Starting phenix.real_space_refine on Thu Jul 2 21:38:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iuj_60907/07_2026/9iuj_60907.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iuj_60907/07_2026/9iuj_60907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iuj_60907/07_2026/9iuj_60907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iuj_60907/07_2026/9iuj_60907.map" model { file = "/net/cci-nas-00/data/ceres_data/9iuj_60907/07_2026/9iuj_60907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iuj_60907/07_2026/9iuj_60907.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.058 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 Ca 7 9.91 5 Mg 1 5.21 5 S 74 5.16 5 C 6285 2.51 5 N 1691 2.21 5 O 2014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10072 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5698 Classifications: {'peptide': 737} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 703} Chain: "B" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3589 Classifications: {'peptide': 465} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 438} Chain breaks: 1 Chain: "C" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 487 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 59} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 2, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 14 Ad-hoc single atom residues: {' CA': 5} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 15 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' MG': 1, 'NAG': 1} Classifications: {'undetermined': 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.19, per 1000 atoms: 0.22 Number of scatterers: 10072 At special positions: 0 Unit cell: (83.74, 127.2, 152.64, 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) Ca 7 19.99 S 74 16.00 Mg 1 11.99 O 2014 8.00 N 1691 7.00 C 6285 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 602 " distance=2.03 Simple disulfide: pdb=" SG CYS A 668 " - pdb=" SG CYS A 681 " distance=2.03 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 23 " distance=2.03 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 435 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 38 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.12 Simple disulfide: pdb=" SG CYS B 406 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 460 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 471 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 19 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 14 " distance=2.03 Simple disulfide: pdb=" SG CYS C 13 " - pdb=" SG CYS C 36 " distance=2.03 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 33 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 57 " distance=2.03 Simple disulfide: pdb=" SG CYS C 45 " - pdb=" SG CYS C 64 " distance=2.03 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 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 6 " ALPHA1-4 " BMA F 4 " - " MAN F 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " BMA F 3 " - " BMA F 4 " NAG-ASN " NAG A1206 " - " ASN A 524 " " NAG B1004 " - " ASN B 99 " " NAG D 1 " - " ASN A 44 " " NAG E 1 " - " ASN A 260 " " NAG F 1 " - " ASN A 266 " " NAG G 1 " - " ASN A 458 " " NAG H 1 " - " ASN A 585 " " NAG J 1 " - " ASN B 320 " " NAG K 1 " - " ASN B 371 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 363.4 milliseconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2336 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 23 sheets defined 13.1% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.565A pdb=" N LYS A 369 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 9 Processing helix chain 'B' and resid 12 through 20 removed outlier: 4.101A pdb=" N SER B 20 " --> pdb=" O CYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 127 through 146 Processing helix chain 'B' and resid 170 through 175 removed outlier: 4.561A pdb=" N GLU B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 179 removed outlier: 4.406A pdb=" N ASP B 179 " --> pdb=" O PRO B 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 176 through 179' Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 221 through 232 removed outlier: 3.671A pdb=" N ALA B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 291 through 303 Processing helix chain 'B' and resid 314 through 325 Processing helix chain 'B' and resid 337 through 350 Processing helix chain 'B' and resid 435 through 441 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.934A