Starting phenix.real_space_refine on Tue Aug 26 12:05:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9exo_50042/08_2025/9exo_50042.cif Found real_map, /net/cci-nas-00/data/ceres_data/9exo_50042/08_2025/9exo_50042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9exo_50042/08_2025/9exo_50042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9exo_50042/08_2025/9exo_50042.map" model { file = "/net/cci-nas-00/data/ceres_data/9exo_50042/08_2025/9exo_50042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9exo_50042/08_2025/9exo_50042.cif" } resolution = 3.0 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= 0.003 sd= 0.028 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 16 5.49 5 Mg 8 5.21 5 S 113 5.16 5 C 23405 2.51 5 N 6285 2.21 5 O 6988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36815 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" Number of atoms: 4317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4317 Classifications: {'peptide': 560} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 536} Chain breaks: 3 Chain: "A" Number of atoms: 5117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5117 Classifications: {'peptide': 658} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 632} Chain breaks: 3 Chain: "B" Number of atoms: 4313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4313 Classifications: {'peptide': 559} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 535} Chain breaks: 3 Chain: "C" Number of atoms: 4317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4317 Classifications: {'peptide': 560} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 536} Chain breaks: 3 Chain: "D" Number of atoms: 5117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5117 Classifications: {'peptide': 658} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 632} Chain breaks: 3 Chain: "E" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3980 Classifications: {'peptide': 517} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 494} Chain breaks: 3 Chain: "F" Number of atoms: 5117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5117 Classifications: {'peptide': 658} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 632} Chain breaks: 3 Chain: "G" Number of atoms: 4313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4313 Classifications: {'peptide': 559} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 535} Chain breaks: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.31, per 1000 atoms: 0.28 Number of scatterers: 36815 At special positions: 0 Unit cell: (165.088, 164.351, 174.669, 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 113 16.00 P 16 15.00 Mg 8 11.99 O 6988 8.00 N 6285 7.00 C 23405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8794 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 32 sheets defined 51.4% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'H' and resid 18 through 29 Processing helix chain 'H' and resid 29 through 51 Processing helix chain 'H' and resid 86 through 94 removed outlier: 3.695A pdb=" N THR H 90 " --> pdb=" O SER H 86 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'H' and resid 120 through 128 Processing helix chain 'H' and resid 208 through 219 removed outlier: 3.644A pdb=" N SER H 219 " --> pdb=" O ASP H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 278 removed outlier: 3.918A pdb=" N SER H 245 " --> pdb=" O PRO H 241 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN H 266 " --> pdb=" O ARG H 262 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASP H 267 " --> pdb=" O GLN H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 404 Processing helix chain 'H' and resid 425 through 452 Processing helix chain 'H' and resid 457 through 465 removed outlier: 4.021A pdb=" N LEU H 461 " --> pdb=" O SER H 457 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE H 464 " --> pdb=" O GLN H 460 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY H 465 " --> pdb=" O LEU H 461 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 501 Processing helix chain 'H' and resid 504 through 521 removed outlier: 3.696A pdb=" N PHE H 519 " --> pdb=" O THR H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 539 through 553 Processing helix chain 'H' and resid 569 through 575 Processing helix chain 'H' and resid 581 through 587 removed outlier: 3.544A pdb=" N PHE H 585 " --> pdb=" O GLY H 581 " (cutoff:3.500A) Processing helix chain 'H' and resid 615 through 620 Processing helix chain 'H' and resid 622 through 633 removed outlier: 4.202A pdb=" N GLU H 626 " --> pdb=" O HIS H 622 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 656 Processing helix chain 'H' and resid 672 through 686 removed outlier: 3.768A pdb=" N SER H 686 " --> pdb=" O ARG H 682 " (cutoff:3.500A) Processing helix chain 'H' and resid 701 through 708 Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 29 through 51 Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.665A pdb=" N ALA A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 107 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.818A pdb=" N SER A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 265 removed outlier: 3.879A pdb=" N SER A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 297 Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 305 through 336 Processing helix chain 'A' and resid 340 through 366 removed outlier: 3.591A pdb=" N SER A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 403 removed outlier: 3.825A pdb=" N VAL A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 403 " --> pdb=" O ASN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 451 Processing helix chain 'A' and resid 457 through 465 removed outlier: 4.053A pdb=" N LEU A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 504 through 521 removed outlier: 3.702A pdb=" N PHE A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 553 Processing helix chain 'A' and resid 569 through 575 Processing helix chain 'A' and resid 581 through 587 removed outlier: 3.569A pdb=" N PHE A 585 " --> pdb=" O GLY A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 622 through 633 removed outlier: 4.386A pdb=" N GLU A 626 " --> pdb=" O HIS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 672 through 686 removed outlier: 3.659A pdb=" N SER A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 708 Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 29 through 51 Processing helix chain 'B' and resid 86 through 94 removed outlier: 3.585A pdb=" N THR B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 120 through 128 Processing helix chain 'B' and resid 208 through 219 removed outlier: 3.613A pdb=" N SER B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 278 removed outlier: 3.961A pdb=" N SER B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASP B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 405 Processing helix chain 'B' and resid 425 through 451 Processing helix chain 'B' and resid 457 through 465 removed outlier: 4.112A pdb=" N LEU B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 504 through 521 removed outlier: 3.730A pdb=" N PHE B 519 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 553 Processing helix chain 'B' and resid 569 through 575 Processing helix chain 'B' and resid 581 through 587 Processing helix chain 'B' and resid 615 through 620 Processing helix chain 'B' and resid 622 through 633 removed outlier: 4.210A pdb=" N GLU B 626 " --> pdb=" O HIS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 656 Processing helix chain 'B' and resid 672 through 686 removed outlier: 3.584A pdb=" N SER B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 708 Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 29 through 51 Processing helix chain 'C' and resid 86 through 94 removed outlier: 3.584A pdb=" N THR C 90 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 107 Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 208 through 219 removed outlier: 3.662A pdb=" N SER C 219 " --> pdb=" O ASP C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 263 removed outlier: 4.033A pdb=" N SER C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 385 through 405 Processing helix chain 'C' and resid 425 through 451 Processing helix chain 'C' and resid 457 through 465 removed outlier: 4.136A pdb=" N LEU C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 501 Processing helix chain 'C' and resid 504 through 521 removed outlier: 3.768A pdb=" N PHE C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 553 Processing helix chain 'C' and resid 569 through 575 Processing helix chain 'C' and resid 581 through 587 Processing helix chain 'C' and resid 615 through 620 Processing helix chain 'C' and resid 622 through 633 removed outlier: 4.167A pdb=" N GLU C 626 " --> pdb=" O HIS C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 656 Processing helix chain 'C' and resid 672 through 686 removed outlier: 3.670A pdb=" N SER C 686 " --> pdb=" O ARG C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 708 Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 29 through 51 Processing helix chain 'D' and resid 86 through 94 removed outlier: 3.589A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 208 through 219 removed outlier: 3.759A pdb=" N SER D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 268 removed outlier: 3.894A pdb=" N SER D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG D 262 " --> pdb=" O GLN D 258 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLN D 263 " --> pdb=" O ASN D 259 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA D 264 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASP D 267 " --> pdb=" O GLN D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 297 Proline residue: D 279 - end of helix Processing helix chain 'D' and resid 305 through 336 Processing helix chain 'D' and resid 340 through 366 removed outlier: 3.586A pdb=" N SER D 366 " --> pdb=" O LYS D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 404 removed outlier: 3.901A pdb=" N VAL D 374 " --> pdb=" O THR D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 451 Processing helix chain 'D' and resid 457 through 465 removed outlier: 4.022A pdb=" N LEU D 461 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 501 Processing helix chain 'D' and resid 504 through 521 removed outlier: 3.738A pdb=" N PHE D 519 " --> pdb=" O THR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 553 Processing helix chain 'D' and resid 569 through 575 Processing helix chain 'D' and resid 581 through 587 removed outlier: 3.522A pdb=" N PHE D 585 " --> pdb=" O GLY D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 620 Processing helix chain 'D' and resid 622 through 633 removed outlier: 4.238A pdb=" N GLU D 626 " --> pdb=" O HIS D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 Processing helix chain 'D' and resid 672 through 686 removed outlier: 3.634A pdb=" N SER D 686 " --> pdb=" O ARG D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 708 Processing helix chain 'E' and resid 18 through 29 Processing helix chain 'E' and