C 720 MET cc_start: 0.5531 (mpp) cc_final: 0.5077 (mmm) REVERT: D 69 CYS cc_start: 0.7295 (p) cc_final: 0.6991 (p) REVERT: D 152 PHE cc_start: 0.5518 (p90) cc_final: 0.5177 (p90) REVERT: D 285 ASN cc_start: 0.8154 (m-40) cc_final: 0.7928 (t0) REVERT: D 449 MET cc_start: 0.7922 (tpt) cc_final: 0.7287 (tpt) REVERT: D 711 ARG cc_start: 0.7137 (tmm160) cc_final: 0.6658 (tmm160) REVERT: D 733 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7851 (mtt-85) REVERT: E 46 MET cc_start: 0.4243 (tpt) cc_final: 0.3934 (tpt) REVERT: E 69 CYS cc_start: 0.7356 (p) cc_final: 0.7056 (p) REVERT: E 285 ASN cc_start: 0.8176 (m-40) cc_final: 0.7946 (t0) REVERT: E 633 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8915 (tp) REVERT: F 62 LYS cc_start: 0.6901 (mttp) cc_final: 0.6526 (ttpp) REVERT: F 69 CYS cc_start: 0.7644 (p) cc_final: 0.7382 (p) REVERT: F 236 LYS cc_start: 0.8418 (tttt) cc_final: 0.8204 (tttm) REVERT: F 457 SER cc_start: 0.9001 (t) cc_final: 0.8476 (p) REVERT: F 720 MET cc_start: 0.5532 (mpp) cc_final: 0.5078 (mmm) REVERT: F 742 PHE cc_start: 0.7781 (m-80) cc_final: 0.7358 (m-10) outliers start: 34 outliers final: 22 residues processed: 309 average time/residue: 0.2413 time to fit residues: 119.7056 Evaluate side-chains 289 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 263 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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 445 LEU 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 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 633 ILE Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 337 GLN Chi-restraints excluded: chain D residue 445 LEU 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 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 633 ILE Chi-restraints excluded: chain F residue 670 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 17 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 402 optimal weight: 7.9990 chunk 235 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 296 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN C 558 ASN D 91 ASN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 ASN ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.175327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110647 restraints weight = 47241.463| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.70 r_work: 0.3139 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 36298 Z= 0.255 Angle : 0.653 10.632 49086 Z= 0.318 Chirality : 0.049 0.151 5496 Planarity : 0.005 0.057 6474 Dihedral : 7.077 113.842 5028 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.99 % Allowed : 8.23 % Favored : 90.78 % 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 (0.13), residues: 4494 helix: 0.92 (0.12), residues: 1872 sheet: 0.41 (0.22), residues: 612 loop : -0.64 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 338 TYR 0.017 0.002 TYR A 244 PHE 0.020 0.002 PHE A 682 TRP 0.015 0.003 TRP B 551 HIS 0.004 0.001 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.26 (36294) covalent geometry : angle 0.65284 / 0.32 (49086) hydrogen bonds : bond 0.05152 / 3.45 ( 1356) hydrogen bonds : angle 3.97791 / 2.79 ( 3942) Misc. bond : bond 0.00206 / 0.10 ( 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 300 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 262 time to evaluate : 1.373 Fit side-chains REVERT: A 69 CYS cc_start: 0.7335 (p) cc_final: 0.7013 (p) REVERT: A 152 PHE cc_start: 0.5546 (p90) cc_final: 0.5129 (p90) REVERT: A 449 MET cc_start: 0.8036 (tpt) cc_final: 0.7832 (tpt) REVERT: A 711 ARG cc_start: 0.7014 (tmm160) cc_final: 0.6590 (tmm160) REVERT: A 742 PHE cc_start: 0.7642 (m-80) cc_final: 0.7198 (m-10) REVERT: B 46 MET cc_start: 0.4165 (tpt) cc_final: 0.3902 (tpt) REVERT: B 69 CYS cc_start: 0.7459 (p) cc_final: 0.7109 (p) REVERT: B 285 ASN cc_start: 0.8353 (m-40) cc_final: 0.8118 (t0) REVERT: B 442 MET cc_start: 0.7018 (ttp) cc_final: 0.6618 (tmm) REVERT: C 62 LYS cc_start: 0.6903 (mttp) cc_final: 0.6543 (ttpp) REVERT: C 69 CYS cc_start: 0.7832 (p) cc_final: 0.7555 (p) REVERT: C 720 MET cc_start: 0.5636 (mpp) cc_final: 0.5218 (mmm) REVERT: D 69 CYS cc_start: 0.7337 (p) cc_final: 0.7018 (p) REVERT: D 152 PHE cc_start: 0.5535 (p90) cc_final: 0.5120 (p90) REVERT: D 285 ASN cc_start: 0.8260 (m-40) cc_final: 0.8055 (t0) REVERT: D 449 MET cc_start: 0.8064 (tpt) cc_final: 0.7845 (tpt) REVERT: D 711 ARG cc_start: 0.7013 (tmm160) cc_final: 0.6591 (tmm160) REVERT: D 742 PHE cc_start: 0.7637 (m-80) cc_final: 0.7194 (m-10) REVERT: E 46 MET cc_start: 0.4154 (tpt) cc_final: 0.3893 (tpt) REVERT: E 69 CYS cc_start: 0.7459 (p) cc_final: 0.7106 (p) REVERT: E 285 ASN cc_start: 0.8351 (m-40) cc_final: 0.8122 (t0) REVERT: E 442 MET cc_start: 0.7015 (ttp) cc_final: 0.6621 (tmm) REVERT: F 62 LYS cc_start: 0.6899 (mttp) cc_final: 0.6537 (ttpp) REVERT: F 69 CYS cc_start: 0.7834 (p) cc_final: 0.7555 (p) REVERT: F 720 MET cc_start: 0.5635 (mpp) cc_final: 0.5216 (mmm) REVERT: F 742 PHE cc_start: 0.7768 (m-80) cc_final: 0.7384 (m-10) outliers start: 38 outliers final: 26 residues processed: 294 average time/residue: 0.2519 time to fit residues: 117.9172 Evaluate side-chains 273 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 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 662 ARG Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 337 GLN Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 633 ILE 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 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 662 ARG Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 337 GLN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 633 ILE 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: 0.9980 chunk 366 optimal weight: 0.7980 chunk 274 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 310 optimal weight: 7.9990 chunk 246 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 150 optimal weight: 30.0000 chunk 406 optimal weight: 2.9990 chunk 320 optimal weight: 0.9990 chunk 255 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN D 91 ASN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.175758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110811 restraints weight = 47261.767| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.82 r_work: 0.3136 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.159 36298 Z= 0.217 Angle : 0.817 59.092 49086 Z= 0.436 Chirality : 0.048 0.488 5496 Planarity : 0.005 0.057 6474 Dihedral : 7.074 113.868 5028 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.76 % Allowed : 8.46 % Favored : 90.78 % 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: 0.20 (0.13), residues: 4494 helix: 0.92 (0.12), residues: 1872 sheet: 0.39 (0.22), residues: 612 loop : -0.64 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 239 TYR 0.016 0.002 TYR A 244 PHE 0.016 0.002 PHE A 682 TRP 0.014 0.002 TRP B 551 HIS 0.004 0.001 HIS E 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (36294) covalent geometry : angle 0.81715 / 0.44 (49086) hydrogen bonds : bond 0.04884 / 3.27 ( 1356) hydrogen bonds : angle 3.96919 / 2.79 ( 3942) Misc. bond : bond 0.00143 / 0.07 ( 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 279 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 250 time to evaluate : 1.512 Fit side-chains REVERT: A 69 CYS cc_start: 0.7320 (p) cc_final: 0.6998 (p) REVERT: A 152 PHE cc_start: 0.5485 (p90) cc_final: 0.5077 (p90) REVERT: A 449 MET cc_start: 0.8056 (tpt) cc_final: 0.7835 (tpt) REVERT: A 711 ARG cc_start: 0.7006 (tmm160) cc_final: 0.6581 (tmm160) REVERT: A 742 PHE cc_start: 0.7639 (m-80) cc_final: 0.7228 (m-10) REVERT: B 46 MET cc_start: 0.4152 (tpt) cc_final: 0.3890 (tpt) REVERT: B 69 CYS cc_start: 0.7449 (p) cc_final: 0.7094 (p) REVERT: B 285 ASN cc_start: 0.8344 (m-40) cc_final: 0.8097 (t0) REVERT: B 442 MET cc_start: 0.7009 (ttp) cc_final: 0.6603 (tmm) REVERT: C 62 LYS cc_start: 0.6889 (mttp) cc_final: 0.6509 (ttpp) REVERT: C 69 CYS cc_start: 0.7804 (p) cc_final: 0.7523 (p) REVERT: C 720 MET cc_start: 0.5638 (mpp) cc_final: 0.5222 (mmm) REVERT: D 69 CYS cc_start: 0.7320 (p) cc_final: 0.6997 (p) REVERT: D 152 PHE cc_start: 0.5486 (p90) cc_final: 0.5077 (p90) REVERT: D 285 ASN cc_start: 0.8251 (m-40) cc_final: 0.8034 (t0) REVERT: D 449 MET cc_start: 0.8050 (tpt) cc_final: 0.7826 (tpt) REVERT: D 711 ARG cc_start: 0.7009 (tmm160) cc_final: 0.6585 (tmm160) REVERT: D 742 PHE cc_start: 0.7632 (m-80) cc_final: 0.7221 (m-10) REVERT: E 46 MET cc_start: 0.4144 (tpt) cc_final: 0.3886 (tpt) REVERT: E 69 CYS cc_start: 0.7491 (p) cc_final: 0.7171 (p) REVERT: E 285 ASN cc_start: 0.8340 (m-40) cc_final: 0.8098 (t0) REVERT: E 442 MET cc_start: 0.7013 (ttp) cc_final: 0.6603 (tmm) REVERT: F 62 LYS cc_start: 0.6868 (mttp) cc_final: 0.6492 (ttpp) REVERT: F 69 CYS cc_start: 0.7808 (p) cc_final: 0.7523 (p) REVERT: F 720 MET cc_start: 0.5636 (mpp) cc_final: 0.5220 (mmm) REVERT: F 742 PHE cc_start: 0.7814 (m-80) cc_final: 0.7317 (m-10) outliers start: 29 outliers final: 29 residues processed: 274 average time/residue: 0.2456 time to fit residues: 107.9756 Evaluate side-chains 275 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 246 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 445 LEU Chi-restraints excluded: chain A residue 508 MET 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 662 ARG Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 337 GLN Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 633 ILE 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 445 LEU 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 662 ARG Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 337 GLN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 633 ILE 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: 0.0970 chunk 128 optimal weight: 0.8980 chunk 167 optimal weight: 20.0000 chunk 256 optimal weight: 0.5980 chunk 136 optimal weight: 0.0470 chunk 382 optimal weight: 3.9990 chunk 381 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 282 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 410 optimal weight: 1.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.175688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110844 restraints weight = 47058.429| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.83 r_work: 0.3134 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.250 36298 Z= 0.243 Angle : 0.736 41.421 49086 Z= 0.375 Chirality : 0.048 0.481 5496 Planarity : 0.006 0.182 6474 Dihedral : 7.074 113.868 5028 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.76 % Allowed : 8.46 % Favored : 90.78 % 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: 0.20 (0.13), residues: 4494 helix: 0.92 (0.12), residues: 1872 sheet: 0.39 (0.22), residues: 612 loop : -0.64 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 239 TYR 0.016 0.002 TYR A 244 PHE 0.016 0.002 PHE A 682 TRP 0.014 0.002 TRP B 551 HIS 0.004 0.001 HIS E 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.24 (36294) covalent geometry : angle 0.73550 / 0.38 (49086) hydrogen bonds : bond 0.04883 / 3.27 ( 1356) hydrogen bonds : angle 3.96933 / 2.79 ( 3942) Misc. bond : bond 0.00143 / 0.07 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9494.83 seconds wall clock time: 162 minutes 43.20 seconds (9763.20 seconds total)