pdb=" N SER A 407 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 26 removed outlier: 3.722A pdb=" N ALA A 22 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL A 56 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.734A pdb=" N ASP A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 100 Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 163 Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.508A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE A 255 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 283 Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'A' and resid 343 through 348 removed outlier: 6.253A pdb=" N ILE A 344 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ALA A 361 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ALA A 359 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY A 348 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AB3, first strand: chain 'A' and resid 481 through 483 Processing sheet with id=AB4, first strand: chain 'A' and resid 446 through 449 removed outlier: 3.662A pdb=" N PHE A 477 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB6, first strand: chain 'A' and resid 606 through 611 removed outlier: 3.886A pdb=" N ILE A 628 " --> pdb=" O ASP A 611 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN A 623 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 701 " --> pdb=" O ASN A 623 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 691 " --> pdb=" O ASN A 633 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A 655 " --> pdb=" O ARG A 698 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER A 700 " --> pdb=" O PHE A 653 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE A 653 " --> pdb=" O SER A 700 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 616 through 618 removed outlier: 6.107A pdb=" N ILE A 617 " --> pdb=" O ALA A 737 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 668 through 671 removed outlier: 3.601A pdb=" N CYS A 681 " --> pdb=" O LEU A 643 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ALA A 641 " --> pdb=" O LEU A 683 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AC1, first strand: chain 'B' and resid 60 through 65 removed outlier: 3.504A pdb=" N GLU B 60 " --> pdb=" O ARG B 91 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG B 87 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE B 88 " --> pdb=" O GLN B 428 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THR B 430 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU B 90 " --> pdb=" O THR B 430 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 415 " --> pdb=" O ARG B 360 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.597A pdb=" N SER B 396 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 190 through 197 removed outlier: 6.778A pdb=" N VAL B 193 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ALA B 155 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N THR B 195 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N PHE B 153 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL B 112 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N GLY B 152 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE B 114 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLY B 154 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR B 116 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N PHE B 156 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N MET B 118 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 250 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR B 329 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU B 306 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N GLY B 331 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE B 308 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 455 through 456 Processing sheet with id=AC5, first strand: chain 'C' and resid 33 through 34 299 hydrogen bonds defined for protein. 