resid 29 through 51 Processing helix chain 'E' and resid 86 through 94 removed outlier: 3.692A pdb=" N THR E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN E 94 " --> pdb=" O THR E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 107 Processing helix chain 'E' and resid 120 through 128 Processing helix chain 'E' and resid 208 through 219 removed outlier: 3.675A pdb=" N SER E 219 " --> pdb=" O ASP E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 260 removed outlier: 3.971A pdb=" N SER E 245 " --> pdb=" O PRO E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 451 Processing helix chain 'E' and resid 457 through 465 removed outlier: 4.088A pdb=" N LEU E 461 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE E 464 " --> pdb=" O GLN E 460 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY E 465 " --> pdb=" O LEU E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 501 Processing helix chain 'E' and resid 504 through 521 removed outlier: 3.759A pdb=" N PHE E 519 " --> pdb=" O THR E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 553 Processing helix chain 'E' and resid 569 through 575 Processing helix chain 'E' and resid 581 through 587 removed outlier: 3.546A pdb=" N PHE E 585 " --> pdb=" O GLY E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 620 Processing helix chain 'E' and resid 622 through 633 removed outlier: 4.259A pdb=" N GLU E 626 " --> pdb=" O HIS E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 656 Processing helix chain 'E' and resid 672 through 686 removed outlier: 3.527A pdb=" N SER E 686 " --> pdb=" O ARG E 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 708 Processing helix chain 'F' and resid 18 through 29 Processing helix chain 'F' and resid 29 through 51 Processing helix chain 'F' and resid 86 through 94 removed outlier: 3.866A pdb=" N ALA F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 107 Processing helix chain 'F' and resid 120 through 128 Processing helix chain 'F' and resid 208 through 219 removed outlier: 3.711A pdb=" N SER F 219 " --> pdb=" O ASP F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 266 removed outlier: 3.994A pdb=" N SER F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN F 259 " --> pdb=" O TYR F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 297 Proline residue: F 279 - end of helix Processing helix chain 'F' and resid 305 through 336 Processing helix chain 'F' and resid 340 through 366 Processing helix chain 'F' and resid 368 through 403 removed outlier: 4.153A pdb=" N VAL F 374 " --> pdb=" O THR F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 451 Processing helix chain 'F' and resid 457 through 465 removed outlier: 4.132A pdb=" N LEU F 461 " --> pdb=" O SER F 457 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE F 464 " --> pdb=" O GLN F 460 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY F 465 " --> pdb=" O LEU F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 501 Processing helix chain 'F' and resid 504 through 521 removed outlier: 3.739A pdb=" N PHE F 519 " --> pdb=" O THR F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 553 Processing helix chain 'F' and resid 569 through 575 Processing helix chain 'F' and resid 581 through 587 removed outlier: 3.655A pdb=" N PHE F 585 " --> pdb=" O GLY F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 615 through 620 Processing helix chain 'F' and resid 622 through 633 removed outlier: 4.249A pdb=" N GLU F 626 " --> pdb=" O HIS F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 656 Processing helix chain 'F' and resid 672 through 686 removed outlier: 3.608A pdb=" N SER F 686 " --> pdb=" O ARG F 682 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 708 Processing helix chain 'G' and resid 18 through 29 Processing helix chain 'G' and resid 29 through 51 Processing helix chain 'G' and resid 86 through 94 removed outlier: 3.831A pdb=" N ALA G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 208 through 219 removed outlier: 3.600A pdb=" N SER G 219 " --> pdb=" O ASP G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 277 removed outlier: 3.906A pdb=" N SER G 245 " --> pdb=" O PRO G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 404 Processing helix chain 'G' and resid 425 through 452 Processing helix chain 'G' and resid 457 through 465 removed outlier: 4.074A pdb=" N LEU G 461 " --> pdb=" O SER G 457 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE G 464 " --> pdb=" O GLN G 460 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY G 465 " --> pdb=" O LEU G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 501 Processing helix chain 'G' and resid 504 through 521 removed outlier: 3.703A pdb=" N PHE G 519 " --> pdb=" O THR G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 553 Processing helix chain 'G' and resid 569 through 575 Processing helix chain 'G' and resid 581 through 587 removed outlier: 3.560A pdb=" N PHE G 585 " --> pdb=" O GLY G 581 " (cutoff:3.500A) Processing helix chain 'G' and resid 615 through 620 removed outlier: 3.528A pdb=" N LEU G 620 " --> pdb=" O PRO G 616 " (cutoff:3.500A) Processing helix chain 'G' and resid 622 through 633 removed outlier: 4.220A pdb=" N GLU G 626 " --> pdb=" O HIS G 622 " (cutoff:3.500A) Processing helix chain 'G' and resid 650 through 656 Processing helix chain 'G' and resid 672 through 686 removed outlier: 3.748A pdb=" N SER G 686 " --> pdb=" O ARG G 682 " (cutoff:3.500A) Processing helix chain 'G' and resid 701 through 708 Processing sheet with id=AA1, first strand: chain 'H' and resid 220 through 223 removed outlier: 8.455A pdb=" N ILE H 54 " --> pdb=" O ASP H 418 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ASP H 418 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU H 56 " --> pdb=" O VAL H 416 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL H 416 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP H 58 " --> pdb=" O ASN H 414 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ASN H 414 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU H 60 " --> pdb=" O ILE H 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 110 through 114 Processing sheet with id=AA3, first strand: chain 'H' and resid 134 through 141 removed outlier: 7.372A pdb=" N ASN H 134 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ILE H 194 " --> pdb=" O ASN H 134 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR H 138 " --> pdb=" O LEU H 190 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU H 190 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU H 140 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N SER H 188 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 468 through 473 removed outlier: 7.155A pdb=" N LEU H 695 " --> pdb=" O TYR H 469 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER H 471 " --> pdb=" O LEU H 695 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY H 697 " --> pdb=" O SER H 471 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N CYS H 662 " --> pdb=" O GLY H 692 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ILE H 694 " --> pdb=" O CYS H 662 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU H 664 " --> pdb=" O ILE H 694 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ASN H 696 " --> pdb=" O LEU H 664 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA H 666 " --> pdb=" O ASN H 696 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL H 698 " --> pdb=" O ALA H 666 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU H 559 " --> pdb=" O ILE H 640 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASP H 642 " --> pdb=" O LEU H 559 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE H 561 " --> pdb=" O ASP H 642 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR H 606 " --> pdb=" O ASP H 597 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 220 through 223 removed outlier: 6.822A pdb=" N GLU A 56 " --> pdb=" O THR A 417 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N THR A 417 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP A 58 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA A 415 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN A 62 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ILE A 411 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA7, first strand: chain 'A' and resid 134 through 141 removed outlier: 7.317A pdb=" N ASN A 134 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE A 194 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A 190 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 140 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER A 188 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 468 through 473 removed outlier: 7.201A pdb=" N LEU A 695 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER A 471 " --> pdb=" O LEU A 695 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY A 697 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 692 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU A 559 " --> pdb=" O ILE A 640 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASP A 642 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE A 561 " --> pdb=" O ASP A 642 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 606 " --> pdb=" O ASP A 597 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 220 through 223 removed outlier: 8.447A pdb=" N ILE B 54 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ASP B 418 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLU B 56 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL B 416 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASP B 58 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASN B 414 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU B 60 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AB2, first strand: chain 'B' and resid 134 through 141 removed outlier: 7.386A pdb=" N ASN B 134 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE B 194 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 138 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU B 190 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU B 140 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER B 188 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 468 through 473 removed outlier: 7.205A pdb=" N LEU B 695 " --> pdb=" O TYR B 469 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER B 471 " --> pdb=" O LEU B 695 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY B 697 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY B 692 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 559 " --> pdb=" O ILE B 640 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASP B 642 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE B 561 " --> pdb=" O ASP B 642 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 220 through 223 removed outlier: 8.468A pdb=" N ILE C 54 " --> pdb=" O ASP C 418 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ASP C 418 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLU C 56 " --> pdb=" O VAL C 416 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL C 416 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASP C 58 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ASN C 414 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU C 60 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AB6, first strand: chain 'C' and resid 134 through 141 removed outlier: 7.357A pdb=" N ASN C 134 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ILE C 194 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 138 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU C 190 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU C 140 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER C 188 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 468 through 473 removed outlier: 7.252A pdb=" N LEU C 695 " --> pdb=" O TYR C 469 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER C 471 " --> pdb=" O LEU C 695 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY C 697 " --> pdb=" O SER C 471 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N CYS C 662 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ILE C 694 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU C 664 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ASN C 696 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA C 666 " --> pdb=" O ASN C 696 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL C 698 " --> pdb=" O ALA C 666 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU C 559 " --> pdb=" O ILE C 640 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASP C 642 " --> pdb=" O LEU C 559 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE C 561 " --> pdb=" O ASP C 642 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 220 through 223 removed outlier: 8.452A pdb=" N ILE D 54 " --> pdb=" O ASP D 418 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASP D 418 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU D 56 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL D 416 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP D 58 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ASN D 414 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU D 60 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 110 through 114 Processing sheet with id=AC1, first strand: chain 'D' and resid 134 through 141 removed outlier: 7.322A pdb=" N ASN D 134 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE D 194 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU D 190 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU D 140 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER D 188 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 468 through 473 removed outlier: 7.209A pdb=" N LEU D 695 " --> pdb=" O TYR D 469 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER D 471 " --> pdb=" O LEU D 695 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLY D 697 " --> pdb=" O SER D 471 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY D 692 " --> pdb=" O CYS D 662 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU D 559 " --> pdb=" O ILE D 640 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ASP D 642 " --> pdb=" O LEU D 559 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE D 561 " --> pdb=" O ASP D 642 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 220 through 223 removed outlier: 7.327A pdb=" N ILE E 54 " --> pdb=" O ASN E 420 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ASN E 420 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU E 56 " --> pdb=" O ASP E 418 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP E 58 " --> pdb=" O VAL E 416 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL E 416 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU E 60 " --> pdb=" O ASN E 414 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ASN E 414 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N GLN E 62 " --> pdb=" O ILE E 412 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE E 412 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 110 through 114 Processing sheet with id=AC5, first strand: chain 'E' and resid 134 through 141 removed outlier: 7.342A pdb=" N ASN E 134 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ILE E 194 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR E 138 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU E 190 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU E 140 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER E 188 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 468 through 473 removed outlier: 7.198A pdb=" N LEU E 695 " --> pdb=" O TYR E 469 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER E 471 " --> pdb=" O LEU E 695 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLY E 697 " --> pdb=" O SER E 471 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY E 692 " --> pdb=" O CYS E 662 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU E 559 " --> pdb=" O ILE E 640 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ASP E 642 " --> pdb=" O LEU E 559 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE E 561 " --> pdb=" O ASP E 642 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 220 through 223 removed outlier: 6.868A pdb=" N GLU F 56 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL F 416 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASP F 58 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASN F 414 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU F 60 " --> pdb=" O ILE F 412 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 110 through 114 Processing sheet with id=AC9, first strand: chain 'F' and resid 134 through 141 removed outlier: 7.257A pdb=" N ASN F 134 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ILE F 194 " --> pdb=" O ASN F 134 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 138 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU F 190 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU F 140 " --> pdb=" O SER F 188 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER F 188 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 468 through 473 removed outlier: 7.201A pdb=" N LEU F 695 " --> pdb=" O TYR F 469 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER F 471 " --> pdb=" O LEU F 695 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY F 697 " --> pdb=" O SER F 471 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N CYS F 662 " --> pdb=" O GLY F 692 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ILE F 694 " --> pdb=" O CYS F 662 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU F 664 " --> pdb=" O ILE F 694 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ASN F 696 " --> pdb=" O LEU F 664 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA F 666 " --> pdb=" O ASN F 696 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL F 698 " --> pdb=" O ALA F 666 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU F 559 " --> pdb=" O ILE F 640 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASP F 642 " --> pdb=" O LEU F 559 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE F 561 " --> pdb=" O ASP F 642 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 220 through 223 removed outlier: 8.523A pdb=" N ILE G 54 " --> pdb=" O ASP G 418 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASP G 418 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLU G 56 " --> pdb=" O VAL G 416 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL G 416 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASP G 58 " --> pdb=" O ASN G 414 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ASN G 414 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU G 60 " --> pdb=" O ILE G 412 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 110 through 114 Processing sheet with id=AD4, first strand: chain 'G' and resid 134 through 141 removed outlier: 7.404A pdb=" N ASN G 134 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ILE G 194 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR G 138 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU G 190 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU G 140 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER G 188 " --> pdb=" O LEU G 140 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 468 through 473 removed outlier: 7.093A pdb=" N LEU G 695 " --> pdb=" O TYR G 469 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER G 471 " --> pdb=" O LEU G 695 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY G 697 " --> pdb=" O SER G 471 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N CYS G 662 " --> pdb=" O GLY G 692 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ILE G 694 " --> pdb=" O CYS G 662 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU G 664 " --> pdb=" O ILE G 694 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASN G 696 " --> pdb=" O LEU G 664 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA G 666 " --> pdb=" O ASN G 696 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL G 698 " --> pdb=" O ALA G 666 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU G 559 " --> pdb=" O ILE G 640 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASP G 642 " --> pdb=" O LEU G 559 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE G 561 " --> pdb=" O ASP G 642 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL G 558 " --> pdb=" O ASP G 605 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE G 607 " --> pdb=" O VAL G 558 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE G 560 " --> pdb=" O ILE G 607 " (cutoff:3.500A) 2073 hydrogen bonds defined for protein. 6114 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: 9.53 Time building geometry restraints manager: 4.