783 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: 1.85 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2780 1.33 - 1.45: 1735 1.45 - 1.57: 5641 1.57 - 1.70: 0 1.70 - 1.82: 100 Bond restraints: 10256 Sorted by residual: bond pdb=" N ARG B 352 " pdb=" CA ARG B 352 " ideal model delta sigma weight residual 1.457 1.413 0.044 1.24e-02 6.50e+03 1.26e+01 bond pdb=" C LYS B 384 " pdb=" N SER B 385 " ideal model delta sigma weight residual 1.333 1.381 -0.048 1.38e-02 5.25e+03 1.21e+01 bond pdb=" C ILE B 351 " pdb=" N ARG B 352 " ideal model delta sigma weight residual 1.331 1.292 0.039 1.38e-02 5.25e+03 8.12e+00 bond pdb=" C ARG B 352 " pdb=" O ARG B 352 " ideal model delta sigma weight residual 1.235 1.210 0.026 1.14e-02 7.69e+03 5.01e+00 bond pdb=" C CYS C 64 " pdb=" N PRO C 65 " ideal model delta sigma weight residual 1.330 1.356 -0.026 1.22e-02 6.72e+03 4.57e+00 ... (remaining 10251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 13531 1.89 - 3.77: 301 3.77 - 5.66: 42 5.66 - 7.55: 11 7.55 - 9.43: 2 Bond angle restraints: 13887 Sorted by residual: angle pdb=" N GLY B 392 " pdb=" CA GLY B 392 " pdb=" C GLY B 392 " ideal model delta sigma weight residual 115.08 111.15 3.93 1.19e+00 7.06e-01 1.09e+01 angle pdb=" CA VAL B 107 " pdb=" C VAL B 107 " pdb=" N GLU B 108 " ideal model delta sigma weight residual 119.31 115.55 3.76 1.15e+00 7.56e-01 1.07e+01 angle pdb=" CB MET B 22 " pdb=" CG MET B 22 " pdb=" SD MET B 22 " ideal model delta sigma weight residual 112.70 122.13 -9.43 3.00e+00 1.11e-01 9.88e+00 angle pdb=" C VAL B 107 " pdb=" N GLU B 108 " pdb=" CA GLU B 108 " ideal model delta sigma weight residual 120.87 116.82 4.05 1.42e+00 4.96e-01 8.13e+00 angle pdb=" CA ARG A 566 " pdb=" CB ARG A 566 " pdb=" CG ARG A 566 " ideal model delta sigma weight residual 114.10 119.61 -5.51 2.00e+00 2.50e-01 7.59e+00 ... (remaining 13882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 5853 21.52 - 43.03: 545 43.03 - 64.55: 96 64.55 - 86.07: 36 86.07 - 107.58: 34 Dihedral angle restraints: 6564 sinusoidal: 2922 harmonic: 3642 Sorted by residual: dihedral pdb=" CB CYS C 45 " pdb=" SG CYS C 45 " pdb=" SG CYS C 64 " pdb=" CB CYS C 64 " ideal model delta sinusoidal sigma weight residual -86.00 -170.90 84.90 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CB CYS B 406 " pdb=" SG CYS B 406 " pdb=" SG CYS B 433 " pdb=" CB CYS B 433 " ideal model delta sinusoidal sigma weight residual 93.00 51.43 41.57 1 1.00e+01 1.00e-02 2.42e+01 dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual 93.00 51.78 41.22 1 1.00e+01 1.00e-02 2.38e+01 ... (remaining 6561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1380 0.070 - 0.140: 194 0.140 - 0.209: 13 0.209 - 0.279: 4 0.279 - 0.349: 2 Chirality restraints: 1593 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-02 2.50e+03 3.04e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.32e+01 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 1590 not shown) Planarity restraints: 1817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.093 2.00e-02 2.50e+03 7.60e-02 7.22e+01 pdb=" C7 NAG H 2 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.070 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.119 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " -0.063 2.00e-02 2.50e+03 5.15e-02 3.32e+01 pdb=" C7 NAG K 2 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " -0.047 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " 0.082 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 107 " 0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C VAL B 107 " -0.066 2.00e-02 2.50e+03 pdb=" O VAL B 107 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU B 108 " 0.023 2.00e-02 2.50e+03 ... (remaining 1814 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 7 2.24 - 2.90: 4175 2.90 - 3.57: 13777 3.57 - 4.23: 24761 4.23 - 4.90: 41827 Nonbonded interactions: 84547 Sorted by model distance: nonbonded pdb=" OG SER B 123 " pdb="MG MG B1001 " model vdw 1.573 2.170 nonbonded pdb=" OD1 ASP C 51 " pdb="MG MG B1001 " model vdw 2.091 2.170 nonbonded pdb=" O SER B 123 " pdb="CA CA B1002 " model vdw 2.095 3.250 nonbonded pdb=" OD1 ASN A 232 " pdb="CA CA A1202 " model vdw 2.100 3.250 nonbonded pdb=" OD1 ASP A 415 " pdb="CA CA A1205 " model vdw 2.134 3.250 ... (remaining 84542 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 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' selection = chain 'K' } 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: 4.110 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.710 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 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 : 0.004 0.087 10302 Z= 0.193 Angle : 0.668 9.432 14001 Z= 0.333 Chirality : 0.049 0.349 1593 Planarity : 0.004 0.076 1808 Dihedral : 18.849 107.581 4156 Min Nonbonded Distance : 1.573 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.56 % Allowed : 21.87 