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12103 1.34 - 1.46: 4124 1.46 - 1.57: 20884 1.57 - 1.69: 40 1.69 - 1.81: 210 Bond restraints: 37361 Sorted by residual: bond pdb=" C3' ADP A1000 " pdb=" C4' ADP A1000 " ideal model delta sigma weight residual 1.524 1.273 0.251 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C3' ADP B1000 " pdb=" C4' ADP B1000 " ideal model delta sigma weight residual 1.524 1.273 0.251 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C3' ADP C1000 " pdb=" C4' ADP C1000 " ideal model delta sigma weight residual 1.524 1.273 0.251 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C3' ADP H1000 " pdb=" C4' ADP H1000 " ideal model delta sigma weight residual 1.524 1.273 0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C3' ADP G1000 " pdb=" C4' ADP G1000 " ideal model delta sigma weight residual 1.524 1.273 0.251 2.00e-02 2.50e+03 1.57e+02 ... (remaining 37356 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 49896 2.32 - 4.65: 586 4.65 - 6.97: 76 6.97 - 9.29: 15 9.29 - 11.61: 56 Bond angle restraints: 50629 Sorted by residual: angle pdb=" O2B ADP C1000 " pdb=" PB ADP C1000 " pdb=" O3B ADP C1000 " ideal model delta sigma weight residual 119.90 108.29 11.61 3.00e+00 1.11e-01 1.50e+01 angle pdb=" O1A ADP B1000 " pdb=" PA ADP B1000 " pdb=" O2A ADP B1000 " ideal model delta sigma weight residual 119.90 108.33 11.57 3.00e+00 1.11e-01 1.49e+01 angle pdb=" O2B ADP B1000 " pdb=" PB ADP B1000 " pdb=" O3B ADP B1000 " ideal model delta sigma weight residual 119.90 108.38 11.52 3.00e+00 1.11e-01 1.47e+01 angle pdb=" O1A ADP G1000 " pdb=" PA ADP G1000 " pdb=" O2A ADP G1000 " ideal model delta sigma weight residual 119.90 108.45 11.45 3.00e+00 1.11e-01 1.46e+01 angle pdb=" O2B ADP H1000 " pdb=" PB ADP H1000 " pdb=" O3B ADP H1000 " ideal model delta sigma weight residual 119.90 108.45 11.45 3.00e+00 1.11e-01 1.46e+01 ... (remaining 50624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.62: 22274 26.62 - 53.24: 474 53.24 - 79.86: 53 79.86 - 106.48: 10 106.48 - 133.10: 16 Dihedral angle restraints: 22827 sinusoidal: 9192 harmonic: 13635 Sorted by residual: dihedral pdb=" C5' ADP E1000 " pdb=" O5' ADP E1000 " pdb=" PA ADP E1000 " pdb=" O2A ADP E1000 " ideal model delta sinusoidal sigma weight residual -60.00 73.11 -133.10 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" C5' ADP B1000 " pdb=" O5' ADP B1000 " pdb=" PA ADP B1000 " pdb=" O2A ADP B1000 " ideal model delta sinusoidal sigma weight residual -60.00 73.04 -133.04 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" O1B ADP B1000 " pdb=" O3A ADP B1000 " pdb=" PB ADP B1000 " pdb=" PA ADP B1000 " ideal model delta sinusoidal sigma weight residual -60.00 71.61 -131.61 1 2.00e+01 2.50e-03 3.99e+01 ... (remaining 22824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3754 0.036 - 0.073: 1542 0.073 - 0.109: 477 0.109 - 0.145: 222 0.145 - 0.181: 22 Chirality restraints: 6017 Sorted by residual: chirality pdb=" CA ILE F 694 " pdb=" N ILE F 694 " pdb=" C ILE F 694 " pdb=" CB ILE F 694 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.22e-01 chirality pdb=" CA ILE C 694 " pdb=" N ILE C 694 " pdb=" C ILE C 694 " pdb=" CB ILE C 694 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA ILE E 694 " pdb=" N ILE E 694 " pdb=" C ILE E 694 " pdb=" CB ILE E 694 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.22e-01 ... (remaining 6014 not shown) Planarity restraints: 6449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 197 " 0.052 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO C 198 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO C 198 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 198 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 197 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.12e+00 pdb=" N PRO H 198 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO H 198 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO H 198 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 644 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO B 645 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 645 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 645 " -0.032 5.00e-02 4.00e+02 ... (remaining 6446 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 192 2.52 - 3.12: 28064 3.12 - 3.71: 54509 3.71 - 4.31: 75936 4.31 - 4.90: 131779 Nonbonded interactions: 290480 Sorted by model distance: nonbonded pdb=" O1B ADP A1000 " pdb="MG MG A1001 " model vdw 1.931 2.170 nonbonded pdb=" O1B ADP H1000 " pdb="MG MG H1001 " model vdw 1.936 2.170 nonbonded pdb=" O1B ADP G1000 " pdb="MG MG G1001 " model vdw 1.947 2.170 nonbonded pdb=" O1B ADP F1000 " pdb="MG MG F1001 " model vdw 1.964 2.170 nonbonded pdb=" O1B ADP C1000 " pdb="MG MG C1001 " model vdw 1.967 2.170 ... (remaining 290475 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 279 or resid 384 through 1001)) selection = chain 'C' selection = (chain 'D' and (resid 17 through 279 or resid 384 through 1001)) selection = (chain 'F' and (resid 17 through 279 or resid 384 through 1001)) selection = chain 'H' } ncs_group { reference = (chain 'B' and (resid 17 through 261 or resid 409 through 1001)) selection = chain 'E' selection = (chain 'G' and (resid 17 through 261 or resid 409 through 1001)) } 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: 3.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.840 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 38.530 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 0.009 0.251 37361 Z= 0.411 Angle : 0.743 11.614 50629 Z= 0.364 Chirality : 0.047 0.181 6017 Planarity : 0.004 0.079 6449 Dihedral : 12.181 133.103 14033 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 0.30 (0.12), residues: 4665 helix: 1.38 (0.11), residues: 2318 sheet: 0.55 (0.18), residues: 725 loop : -1.75 (0.14), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 609 TYR 0.025 0.001 TYR F 141 PHE 0.021 0.002 PHE B 40 TRP 0.011 0.001 TRP B 477 HIS 0.006 0.001 HIS A 622 Details of bonding type rmsd covalent geometry : bond 0.00870 (37361) covalent geometry : angle 0.74257 (50629) hydrogen bonds : bond 0.12444 ( 2073) hydrogen bonds : angle 5.42567 ( 6114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 58 ASP cc_start: 0.7914 (p0) cc_final: 0.7656 (p0) REVERT: H 113 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7332 (mt-10) REVERT: H 130 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7442 (mt-10) REVERT: A 58 ASP cc_start: 0.8254 (p0) cc_final: 0.7948 (p0) REVERT: A 139 ARG cc_start: 0.7807 (tpt90) cc_final: 0.7551 (tpt170) REVERT: A 141 TYR cc_start: 0.8510 (t80) cc_final: 0.8309 (t80) REVERT: A 164 ASN cc_start: 0.8998 (m-40) cc_final: 0.8728 (m-40) REVERT: B 47 TYR cc_start: 0.8342 (t80) cc_final: 0.8105 (t80) REVERT: B 139 ARG cc_start: 0.7613 (mtp-110) cc_final: 0.7294 (mtm110) REVERT: B 218 LYS cc_start: 0.8028 (tptp) cc_final: 0.7616 (ttpt) REVERT: C 58 ASP cc_start: 0.8475 (p0) cc_final: 0.8151 (p0) REVERT: C 136 ASP cc_start: 0.7597 (t0) cc_final: 0.7385 (t0) REVERT: C 594 MET cc_start: 0.7721 (mtm) cc_final: 0.7508 (mtp) REVERT: D 58 ASP cc_start: 0.8423 (p0) cc_final: 0.8223 (p0) REVERT: D 131 LYS cc_start: 0.9176 (ptmt) cc_final: 0.8965 (pmtt) REVERT: D 162 LYS cc_start: 0.9006 (tppt) cc_final: 0.8781 (tppp) REVERT: D 194 ILE cc_start: 0.8557 (mt) cc_final: 0.8260 (tt) REVERT: E 31 LYS cc_start: 0.7053 (tttm) cc_final: 0.6585 (tppt) REVERT: E 54 ILE cc_start: 0.8643 (mm) cc_final: 0.8426 (mp) REVERT: E 124 LEU cc_start: 0.8571 (pp) cc_final: 0.8371 (pp) REVERT: E 128 MET cc_start: 0.8606 (mtm) cc_final: 0.8230 (mpp) REVERT: E 410 ARG cc_start: 0.7366 (ptm160) cc_final: 0.7057 (ptm160) REVERT: F 105 ASP cc_start: 0.8533 (t0) cc_final: 0.8249 (m-30) REVERT: F 700 LYS cc_start: 0.8570 (mttt) cc_final: 0.8270 (mptt) REVERT: G 31 LYS cc_start: 0.7051 (tttt) cc_final: 0.6649 (tppt) REVERT: G 130 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8112 (tp30) REVERT: G 139 ARG cc_start: 0.7695 (tpt-90) cc_final: 0.7334 (tpt-90) REVERT: G 174 LEU cc_start: 0.6944 (mp) cc_final: 0.6613 (mp) outliers start: 0 outliers final: 1 residues processed: 455 average time/residue: 0.7252 time to fit residues: 399.8486 Evaluate side-chains 333 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 332 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 130 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 258 GLN H 671 ASN H 711 ASN A 206 GLN A 671 ASN C 399 ASN ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN ** D 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN F 314 GLN F 571 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.184554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114866 restraints weight = 40531.748| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.68 r_work: 0.3230 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37361 Z= 0.134 Angle : 0.595 9.039 50629 Z= 0.288 Chirality : 0.044 0.161 6017 Planarity : 0.004 0.057 6449 Dihedral : 5.831 80.740 5142 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.14 % Allowed : 6.65 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 0.83 (0.13), residues: 4665 helix: 1.81 (0.11), residues: 2329 sheet: 0.97 (0.19), residues: 725 loop : -1.60 (0.14), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 139 TYR 0.022 0.001 TYR A 343 PHE 0.014 0.001 PHE F 117 TRP 0.006 0.001 TRP B 477 HIS 0.002 0.001 HIS D 571 Details of bonding type rmsd covalent geometry : bond 0.00309 (37361) covalent geometry : angle 0.59534 (50629) hydrogen bonds : bond 0.03896 ( 2073) hydrogen bonds : angle 4.33533 ( 6114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 379 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 58 ASP cc_start: 0.8322 (p0) cc_final: 0.8105 (p0) REVERT: H 113 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7429 (mt-10) REVERT: H 136 ASP cc_start: 0.7485 (t0) cc_final: 0.7263 (t0) REVERT: H 167 ILE cc_start: 0.7863 (mt) cc_final: 0.7652 (mp) REVERT: H 195 ASP cc_start: 0.8135 (t0) cc_final: 0.7613 (m-30) REVERT: H 258 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7240 (tm-30) REVERT: A 58 ASP cc_start: 0.8561 (p0) cc_final: 0.8252 (p0) REVERT: A 120 ILE cc_start: 0.8647 (pt) cc_final: 0.8321 (pp) REVERT: A 139 ARG cc_start: 0.7572 (tpt90) cc_final: 0.7206 (tpt170) REVERT: A 193 GLU cc_start: 0.7608 (tp30) cc_final: 0.7371 (tp30) REVERT: B 139 ARG cc_start: 0.7794 (mtp-110) cc_final: 0.7328 (mtm110) REVERT: B 218 LYS cc_start: 0.8199 (tptp) cc_final: 0.7689 (ttpt) REVERT: B 611 GLN cc_start: 0.7178 (mm-40) cc_final: 0.6880 (mm110) REVERT: C 58 ASP cc_start: 0.8703 (p0) cc_final: 0.8412 (p0) REVERT: C 523 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7472 (tm-30) REVERT: C 594 MET cc_start: 0.8865 (mtm) cc_final: 0.8602 (mtp) REVERT: D 131 LYS cc_start: 0.9214 (ptmt) cc_final: 0.8883 (pmtt) REVERT: D 139 ARG cc_start: 0.7806 (tpt170) cc_final: 0.7443 (tpt170) REVERT: D 162 LYS cc_start: 0.8794 (tppt) cc_final: 0.8531 (tmmt) REVERT: D 680 MET cc_start: 0.8389 (mtm) cc_final: 0.8041 (mmm) REVERT: E 23 ILE cc_start: 0.8158 (mm) cc_final: 0.7941 (mp) REVERT: E 31 LYS cc_start: 0.7028 (tttm) cc_final: 0.6484 (tppt) REVERT: E 54 ILE cc_start: 0.8589 (mm) cc_final: 0.8345 (mp) REVERT: E 113 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7315 (mt-10) REVERT: E 130 GLU cc_start: 0.7683 (mp0) cc_final: 0.7187 (mp0) REVERT: E 190 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7780 (tm) REVERT: E 231 MET cc_start: 0.8583 (mmt) cc_final: 0.8376 (mmt) REVERT: E 410 ARG cc_start: 0.7633 (ptm160) cc_final: 0.7405 (ttm-80) REVERT: E 634 GLN cc_start: 0.9158 (mt0) cc_final: 0.8704 (mm110) REVERT: F 105 ASP cc_start: 0.8676 (t0) cc_final: 0.8381 (m-30) REVERT: F 130 GLU cc_start: 0.7893 (mp0) cc_final: 0.7438 (OUTLIER) REVERT: F 410 ARG cc_start: 0.7316 (ttp80) cc_final: 0.7102 (ttp80) REVERT: F 447 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6650 (t80) REVERT: F 680 MET cc_start: 0.8242 (mtm) cc_final: 0.7741 (mmm) REVERT: F 700 LYS cc_start: 0.8812 (mttt) cc_final: 0.8289 (mptt) REVERT: G 31 LYS cc_start: 0.7108 (tttt) cc_final: 0.6628 (tppt) REVERT: G 105 ASP cc_start: 0.8592 (t0) cc_final: 0.8351 (m-30) REVERT: G 130 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7931 (tp30) REVERT: G 139 ARG cc_start: 0.7884 (tpt-90) cc_final: 0.7336 (tpt-90) REVERT: G 459 GLU cc_start: 0.7840 (mp0) cc_final: 0.7605 (mp0) REVERT: G 525 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8182 (pttm) REVERT: G 657 ARG cc_start: 0.8474 (mmm160) cc_final: 0.8099 (mtm180) REVERT: G 680 MET cc_start: 0.8125 (mtm) cc_final: 0.7657 (mmm) outliers start: 46 outliers final: 15 residues processed: 406 average time/residue: 0.6844 time to fit residues: 339.9624 Evaluate side-chains 346 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 328 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 258 GLN Chi-restraints excluded: chain H residue 474 ILE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 705 TYR Chi-restraints excluded: chain F residue 447 PHE Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 525 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 383 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 137 optimal weight: 0.3980 chunk 150 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 458 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 202 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 350 optimal weight: 7.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN ** D 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN F 317 ASN F 321 GLN ** F 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.183320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.113158 restraints weight = 40822.768| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.62 r_work: 0.3225 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 37361 Z= 0.156 Angle : 0.588 9.305 50629 Z= 0.283 Chirality : 0.044 0.174 6017 Planarity : 0.004 0.050 6449 Dihedral : 5.323 68.498 5139 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.56 % Allowed : 8.48 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 0.96 (0.13), residues: 4665 helix: 1.93 (0.11), residues: 2328 sheet: 1.04 (0.19), residues: 722 loop : -1.56 (0.14), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 139 TYR 0.021 0.001 TYR A 343 PHE 0.013 0.001 PHE F 117 TRP 0.007 0.001 TRP E 477 HIS 0.003 0.001 HIS A 622 Details of bonding type rmsd covalent geometry : bond 0.00376 (37361) covalent geometry : angle 0.58825 (50629) hydrogen bonds : bond 0.03887 ( 2073) hydrogen bonds : angle 4.15474 ( 6114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 360 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 58 ASP cc_start: 0.8271 (p0) cc_final: 0.8065 (p0) REVERT: H 113 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7415 (mt-10) REVERT: H 136 ASP cc_start: 0.7557 (t0) cc_final: 0.7290 (t0) REVERT: H 185 LYS cc_start: 0.8822 (ttpt) cc_final: 0.8600 (tptp) REVERT: H 195 ASP cc_start: 0.8362 (t0) cc_final: 0.8076 (t0) REVERT: A 58 ASP cc_start: 0.8536 (p0) cc_final: 0.8248 (p0) REVERT: A 120 ILE cc_start: 0.8606 (pt) cc_final: 0.8267 (pp) REVERT: A 139 ARG cc_start: 0.7713 (tpt90) cc_final: 0.7320 (tpt170) REVERT: A 185 LYS cc_start: 0.8700 (mppt) cc_final: 0.8376 (pttt) REVERT: A 193 GLU cc_start: 0.7413 (tp30) cc_final: 0.6995 (tp30) REVERT: A 540 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7663 (mtp) REVERT: B 25 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8334 (mm-30) REVERT: B 139 ARG cc_start: 0.7765 (mtp-110) cc_final: 0.7330 (mtm110) REVERT: B 218 LYS cc_start: 0.8183 (tptp) cc_final: 0.7602 (ttmt) REVERT: B 657 ARG cc_start: 0.8255 (mmm160) cc_final: 0.7731 (mtt180) REVERT: C 58 ASP cc_start: 0.8627 (p0) cc_final: 0.8363 (p0) REVERT: C 195 ASP cc_start: 0.8042 (t0) cc_final: 0.7758 (t0) REVERT: C 410 ARG cc_start: 0.6530 (ptp-110) cc_final: 0.6305 (ptp-110) REVERT: C 594 MET cc_start: 0.8860 (mtm) cc_final: 0.8581 (mtp) REVERT: D 131 LYS cc_start: 0.9196 (ptmt) cc_final: 0.8868 (pmtt) REVERT: D 139 ARG cc_start: 0.7882 (tpt170) cc_final: 0.7566 (tpt170) REVERT: D 680 MET cc_start: 0.8298 (mtm) cc_final: 0.7949 (mmm) REVERT: E 31 LYS cc_start: 0.6985 (tttm) cc_final: 0.6462 (tppt) REVERT: E 54 ILE cc_start: 0.8536 (mm) cc_final: 0.8288 (mp) REVERT: E 113 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7227 (mt-10) REVERT: E 130 GLU cc_start: 0.7743 (mp0) cc_final: 0.7305 (mp0) REVERT: E 634 GLN cc_start: 0.9153 (mt0) cc_final: 0.8690 (mm110) REVERT: F 105 ASP cc_start: 0.8679 (t0) cc_final: 0.8374 (m-30) REVERT: F 130 GLU cc_start: 0.7888 (mp0) cc_final: 0.7367 (OUTLIER) REVERT: F 680 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7683 (mmm) REVERT: F 700 LYS cc_start: 0.8812 (mttt) cc_final: 0.8290 (mptt) REVERT: G 31 LYS cc_start: 0.7074 (tttt) cc_final: 0.6606 (tppt) REVERT: G 105 ASP cc_start: 0.8563 (t0) cc_final: 0.8324 (m-30) REVERT: G 130 GLU cc_start: 0.8517 (mt-10) cc_final: 0.7597 (mp0) REVERT: G 139 ARG cc_start: 0.7931 (tpt-90) cc_final: 0.7409 (tpt-90) REVERT: G 162 LYS cc_start: 0.8557 (tppp) cc_final: 0.7937 (tptp) REVERT: G 657 ARG cc_start: 0.8480 (mmm160) cc_final: 0.8084 (mtm180) REVERT: G 680 MET cc_start: 0.8081 (mtm) cc_final: 0.7655 (mmm) outliers start: 63 outliers final: 26 residues processed: 392 average time/residue: 0.6900 time to fit residues: 330.6832 Evaluate side-chains 354 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 327 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 474 ILE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 705 TYR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 680 MET Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 229 THR Chi-restraints excluded: chain G residue 522 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 340 optimal weight: 1.9990 chunk 433 optimal weight: 0.0970 chunk 221 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 395 optimal weight: 0.4980 chunk 348 optimal weight: 10.0000 chunk 282 optimal weight: 3.9990 chunk 299 optimal weight: 6.9990 chunk 291 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 396 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 258 GLN H 710 HIS ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 ASN ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN D 107 ASN ** D 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** E 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.185867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.115538 restraints weight = 40626.720| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.65 r_work: 0.3268 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 37361 Z= 0.107 Angle : 0.553 8.515 50629 Z= 0.263 Chirality : 0.043 0.158 6017 Planarity : 0.003 0.045 6449 Dihedral : 4.988 60.765 5139 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.19 % Allowed : 10.34 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 1.22 (0.13), residues: 4665 helix: 2.16 (0.11), residues: 2333 sheet: 1.21 (0.19), residues: 723 loop : -1.51 (0.14), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 139 TYR 0.017 0.001 TYR A 343 PHE 0.013 0.001 PHE F 117 TRP 0.004 0.001 TRP B 477 HIS 0.003 0.000 HIS E 710 Details of bonding type rmsd covalent geometry : bond 0.00236 (37361) covalent geometry : angle 0.55306 (50629) hydrogen bonds : bond 0.03343 ( 2073) hydrogen bonds : angle 3.92796 ( 6114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 379 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 58 ASP cc_start: 0.8276 (p0) cc_final: 0.8032 (p0) REVERT: H 113 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7500 (mt-10) REVERT: H 185 LYS cc_start: 0.8853 (ttpt) cc_final: 0.8560 (tptp) REVERT: H 195 ASP cc_start: 0.8386 (t0) cc_final: 0.8003 (t0) REVERT: A 58 ASP cc_start: 0.8516 (p0) cc_final: 0.8274 (p0) REVERT: A 120 ILE cc_start: 0.8655 (pt) cc_final: 0.8281 (pp) REVERT: A 139 ARG cc_start: 0.7778 (tpt90) cc_final: 0.7438 (tpt170) REVERT: A 184 GLU cc_start: 0.7130 (mp0) cc_final: 0.6356 (pm20) REVERT: A 193 GLU cc_start: 0.7430 (tp30) cc_final: 0.6877 (tp30) REVERT: A 657 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7779 (mtp180) REVERT: B 139 ARG cc_start: 0.7869 (mtp-110) cc_final: 0.7347 (mtm110) REVERT: B 218 LYS cc_start: 0.8179 (tptp) cc_final: 0.7602 (ttpt) REVERT: B 611 GLN cc_start: 0.7172 (mm-40) cc_final: 0.6872 (mm110) REVERT: B 657 ARG cc_start: 0.8261 (mmm160) cc_final: 0.7735 (mtt180) REVERT: B 684 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7526 (mp0) REVERT: C 58 ASP cc_start: 0.8672 (p0) cc_final: 0.8468 (p0) REVERT: C 131 LYS cc_start: 0.9227 (ptpp) cc_final: 0.9001 (ptmm) REVERT: C 594 MET cc_start: 0.8865 (mtm) cc_final: 0.8596 (mtp) REVERT: D 85 GLN cc_start: 0.5691 (OUTLIER) cc_final: 0.5463 (pm20) REVERT: D 89 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8038 (mm-30) REVERT: D 92 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7877 (tt) REVERT: D 131 LYS cc_start: 0.9180 (ptmt) cc_final: 0.8866 (pmtt) REVERT: D 139 ARG cc_start: 0.7852 (tpt170) cc_final: 0.7567 (tpt170) REVERT: D 174 LEU cc_start: 0.7039 (mm) cc_final: 0.6779 (mp) REVERT: D 680 MET cc_start: 0.8231 (mtm) cc_final: 0.7866 (mmm) REVERT: E 23 ILE cc_start: 0.8149 (mm) cc_final: 0.7940 (mp) REVERT: E 31 LYS cc_start: 0.6994 (tttm) cc_final: 0.6505 (tppt) REVERT: E 54 ILE cc_start: 0.8566 (mm) cc_final: 0.8299 (mp) REVERT: E 113 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7267 (mt-10) REVERT: E 130 GLU cc_start: 0.7793 (mp0) cc_final: 0.7290 (mp0) REVERT: E 190 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7804 (tm) REVERT: E 634 GLN cc_start: 0.9158 (mt0) cc_final: 0.8695 (mm110) REVERT: E 658 TYR cc_start: 0.8907 (m-80) cc_final: 0.8669 (m-80) REVERT: F 105 ASP cc_start: 0.8656 (t0) cc_final: 0.8384 (m-30) REVERT: F 113 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7218 (mt-10) REVERT: F 130 GLU cc_start: 0.7929 (mp0) cc_final: 0.7393 (OUTLIER) REVERT: F 447 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6594 (t80) REVERT: F 680 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7776 (mmm) REVERT: F 700 LYS cc_start: 0.8774 (mttt) cc_final: 0.8282 (mptt) REVERT: G 31 LYS cc_start: 0.7086 (tttt) cc_final: 0.6624 (tppt) REVERT: G 105 ASP cc_start: 0.8555 (t0) cc_final: 0.8321 (m-30) REVERT: G 130 GLU cc_start: 0.8503 (mt-10) cc_final: 0.7620 (OUTLIER) REVERT: G 139 ARG cc_start: 0.7982 (tpt-90) cc_final: 0.7461 (tpt-90) REVERT: G 162 LYS cc_start: 0.8597 (tppp) cc_final: 0.7996 (tptp) REVERT: G 657 ARG cc_start: 0.8519 (mmm160) cc_final: 0.8141 (mtm180) REVERT: G 680 MET cc_start: 0.8110 (mtm) cc_final: 0.7647 (mmm) outliers start: 48 outliers final: 16 residues processed: 408 average time/residue: 0.6761 time to fit residues: 338.4740 Evaluate side-chains 368 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 348 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 447 PHE Chi-restraints excluded: chain F residue 680 MET Chi-restraints excluded: chain G residue 444 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 67 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 310 optimal weight: 0.9990 chunk 269 optimal weight: 9.9990 chunk 260 optimal weight: 30.0000 chunk 102 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN D 164 ASN ** D 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** E 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 711 ASN ** F 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.183712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.113105 restraints weight = 40808.403| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.64 r_work: 0.3234 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 37361 Z= 0.153 Angle : 0.577 8.455 50629 Z= 0.276 Chirality : 0.044 0.165 6017 Planarity : 0.004 0.092 6449 Dihedral : 5.164 67.731 5139 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.64 % Allowed : 11.18 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 1.16 (0.13), residues: 4665 helix: 2.12 (0.11), residues: 2335 sheet: 1.19 (0.20), residues: 681 loop : -1.51 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 139 TYR 0.017 0.001 TYR E 165 PHE 0.013 0.001 PHE A 117 TRP 0.006 0.001 TRP E 477 HIS 0.003 0.001 HIS A 622 Details of bonding type rmsd covalent geometry : bond 0.00371 (37361) covalent geometry : angle 0.57712 (50629) hydrogen bonds : bond 0.03641 ( 2073) hydrogen bonds : angle 3.95175 ( 6114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 362 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 58 ASP cc_start: 0.8273 (p0) cc_final: 0.8038 (p0) REVERT: H 113 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7479 (mt-10) REVERT: H 185 LYS cc_start: 0.8862 (ttpt) cc_final: 0.8519 (tptp) REVERT: H 195 ASP cc_start: 0.8671 (t0) cc_final: 0.8307 (OUTLIER) REVERT: H 410 ARG cc_start: 0.6727 (mtt-85) cc_final: 0.6494 (mtp85) REVERT: A 58 ASP cc_start: 0.8521 (p0) cc_final: 0.8286 (p0) REVERT: A 120 ILE cc_start: 0.8609 (pt) cc_final: 0.8279 (pp) REVERT: A 139 ARG cc_start: 0.7918 (tpt90) cc_final: 0.7530 (tpt170) REVERT: A 193 GLU cc_start: 0.7371 (tp30) cc_final: 0.6750 (tp30) REVERT: A 343 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.6841 (t80) REVERT: A 657 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7771 (mtp180) REVERT: B 131 LYS cc_start: 0.9194 (mtpp) cc_final: 0.8946 (mmmm) REVERT: B 139 ARG cc_start: 0.7851 (mtp-110) cc_final: 0.7373 (mtm110) REVERT: B 218 LYS cc_start: 0.8196 (tptp) cc_final: 0.7610 (ttpt) REVERT: B 410 ARG cc_start: 0.7528 (ttp-170) cc_final: 0.7181 (ttm170) REVERT: B 657 ARG cc_start: 0.8285 (mmm160) cc_final: 0.7760 (mtt180) REVERT: C 58 ASP cc_start: 0.8686 (p0) cc_final: 0.8472 (p0) REVERT: C 594 MET cc_start: 0.8852 (mtm) cc_final: 0.8582 (mtp) REVERT: D 89 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8134 (mm-30) REVERT: D 92 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7962 (tt) REVERT: D 131 LYS cc_start: 0.9163 (ptmt) cc_final: 0.8844 (pmtt) REVERT: D 139 ARG cc_start: 0.7904 (tpt170) cc_final: 0.7562 (tpt170) REVERT: D 200 ASP cc_start: 0.8416 (m-30) cc_final: 0.8139 (m-30) REVERT: D 680 MET cc_start: 0.8295 (mtm) cc_final: 0.7953 (mmm) REVERT: E 23 ILE cc_start: 0.8183 (mm) cc_final: 0.7967 (mp) REVERT: E 31 LYS cc_start: 0.7017 (tttm) cc_final: 0.6512 (tppt) REVERT: E 113 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7264 (mt-10) REVERT: E 130 GLU cc_start: 0.7845 (mp0) cc_final: 0.7286 (mp0) REVERT: E 190 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7763 (tm) REVERT: E 634 GLN cc_start: 0.9154 (mt0) cc_final: 0.8697 (mm110) REVERT: E 658 TYR cc_start: 0.8918 (m-80) cc_final: 0.8665 (m-80) REVERT: F 105 ASP cc_start: 0.8680 (t0) cc_final: 0.8389 (m-30) REVERT: F 113 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7217 (mt-10) REVERT: F 130 GLU cc_start: 0.7966 (mp0) cc_final: 0.7402 (OUTLIER) REVERT: F 447 PHE cc_start: 0.7314 (OUTLIER) cc_final: 0.6671 (t80) REVERT: F 680 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7812 (mmm) REVERT: F 700 LYS cc_start: 0.8809 (mttt) cc_final: 0.8298 (mptt) REVERT: G 31 LYS cc_start: 0.7147 (tttt) cc_final: 0.6663 (tppt) REVERT: G 105 ASP cc_start: 0.8570 (t0) cc_final: 0.8346 (m-30) REVERT: G 130 GLU cc_start: 0.8555 (mt-10) cc_final: 0.7640 (mp0) REVERT: G 139 ARG cc_start: 0.8042 (tpt-90) cc_final: 0.7475 (tpt-90) REVERT: G 162 LYS cc_start: 0.8665 (tppp) cc_final: 0.8052 (tptp) REVERT: G 207 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6950 (pp) REVERT: G 657 ARG cc_start: 0.8523 (mmm160) cc_final: 0.8128 (mtm180) REVERT: G 680 MET cc_start: 0.8164 (mtm) cc_final: 0.7726 (mmm) outliers start: 66 outliers final: 37 residues processed: 401 average time/residue: 0.6394 time to fit residues: 316.5561 Evaluate side-chains 386 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 344 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 447 PHE Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 680 MET Chi-restraints excluded: chain F residue 705 TYR Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 229 THR Chi-restraints excluded: chain G residue 444 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 185 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 341 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 343 optimal weight: 0.9990 chunk 330 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 258 optimal weight: 7.9990 chunk 257 optimal weight: 20.0000 chunk 387 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** E 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 711 ASN ** F 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.185245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.115808 restraints weight = 40502.122| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.61 r_work: 0.3268 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37361 Z= 0.111 Angle : 0.557 8.883 50629 Z= 0.265 Chirality : 0.043 0.209 6017 Planarity : 0.003 0.043 6449 Dihedral : 4.922 62.611 5139 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.49 % Allowed : 12.05 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 1.34 (0.13), residues: 4665 helix: 2.27 (0.11), residues: 2341 sheet: 1.28 (0.19), residues: 733 loop : -1.52 (0.14), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 139 TYR 0.019 0.001 TYR F 705 PHE 0.013 0.001 PHE F 117 TRP 0.004 0.001 TRP E 477 HIS 0.002 0.000 HIS F 571 Details of bonding type rmsd covalent geometry : bond 0.00251 (37361) covalent geometry : angle 0.55695 (50629) hydrogen bonds : bond 0.03286 ( 2073) hydrogen bonds : angle 3.83041 ( 6114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 365 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 58 ASP cc_start: 0.8255 (p0) cc_final: 0.8035 (p0) REVERT: H 113 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7490 (mt-10) REVERT: H 185 LYS cc_start: 0.8879 (ttpt) cc_final: 0.8545 (tptp) REVERT: H 195 ASP cc_start: 0.8783 (t0) cc_final: 0.8438 (OUTLIER) REVERT: H 216 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7642 (tt) REVERT: A 58 ASP cc_start: 0.8466 (p0) cc_final: 0.8222 (p0) REVERT: A 120 ILE cc_start: 0.8558 (pt) cc_final: 0.8231 (pp) REVERT: A 139 ARG cc_start: 0.7896 (tpt90) cc_final: 0.7533 (tpt170) REVERT: A 193 GLU cc_start: 0.7332 (tp30) cc_final: 0.6676 (tp30) REVERT: A 343 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.6817 (t80) REVERT: A 657 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7747 (mtp180) REVERT: B 131 LYS cc_start: 0.9215 (mtpp) cc_final: 0.8982 (mmmm) REVERT: B 139 ARG cc_start: 0.7961 (mtp-110) cc_final: 0.7418 (mtm110) REVERT: B 218 LYS cc_start: 0.8183 (tptp) cc_final: 0.7591 (ttmt) REVERT: B 410 ARG cc_start: 0.7537 (ttp-170) cc_final: 0.7162 (ttm170) REVERT: B 657 ARG cc_start: 0.8290 (mmm160) cc_final: 0.7757 (mtt180) REVERT: B 684 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7441 (mp0) REVERT: C 594 MET cc_start: 0.8869 (mtm) cc_final: 0.8595 (mtp) REVERT: D 89 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8049 (mm-30) REVERT: D 92 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7887 (tt) REVERT: D 131 LYS cc_start: 0.9165 (ptmt) cc_final: 0.8850 (pmtt) REVERT: D 139 ARG cc_start: 0.7820 (tpt170) cc_final: 0.7519 (tpt170) REVERT: D 200 ASP cc_start: 0.8461 (m-30) cc_final: 0.8172 (m-30) REVERT: D 259 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.7965 (t0) REVERT: D 680 MET cc_start: 0.8223 (mtm) cc_final: 0.7895 (mmm) REVERT: E 31 LYS cc_start: 0.7003 (tttm) cc_final: 0.6504 (tppt) REVERT: E 113 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7246 (mt-10) REVERT: E 120 ILE cc_start: 0.8775 (pp) cc_final: 0.8388 (pp) REVERT: E 124 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8611 (mm) REVERT: E 130 GLU cc_start: 0.7877 (mp0) cc_final: 0.7304 (mp0) REVERT: E 136 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.7225 (p0) REVERT: E 634 GLN cc_start: 0.9148 (mt0) cc_final: 0.8679 (mm110) REVERT: F 105 ASP cc_start: 0.8643 (t0) cc_final: 0.8408 (m-30) REVERT: F 113 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7203 (mt-10) REVERT: F 130 GLU cc_start: 0.8004 (mp0) cc_final: 0.7406 (OUTLIER) REVERT: F 447 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.6613 (t80) REVERT: F 680 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7664 (mmm) REVERT: F 700 LYS cc_start: 0.8844 (mttt) cc_final: 0.8324 (mptt) REVERT: G 31 LYS cc_start: 0.7102 (tttt) cc_final: 0.6628 (tppt) REVERT: G 105 ASP cc_start: 0.8567 (t0) cc_final: 0.8353 (m-30) REVERT: G 130 GLU cc_start: 0.8562 (mt-10) cc_final: 0.7660 (mp0) REVERT: G 139 ARG cc_start: 0.8058 (tpt-90) cc_final: 0.7441 (tpt-90) REVERT: G 162 LYS cc_start: 0.8626 (tppp) cc_final: 0.8066 (tptp) REVERT: G 657 ARG cc_start: 0.8523 (mmm160) cc_final: 0.8113 (mtm180) REVERT: G 680 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7700 (mmm) outliers start: 60 outliers final: 30 residues processed: 403 average time/residue: 0.6079 time to fit residues: 300.1809 Evaluate side-chains 384 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 346 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 447 PHE Chi-restraints excluded: chain F residue 680 MET Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 229 THR Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 521 MET Chi-restraints excluded: chain G residue 680 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 98 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 267 optimal weight: 0.7980 chunk 421 optimal weight: 0.0970 chunk 94 optimal weight: 4.9990 chunk 286 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 696 ASN D 696 ASN D 711 ASN E 696 ASN E 711 ASN ** F 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.186665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117371 restraints weight = 40447.324| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.61 r_work: 0.3296 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 37361 Z= 0.100 Angle : 0.557 9.278 50629 Z= 0.264 Chirality : 0.042 0.185 6017 Planarity : 0.003 0.042 6449 Dihedral : 4.728 59.955 5139 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.19 % Allowed : 12.89 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 1.48 (0.13), residues: 4665 helix: 2.39 (0.11), residues: 2351 sheet: 1.38 (0.19), residues: 733 loop : -1.51 (0.14), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 139 TYR 0.016 0.001 TYR E 165 PHE 0.013 0.001 PHE F 117 TRP 0.004 0.000 TRP B 477 HIS 0.002 0.000 HIS F 571 Details of bonding type rmsd covalent geometry : bond 0.00220 (37361) covalent geometry : angle 0.55683 (50629) hydrogen bonds : bond 0.03110 ( 2073) hydrogen bonds : angle 3.74202 ( 6114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 367 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 113 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7502 (mt-10) REVERT: H 