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.23), residues: 1260 helix: 1.05 (0.50), residues: 121 sheet: 0.32 (0.25), residues: 437 loop : -1.05 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 562 TYR 0.012 0.001 TYR A 639 PHE 0.012 0.001 PHE A 154 TRP 0.012 0.001 TRP A 179 HIS 0.001 0.000 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.19 (10256) covalent geometry : angle 0.65796 / 0.33 (13887) SS BOND : bond 0.01790 / 1.21 ( 24) SS BOND : angle 1.13077 / 0.69 ( 48) hydrogen bonds : bond 0.20819 / 13.32 ( 299) hydrogen bonds : angle 8.95921 / 6.49 ( 783) link_ALPHA1-3 : bond 0.00477 / 0.25 ( 1) link_ALPHA1-3 : angle 1.43977 / 1.22 ( 3) link_ALPHA1-4 : bond 0.00617 / 0.32 ( 1) link_ALPHA1-4 : angle 2.14595 / 1.34 ( 3) link_BETA1-4 : bond 0.00662 / 0.31 ( 10) link_BETA1-4 : angle 1.98285 / 1.13 ( 30) link_BETA1-6 : bond 0.01030 / 0.54 ( 1) link_BETA1-6 : angle 0.74104 / 0.51 ( 3) link_NAG-ASN : bond 0.00221 / 0.11 ( 9) link_NAG-ASN : angle 1.14126 / 0.76 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7703 (tptm) cc_final: 0.7388 (mppt) REVERT: A 368 ASP cc_start: 0.7649 (m-30) cc_final: 0.7351 (t0) REVERT: A 474 ASN cc_start: 0.7906 (m-40) cc_final: 0.6863 (p0) REVERT: A 476 ARG cc_start: 0.6919 (mtp85) cc_final: 0.6666 (mtp85) REVERT: A 533 MET cc_start: 0.7717 (mmt) cc_final: 0.7386 (mmt) REVERT: A 536 GLU cc_start: 0.6498 (mp0) cc_final: 0.6283 (pm20) REVERT: C 46 ARG cc_start: 0.7952 (ttp-170) cc_final: 0.7695 (ttp-110) outliers start: 6 outliers final: 2 residues processed: 123 average time/residue: 0.4416 time to fit residues: 59.8581 Evaluate side-chains 84 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 207 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0980 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 ASN ** B 82 GLN ** 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 = 0.4578 r_free = 0.4578 target = 0.219705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.132606 restraints weight = 11398.822| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.22 r_work: 0.3653 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10302 Z= 0.216 Angle : 0.706 9.740 14001 Z= 0.352 Chirality : 0.050 0.285 1593 Planarity : 0.004 0.032 1808 Dihedral : 11.414 80.898 1821 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.43 % Allowed : 21.59 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.23), residues: 1260 helix: 0.66 (0.48), residues: 120 sheet: 0.32 (0.25), residues: 417 loop : -1.08 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 93 TYR 0.022 0.002 TYR B 178 PHE 0.022 0.002 PHE A 154 TRP 0.014 0.002 TRP B 238 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (10256) covalent geometry : angle 0.68732 / 0.35 (13887) SS BOND : bond 0.00498 / 0.34 ( 24) SS BOND : angle 1.39486 / 0.86 ( 48) hydrogen bonds : bond 0.04139 / 2.76 ( 299) hydrogen bonds : angle 6.95055 / 4.95 ( 783) link_ALPHA1-3 : bond 0.00918 / 0.48 ( 1) link_ALPHA1-3 : angle 3.17998 / 1.91 ( 3) link_ALPHA1-4 : bond 0.00061 / 0.03 ( 1) link_ALPHA1-4 : angle 2.49085 / 1.80 ( 3) link_BETA1-4 : bond 0.00500 / 0.28 ( 10) link_BETA1-4 : angle 2.66149 / 1.85 ( 30) link_BETA1-6 : bond 0.00004 / 0.00 ( 1) link_BETA1-6 : angle 2.17225 / 1.86 ( 3) link_NAG-ASN : bond 0.00297 / 0.14 ( 9) link_NAG-ASN : angle 1.47381 / 1.00 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 90 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8095 (t70) REVERT: A 194 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8284 (mttm) REVERT: A 236 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7889 (mm) REVERT: A 368 ASP cc_start: 0.7938 (m-30) cc_final: 0.7219 (t0) REVERT: A 394 GLN cc_start: 0.8232 (mm110) cc_final: 0.7998 (mm-40) REVERT: A 435 TYR cc_start: 0.8630 (m-80) cc_final: 0.8322 (m-80) REVERT: A 474 ASN cc_start: 0.7716 (m-40) cc_final: 0.6633 (p0) REVERT: A 477 PHE cc_start: 0.7811 (p90) cc_final: 0.7516 (p90) REVERT: A 512 LEU cc_start: 0.7816 (mp) cc_final: 0.6786 (pt) REVERT: A 539 ILE cc_start: 0.7533 (mm) cc_final: 0.7301 (mm) REVERT: A 612 SER cc_start: 0.4949 (OUTLIER) cc_final: 0.4563 (t) REVERT: B 10 VAL cc_start: -0.2303 (OUTLIER) cc_final: -0.2702 (p) REVERT: B 173 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7835 (mm) REVERT: B 174 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6962 (pm20) REVERT: C 46 ARG cc_start: 0.7947 (ttp-170) cc_final: 0.7664 (ttp-110) outliers start: 37 outliers final: 10 residues processed: 117 average