185 LYS cc_start: 0.8887 (ttpt) cc_final: 0.8543 (tptp) REVERT: H 195 ASP cc_start: 0.8887 (t0) cc_final: 0.8564 (t0) REVERT: H 216 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7676 (tt) REVERT: A 58 ASP cc_start: 0.8437 (p0) cc_final: 0.8165 (p0) REVERT: A 139 ARG cc_start: 0.7965 (tpt90) cc_final: 0.7603 (tpt170) REVERT: A 193 GLU cc_start: 0.7355 (tp30) cc_final: 0.6650 (tp30) REVERT: A 343 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.6845 (t80) REVERT: A 657 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7716 (mtp180) REVERT: B 131 LYS cc_start: 0.9213 (mtpp) cc_final: 0.8998 (mmmm) REVERT: B 139 ARG cc_start: 0.7955 (mtp-110) cc_final: 0.7457 (mtm110) REVERT: B 218 LYS cc_start: 0.8160 (tptp) cc_final: 0.7560 (ttmt) REVERT: B 410 ARG cc_start: 0.7462 (ttp-170) cc_final: 0.7093 (ttm170) REVERT: B 657 ARG cc_start: 0.8267 (mmm160) cc_final: 0.7741 (mtt180) REVERT: B 684 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7392 (mp0) REVERT: C 136 ASP cc_start: 0.7855 (t0) cc_final: 0.6694 (p0) REVERT: C 193 GLU cc_start: 0.7659 (mp0) cc_final: 0.6942 (mp0) REVERT: C 447 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7630 (t80) REVERT: C 594 MET cc_start: 0.8868 (mtm) cc_final: 0.8604 (mtp) REVERT: D 89 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7944 (mm-30) REVERT: D 92 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7844 (tt) REVERT: D 105 ASP cc_start: 0.8402 (m-30) cc_final: 0.8130 (m-30) REVERT: D 131 LYS cc_start: 0.9164 (ptmt) cc_final: 0.8865 (pmtt) REVERT: D 139 ARG cc_start: 0.7885 (tpt170) cc_final: 0.7513 (tpt170) REVERT: D 200 ASP cc_start: 0.8428 (m-30) cc_final: 0.8162 (m-30) REVERT: D 259 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.7838 (t0) REVERT: D 680 MET cc_start: 0.8156 (mtm) cc_final: 0.7823 (mmm) REVERT: E 23 ILE cc_start: 0.8211 (mm) cc_final: 0.8009 (mp) REVERT: E 31 LYS cc_start: 0.7045 (tttm) cc_final: 0.6549 (tppt) REVERT: E 62 GLN cc_start: 0.8318 (tt0) cc_final: 0.8035 (pt0) REVERT: E 113 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7203 (mt-10) REVERT: E 120 ILE cc_start: 0.8734 (pp) cc_final: 0.8335 (pp) REVERT: E 124 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8546 (mm) REVERT: E 130 GLU cc_start: 0.7904 (mp0) cc_final: 0.7310 (mp0) REVERT: E 136 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7300 (p0) REVERT: E 410 ARG cc_start: 0.7336 (ttp-110) cc_final: 0.6952 (ptm-80) REVERT: E 626 GLU cc_start: 0.7426 (tt0) cc_final: 0.6756 (tp30) REVERT: E 634 GLN cc_start: 0.9161 (mt0) cc_final: 0.8685 (mm110) REVERT: E 658 TYR cc_start: 0.8582 (m-80) cc_final: 0.8232 (m-80) REVERT: F 105 ASP cc_start: 0.8631 (t0) cc_final: 0.8404 (m-30) REVERT: F 113 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7161 (mt-10) REVERT: F 130 GLU cc_start: 0.8005 (mp0) cc_final: 0.7394 (OUTLIER) REVERT: F 447 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6591 (t80) REVERT: F 680 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7675 (mmm) REVERT: F 700 LYS cc_start: 0.8819 (mttt) cc_final: 0.8285 (mptt) REVERT: G 105 ASP cc_start: 0.8561 (t0) cc_final: 0.8351 (m-30) REVERT: G 130 GLU cc_start: 0.8569 (mt-10) cc_final: 0.7671 (mp0) REVERT: G 139 ARG cc_start: 0.8106 (tpt-90) cc_final: 0.7484 (tpt-90) REVERT: G 162 LYS cc_start: 0.8727 (tppp) cc_final: 0.8178 (tptp) REVERT: G 657 ARG cc_start: 0.8528 (mmm160) cc_final: 0.8138 (mtm180) REVERT: G 680 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7669 (mmm) outliers start: 48 outliers final: 22 residues processed: 397 average time/residue: 0.6572 time to fit residues: 320.7212 Evaluate side-chains 387 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 355 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 447 PHE Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 680 MET Chi-restraints excluded: chain F residue 705 TYR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 229 THR Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 680 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 356 optimal weight: 8.9990 chunk 406 optimal weight: 0.9980 chunk 414 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 241 optimal weight: 2.9990 chunk 265 optimal weight: 40.0000 chunk 335 optimal weight: 0.0070 chunk 176 optimal weight: 10.0000 chunk 296 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 328 optimal weight: 0.7980 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN D 164 ASN D 711 ASN E 711 ASN ** F 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.188283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.118041 restraints weight = 40276.562| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.63 r_work: 0.3296 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 37361 Z= 0.103 Angle : 0.557 10.067 50629 Z= 0.264 Chirality : 0.042 0.196 6017 Planarity : 0.003 0.042 6449 Dihedral : 4.692 60.029 5139 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.07 % Allowed : 13.54 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 1.58 (0.13), residues: 4665 helix: 2.46 (0.11), residues: 2353 sheet: 1.45 (0.19), residues: 733 loop : -1.47 (0.14), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 139 TYR 0.017 0.001 TYR B 141 PHE 0.014 0.001 PHE F 117 TRP 0.004 0.000 TRP B 477 HIS 0.002 0.000 HIS F 571 Details of bonding type rmsd covalent geometry : bond 0.00231 (37361) covalent geometry : angle 0.55686 (50629) hydrogen bonds : bond 0.03107 ( 2073) hydrogen bonds : angle 3.71593 ( 6114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 363 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 113 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7544 (mt-10) REVERT: H 185 LYS cc_start: 0.8892 (ttpt) cc_final: 0.8572 (tptp) REVERT: H 195 ASP cc_start: 0.8946 (t0) cc_final: 0.7994 (p0) REVERT: H 216 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7661 (tt) REVERT: A 58 ASP cc_start: 0.8448 (p0) cc_final: 0.8171 (p0) REVERT: A 139 ARG cc_start: 0.7936 (tpt90) cc_final: 0.7590 (tpt170) REVERT: A 193 GLU cc_start: 0.7464 (tp30) cc_final: 0.7160 (tp30) REVERT: A 343 TYR cc_start: 0.7229 (OUTLIER) cc_final: 0.6763 (t80) REVERT: A 657 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7707 (mtp180) REVERT: B 139 ARG cc_start: 0.8028 (mtp-110) cc_final: 0.7484 (mtm110) REVERT: B 218 LYS cc_start: 0.8166 (tptp) cc_final: 0.7581 (ttmt) REVERT: B 410 ARG cc_start: 0.7478 (ttp-170) cc_final: 0.7130 (ttm170) REVERT: B 657 ARG cc_start: 0.8299 (mmm160) cc_final: 0.7797 (mtt180) REVERT: B 684 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7473 (mp0) REVERT: C 131 LYS cc_start: 0.9190 (ptpp) cc_final: 0.8988 (ptmm) REVERT: C 136 ASP cc_start: 0.7923 (t0) cc_final: 0.6801 (p0) REVERT: C 193 GLU cc_start: 0.7600 (mp0) cc_final: 0.6888 (mp0) REVERT: C 224 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7332 (t0) REVERT: C 410 ARG cc_start: 0.6399 (ptp-110) cc_final: 0.5722 (ptp90) REVERT: C 447 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7659 (t80) REVERT: C 594 MET cc_start: 0.8790 (mtm) cc_final: 0.8516 (mtp) REVERT: D 89 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8032 (mm-30) REVERT: D 92 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7977 (tt) REVERT: D 131 LYS cc_start: 0.9131 (ptmt) cc_final: 0.8840 (pmtt) REVERT: D 139 ARG cc_start: 0.7845 (tpt170) cc_final: 0.7555 (tpt170) REVERT: D 200 ASP cc_start: 0.8424 (m-30) cc_final: 0.8163 (m-30) REVERT: D 259 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.7821 (t0) REVERT: D 680 MET cc_start: 0.8191 (mtm) cc_final: 0.7856 (mmm) REVERT: E 31 LYS cc_start: 0.7134 (tttm) cc_final: 0.6630 (tppt) REVERT: E 113 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7212 (mt-10) REVERT: E 120 ILE cc_start: 0.8745 (pp) cc_final: 0.8340 (pp) REVERT: E 124 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8547 (mm) REVERT: E 130 GLU cc_start: 0.7922 (mp0) cc_final: 0.7313 (mp0) REVERT: E 136 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.7359 (p0) REVERT: E 626 GLU cc_start: 0.7459 (tt0) cc_final: 0.6749 (tp30) REVERT: E 634 GLN cc_start: 0.9167 (mt0) cc_final: 0.8691 (mm110) REVERT: E 658 TYR cc_start: 0.8652 (m-80) cc_final: 0.8311 (m-80) REVERT: F 105 ASP cc_start: 0.8684 (t0) cc_final: 0.8457 (m-30) REVERT: F 113 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7202 (mt-10) REVERT: F 130 GLU cc_start: 0.8038 (mp0) cc_final: 0.7449 (OUTLIER) REVERT: F 447 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.6653 (t80) REVERT: F 680 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7735 (mmm) REVERT: F 700 LYS cc_start: 0.8743 (mttt) cc_final: 0.8228 (mptt) REVERT: G 105 ASP cc_start: 0.8591 (t0) cc_final: 0.8387 (m-30) REVERT: G 130 GLU cc_start: 0.8591 (mt-10) cc_final: 0.7660 (mp0) REVERT: G 139 ARG cc_start: 0.8165 (tpt-90) cc_final: 0.7587 (tpt-90) REVERT: G 162 LYS cc_start: 0.8806 (tppp) cc_final: 0.8249 (tptp) REVERT: G 657 ARG cc_start: 0.8554 (mmm160) cc_final: 0.8170 (mtm180) REVERT: G 680 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7758 (mmm) outliers start: 43 outliers final: 23 residues processed: 388 average time/residue: 0.6649 time to fit residues: 316.8118 Evaluate side-chains 378 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 344 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 447 PHE Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 680 MET Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 229 THR Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 680 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 386 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 434 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 321 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 chunk 87 optimal weight: 40.0000 chunk 359 optimal weight: 0.0770 chunk 278 optimal weight: 0.0980 overall best weight: 2.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN E 62 GLN E 711 ASN ** F 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 710 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.184308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113689 restraints weight = 40629.800| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.71 r_work: 0.3240 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 37361 Z= 0.160 Angle : 0.598 10.143 50629 Z= 0.286 Chirality : 0.044 0.186 6017 Planarity : 0.003 0.042 6449 Dihedral : 5.087 67.960 5139 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.21 % Allowed : 13.56 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 1.38 (0.13), residues: 4665 helix: 2.28 (0.11), residues: 2346 sheet: 1.35 (0.19), residues: 723 loop : -1.48 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 139 TYR 0.019 0.001 TYR C 705 PHE 0.014 0.001 PHE F 117 TRP 0.006 0.001 TRP E 477 HIS 0.003 0.001 HIS A 622 Details of bonding type rmsd covalent geometry : bond 0.00389 (37361) covalent geometry : angle 0.59830 (50629) hydrogen bonds : bond 0.03628 ( 2073) hydrogen bonds : angle 3.86521 ( 6114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 345 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 113 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7495 (mt-10) REVERT: H 195 ASP cc_start: 0.8965 (t0) cc_final: 0.8004 (p0) REVERT: H 216 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7565 (tt) REVERT: A 58 ASP cc_start: 0.8417 (p0) cc_final: 0.8177 (p0) REVERT: A 139 ARG cc_start: 0.7895 (tpt90) cc_final: 0.7538 (tpt170) REVERT: A 193 GLU cc_start: 0.7356 (tp30) cc_final: 0.6711 (tp30) REVERT: A 343 TYR cc_start: 0.7209 (OUTLIER) cc_final: 0.6804 (t80) REVERT: A 367 MET cc_start: 0.8628 (pmm) cc_final: 0.7120 (tmm) REVERT: A 523 GLU cc_start: 0.8328 (pm20) cc_final: 0.8079 (pp20) REVERT: A 657 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7717 (mtp180) REVERT: B 139 ARG cc_start: 0.7983 (mtp-110) cc_final: 0.7434 (mtm110) REVERT: B 218 LYS cc_start: 0.8176 (tptp) cc_final: 0.7584 (ttmt) REVERT: B 657 ARG cc_start: 0.8279 (mmm160) cc_final: 0.7737 (mtt180) REVERT: C 131 LYS cc_start: 0.9185 (ptpp) cc_final: 0.8962 (ptmm) REVERT: C 136 ASP cc_start: 0.7860 (t0) cc_final: 0.6745 (p0) REVERT: C 193 GLU cc_start: 0.7546 (mp0) cc_final: 0.6833 (mp0) REVERT: C 446 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7249 (mp) REVERT: C 594 MET cc_start: 0.8849 (mtm) cc_final: 0.8574 (mtp) REVERT: D 89 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8111 (mm-30) REVERT: D 92 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7940 (tt) REVERT: D 131 LYS cc_start: 0.9157 (ptmt) cc_final: 0.8846 (pmtt) REVERT: D 139 ARG cc_start: 0.7701 (tpt170) cc_final: 0.7309 (tpt170) REVERT: D 173 GLN cc_start: 0.8404 (mm-40) cc_final: 0.7845 (tm-30) REVERT: D 200 ASP cc_start: 0.8431 (m-30) cc_final: 0.8149 (m-30) REVERT: D 259 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7876 (t0) REVERT: D 347 MET cc_start: 0.9302 (pp-130) cc_final: 0.9058 (pmm) REVERT: D 680 MET cc_start: 0.8240 (mtm) cc_final: 0.7889 (mmm) REVERT: E 31 LYS cc_start: 0.7017 (tttm) cc_final: 0.6505 (tppt) REVERT: E 62 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7893 (pt0) REVERT: E 113 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7221 (mt-10) REVERT: E 120 ILE cc_start: 0.8709 (pp) cc_final: 0.8354 (pp) REVERT: E 124 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8562 (mm) REVERT: E 130 GLU cc_start: 0.7936 (mp0) cc_final: 0.7306 (mp0) REVERT: E 136 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7279 (p0) REVERT: E 410 ARG cc_start: 0.7388 (ttp-110) cc_final: 0.7007 (ptp-110) REVERT: E 626 GLU cc_start: 0.7486 (tt0) cc_final: 0.7203 (tp30) REVERT: E 634 GLN cc_start: 0.9153 (mt0) cc_final: 0.8688 (mm-40) REVERT: E 658 TYR cc_start: 0.8796 (m-80) cc_final: 0.8573 (m-80) REVERT: F 105 ASP cc_start: 0.8677 (t0) cc_final: 0.8404 (m-30) REVERT: F 113 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7130 (mt-10) REVERT: F 130 GLU cc_start: 0.8035 (mp0) cc_final: 0.7500 (mp0) REVERT: F 680 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7741 (mmm) REVERT: F 700 LYS cc_start: 0.8857 (mttt) cc_final: 0.8313 (mptt) REVERT: G 31 LYS cc_start: 0.7171 (tttt) cc_final: 0.6668 (tppt) REVERT: G 105 ASP cc_start: 0.8580 (t0) cc_final: 0.8357 (m-30) REVERT: G 130 GLU cc_start: 0.8599 (mt-10) cc_final: 0.7643 (mp0) REVERT: G 139 ARG cc_start: 0.8100 (tpt-90) cc_final: 0.7518 (tpt-90) REVERT: G 162 LYS cc_start: 0.8842 (tppp) cc_final: 0.8451 (tptp) REVERT: G 657 ARG cc_start: 0.8518 (mmm160) cc_final: 0.8103 (mtm180) REVERT: G 680 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7759 (mmm) outliers start: 49 outliers final: 23 residues processed: 376 average time/residue: 0.6903 time to fit residues: 317.1963 Evaluate side-chains 364 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 330 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 705 TYR Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 680 MET Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 229 THR Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 680 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 329 optimal weight: 0.6980 chunk 327 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 chunk 441 optimal weight: 0.9990 chunk 231 optimal weight: 3.9990 chunk 295 optimal weight: 1.9990 chunk 359 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 385 optimal weight: 0.9990 chunk 237 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN E 62 GLN E 711 ASN F 183 ASN ** F 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.194406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125884 restraints weight = 41250.898| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.48 r_work: 0.3205 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 37361 Z= 0.110 Angle : 0.578 11.325 50629 Z= 0.276 Chirality : 0.043 0.202 6017 Planarity : 0.003 0.042 6449 Dihedral : 4.873 62.707 5139 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.99 % Allowed : 14.01 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 1.52 (0.13), residues: 4665 helix: 2.39 (0.11), residues: 2351 sheet: 1.40 (0.19), residues: 733 loop : -1.45 (0.14), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 139 TYR 0.019 0.001 TYR E 705 PHE 0.015 0.001 PHE F 117 TRP 0.004 0.001 TRP E 477 HIS 0.002 0.000 HIS E 710 Details of bonding type rmsd covalent geometry : bond 0.00250 (37361) covalent geometry : angle 0.57798 (50629) hydrogen bonds : bond 0.03260 ( 2073) hydrogen bonds : angle 3.78596 ( 6114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9330 Ramachandran restraints generated. 4665 Oldfield, 0 Emsley, 4665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 346 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 113 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7485 (mt-10) REVERT: H 195 ASP cc_start: 0.8979 (t0) cc_final: 0.8066 (p0) REVERT: H 216 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7618 (tt) REVERT: A 58 ASP cc_start: 0.8389 (p0) cc_final: 0.8142 (p0) REVERT: A 139 ARG cc_start: 0.8003 (tpt90) cc_final: 0.7649 (tpt170) REVERT: A 193 GLU cc_start: 0.7377 (tp30) cc_final: 0.6736 (tp30) REVERT: A 343 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.6903 (t80) REVERT: A 367 MET cc_start: 0.8621 (pmm) cc_final: 0.7034 (tmm) REVERT: A 657 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7700 (mtp180) REVERT: B 139 ARG cc_start: 0.7980 (mtp-110) cc_final: 0.7444 (mtm110) REVERT: B 218 LYS cc_start: 0.8131 (tptp) cc_final: 0.7552 (ttmt) REVERT: B 657 ARG cc_start: 0.8252 (mmm160) cc_final: 0.7719 (mtt180) REVERT: B 684 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7347 (mp0) REVERT: C 131 LYS cc_start: 0.9174 (ptpp) cc_final: 0.8957 (ptmm) REVERT: C 136 ASP cc_start: 0.7986 (t0) cc_final: 0.6965 (p0) REVERT: C 193 GLU cc_start: 0.7588 (mp0) cc_final: 0.6961 (mp0) REVERT: C 446 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7273 (mp) REVERT: C 594 MET cc_start: 0.8772 (mtm) cc_final: 0.8494 (mtp) REVERT: D 89 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8063 (mm-30) REVERT: D 92 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7935 (tt) REVERT: D 131 LYS cc_start: 0.9096 (ptmt) cc_final: 0.8829 (pmtt) REVERT: D 139 ARG cc_start: 0.7637 (tpt170) cc_final: 0.7303 (tpt170) REVERT: D 173 GLN cc_start: 0.8383 (mm-40) cc_final: 0.7837 (tm-30) REVERT: D 200 ASP cc_start: 0.8437 (m-30) cc_final: 0.8156 (m-30) REVERT: D 259 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7807 (t0) REVERT: D 347 MET cc_start: 0.9251 (pp-130) cc_final: 0.9035 (pmm) REVERT: D 680 MET cc_start: 0.8257 (mtm) cc_final: 0.7903 (mmm) REVERT: E 31 LYS cc_start: 0.7064 (tttm) cc_final: 0.6561 (tppt) REVERT: E 62 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7968 (pt0) REVERT: E 113 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7222 (mt-10) REVERT: E 120 ILE cc_start: 0.8725 (pp) cc_final: 0.8361 (pp) REVERT: E 124 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8555 (mm) REVERT: E 130 GLU cc_start: 0.7987 (mp0) cc_final: 0.7362 (mp0) REVERT: E 136 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.7281 (p0) REVERT: E 410 ARG cc_start: 0.7246 (ttp-110) cc_final: 0.6915 (ptp-110) REVERT: E 626 GLU cc_start: 0.7450 (tt0) cc_final: 0.7022 (tp30) REVERT: E 634 GLN cc_start: 0.9142 (mt0) cc_final: 0.8670 (mm-40) REVERT: E 658 TYR cc_start: 0.8737 (m-80) cc_final: 0.8478 (m-80) REVERT: F 113 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7127 (mt-10) REVERT: F 130 GLU cc_start: 0.8064 (mp0) cc_final: 0.7466 (OUTLIER) REVERT: F 680 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7745 (mmm) REVERT: F 700 LYS cc_start: 0.8810 (mttt) cc_final: 0.8276 (mptt) REVERT: G 31 LYS cc_start: 0.7153 (tttt) cc_final: 0.6672 (tppt) REVERT: G 105 ASP cc_start: 0.8542 (t0) cc_final: 0.8342 (m-30) REVERT: G 130 GLU cc_start: 0.8623 (mt-10) cc_final: 0.7724 (mp0) REVERT: G 139 ARG cc_start: 0.8115 (tpt-90) cc_final: 0.7538 (tpt-90) REVERT: G 162 LYS cc_start: 0.8905 (tppp) cc_final: 0.8546 (tptp) REVERT: G 657 ARG cc_start: 0.8517 (mmm160) cc_final: 0.8122 (mtm180) REVERT: G 680 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7748 (mmm) outliers start: 40 outliers final: 23 residues processed: 372 average time/residue: 0.6896 time to fit residues: 313.7623 Evaluate side-chains 365 residues out of total 4033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 332 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 711 ASN Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 680 MET Chi-restraints excluded: chain F residue 705 TYR Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 229 THR Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 680 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 426 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 309 optimal weight: 2.9990 chunk 358 optimal weight: 0.8980 chunk 394 optimal weight: 2.9990 chunk 223 optimal weight: 7.9990 chunk 347 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 321 optimal weight: 0.0040 chunk 410 optimal weight: 1.9990 chunk 137 optimal weight: 0.2980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN E 62 GLN E 711 ASN ** F 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.195478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.127284 restraints weight = 40958.351| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.48 r_work: 0.3221 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 37361 Z= 0.104 Angle : 0.580 12.555 50629 Z= 0.276 Chirality : 0.043 0.223 6017 Planarity : 0.003 0.041 6449 Dihedral : 4.734 60.204 5139 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.79 % Allowed : 14.41 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 aren not related in a simple way. whole: 1.64 (0.13), residues: 4665 helix: 2.51 (0.11), residues: 2345 sheet: 1.46 (0.19), residues: 735 loop : -1.42 (0.14), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 139 TYR 0.021 0.001 TYR C 705 PHE 0.015 0.001 PHE F 117 TRP 0.003 0.000 TRP B 477 HIS 0.004 0.000 HIS D 712 Details of bonding type rmsd covalent geometry : bond 0.00230 (37361) covalent geometry : angle 0.57953 (50629) hydrogen bonds : bond 0.03114 ( 2073) hydrogen bonds : angle 3.74526 ( 6114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16571.24 seconds wall clock time: 282 minutes 30.62 seconds (16950.62 seconds total)