time/residue: 0.4655 time to fit residues: 59.6942 Evaluate side-chains 100 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 101 optimal weight: 0.7980 chunk 75 optimal weight: 20.0000 chunk 93 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 122 optimal weight: 8.9990 chunk 18 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 591 HIS ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.217617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.129737 restraints weight = 11358.278| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.23 r_work: 0.3603 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10302 Z= 0.187 Angle : 0.644 9.761 14001 Z= 0.320 Chirality : 0.048 0.256 1593 Planarity : 0.004 0.040 1808 Dihedral : 9.052 68.752 1819 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.80 % Allowed : 20.95 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.23), residues: 1260 helix: 0.40 (0.47), residues: 127 sheet: 0.25 (0.25), residues: 412 loop : -1.18 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 566 TYR 0.020 0.002 TYR B 178 PHE 0.017 0.002 PHE A 154 TRP 0.013 0.002 TRP A 179 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (10256) covalent geometry : angle 0.62915 / 0.32 (13887) SS BOND : bond 0.00153 / 0.09 ( 24) SS BOND : angle 1.10992 / 0.66 ( 48) hydrogen bonds : bond 0.04071 / 2.68 ( 299) hydrogen bonds : angle 6.62700 / 4.72 ( 783) link_ALPHA1-3 : bond 0.01331 / 0.70 ( 1) link_ALPHA1-3 : angle 1.82113 / 1.15 ( 3) link_ALPHA1-4 : bond 0.00156 / 0.08 ( 1) link_ALPHA1-4 : angle 2.45055 / 1.48 ( 3) link_BETA1-4 : bond 0.00482 / 0.29 ( 10) link_BETA1-4 : angle 2.37132 / 1.68 ( 30) link_BETA1-6 : bond 0.00373 / 0.20 ( 1) link_BETA1-6 : angle 1.15038 / 0.68 ( 3) link_NAG-ASN : bond 0.00286 / 0.14 ( 9) link_NAG-ASN : angle 1.28148 / 0.86 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 94 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7001 (p0) cc_final: 0.6622 (p0) REVERT: A 60 ASP cc_start: 0.7976 (m-30) cc_final: 0.7764 (m-30) REVERT: A 368 ASP cc_start: 0.7848 (m-30) cc_final: 0.7022 (t0) REVERT: A 394 GLN cc_start: 0.8272 (mm110) cc_final: 0.7976 (mm-40) REVERT: A 435 TYR cc_start: 0.8728 (m-80) cc_final: 0.8436 (m-80) REVERT: A 474 ASN cc_start: 0.7619 (m-40) cc_final: 0.6570 (p0) REVERT: A 512 LEU cc_start: 0.7895 (mp) cc_final: 0.6983 (pt) REVERT: A 539 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.7082 (mm) REVERT: A 586 ILE cc_start: 0.8415 (pt) cc_final: 0.8146 (pp) REVERT: A 612 SER cc_start: 0.4930 (OUTLIER) cc_final: 0.4449 (t) REVERT: B 122 TYR cc_start: 0.9077 (t80) cc_final: 0.8743 (t80) REVERT: B 173 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7798 (mm) REVERT: C 46 ARG cc_start: 0.7905 (ttp-170) cc_final: 0.7553 (ttp-110) outliers start: 41 outliers final: 13 residues processed: 126 average time/residue: 0.4131 time to fit residues: 57.7200 Evaluate side-chains 103 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 155 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 80 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 120 optimal weight: 30.0000 chunk 88 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.0070 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.217528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.130129 restraints weight = 11395.821| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.22 r_work: 0.3608 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10302 Z= 0.172 Angle : 0.627 9.909 14001 Z= 0.310 Chirality : 0.047 0.257 1593 Planarity : 0.004 0.031 1808 Dihedral : 7.873 57.988 1818 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.24 % Allowed : 21.78 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.23), residues: 1260 helix: 0.56 (0.48), residues: 121 sheet: 0.27 (0.25), residues: 413 loop : -1.10 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 93 TYR 0.016 0.002 TYR B 178 PHE 0.017 0.002 PHE A 154 TRP 0.014 0.002 TRP A 179 HIS 0.002 0.000 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (10256) covalent geometry : angle 0.61172 / 0.31 (13887) SS BOND : bond 0.00131 / 0.07 ( 24) SS BOND : angle 1.00313 / 0.60 ( 48) hydrogen bonds : bond 0.03675 / 2.44 ( 299) hydrogen bonds : angle 6.46808 / 4.58 ( 783) link_ALPHA1-3 : bond 0.00999 / 0.53 ( 1) link_ALPHA1-3 : angle 2.06957 / 1.39 ( 3) link_ALPHA1-4 : bond 0.00137 / 0.07 ( 1) link_ALPHA1-4 : angle 2.51440 / 1.55 ( 3) link_BETA1-4 : bond 0.00450 / 0.26 ( 10) link_BETA1-4 : angle 2.37848 / 1.58 ( 30) link_BETA1-6 : bond 0.00109 / 0.06 ( 1) link_BETA1-6 : angle 1.67343 / 1.03 ( 3) link_NAG-ASN : bond 0.00283 / 0.14 ( 9) link_NAG-ASN : angle 1.28916 / 0.88 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7038 (p0) cc_final: 0.6607 (p0) REVERT: A 60 ASP cc_start: 0.8025 (m-30) cc_final: 0.7822 (m-30) REVERT: A 368 ASP cc_start: 0.7955 (m-30) cc_final: 0.7238 (t0) REVERT: A 369 LYS cc_start: 0.7013 (mtpt) cc_final: 0.6727 (mmpt) REVERT: A 394 GLN cc_start: 0.8248 (mm110) cc_final: 0.7973 (mm-40) REVERT: A 435 TYR cc_start: 0.8757 (m-80) cc_final: 0.8428 (m-80) REVERT: A 474 ASN cc_start: 0.7689 (m-40) cc_final: 0.6499 (p0) REVERT: A 512 LEU cc_start: 0.7928 (mp) cc_final: 0.7076 (pt) REVERT: A 533 MET cc_start: 0.7539 (mmt) cc_final: 0.7320 (mmt) REVERT: A 539 ILE cc_start: 0.7349 (mm) cc_final: 0.7115 (mm) REVERT: A 612 SER cc_start: 0.4906 (OUTLIER) cc_final: 0.4522 (p) REVERT: B 122 TYR cc_start: 0.9098 (t80) cc_final: 0.8778 (t80) REVERT: B 173 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7869 (mm) REVERT: B 174 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: B 199 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7503 (mm-40) REVERT: C 46 ARG cc_start: 0.7905 (ttp-170) cc_final: 0.7513 (ttp-110) outliers start: 35 outliers final: 18 residues processed: 115 average time/residue: 0.4586 time to fit residues: 57.7962 Evaluate side-chains 106 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 83 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 120 optimal weight: 30.0000 chunk 107 optimal weight: 0.1980 chunk 101 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 91 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 GLN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.217513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.129850 restraints weight = 11420.822| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.24 r_work: 0.3608 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10302 Z= 0.168 Angle : 0.618 9.877 14001 Z= 0.306 Chirality : 0.047 0.255 1593 Planarity : 0.004 0.032 1808 Dihedral : 7.003 57.355 1818 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.61 % Allowed : 21.59 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.23), residues: 1260 helix: 0.58 (0.48), residues: 121 sheet: 0.20 (0.25), residues: 423 loop : -1.10 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 476 TYR 0.014 0.001 TYR B 178 PHE 0.017 0.002 PHE A 154 TRP 0.014 0.002 TRP A 179 HIS 0.002 0.000 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (10256) covalent geometry : angle 0.60425 / 0.30 (13887) SS BOND : bond 0.00129 / 0.07 ( 24) SS BOND : angle 1.02745 / 0.61 ( 48) hydrogen bonds : bond 0.03618 / 2.40 ( 299) hydrogen bonds : angle 6.36639 / 4.50 ( 783) link_ALPHA1-3 : bond 0.01054 / 0.55 ( 1) link_ALPHA1-3 : angle 1.89371 / 1.27 ( 3) link_ALPHA1-4 : bond 0.00297 / 0.16 ( 1) link_ALPHA1-4 : angle 2.55551 / 1.56 ( 3) link_BETA1-4 : bond 0.00403 / 0.22 ( 10) link_BETA1-4 : angle 2.21443 / 1.46 ( 30) link_BETA1-6 : bond 0.00227 / 0.12 ( 1) link_BETA1-6 : angle 1.66583 / 1.02 ( 3) link_NAG-ASN : bond 0.00275 / 0.14 ( 9) link_NAG-ASN : angle 1.28323 / 0.87 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 83 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7056 (p0) cc_final: 0.6605 (p0) REVERT: A 162 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7857 (t70) REVERT: A 236 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7863 (mm) REVERT: A 368 ASP cc_start: 0.7936 (m-30) cc_final: 0.7188 (t0) REVERT: A 369 LYS cc_start: 0.7094 (mtpt) cc_final: 0.6830 (mmpt) REVERT: A 394 GLN cc_start: 0.8251 (mm110) cc_final: 0.7987 (mm-40) REVERT: A 435 TYR cc_start: 0.8755 (m-80) cc_final: 0.8421 (m-80) REVERT: A 474 ASN cc_start: 0.7558 (m-40) cc_final: 0.6535 (p0) REVERT: A 476 ARG cc_start: 0.7511 (mtp85) cc_final: 0.7297 (mtp85) REVERT: A 512 LEU cc_start: 0.7901 (mp) cc_final: 0.7090 (pt) REVERT: A 533 MET cc_start: 0.7492 (mmt) cc_final: 0.7192 (mmt) REVERT: A 539 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.7091 (mm) REVERT: A 612 SER cc_start: 0.4655 (OUTLIER) cc_final: 0.4266 (p) REVERT: A 709 THR cc_start: 0.5442 (OUTLIER) cc_final: 0.5022 (p) REVERT: B 122 TYR cc_start: 0.9077 (t80) cc_final: 0.8724 (t80) REVERT: B 173 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7882 (mm) REVERT: C 46 ARG cc_start: 0.7906 (ttp-170) cc_final: 0.7494 (ttp-110) outliers start: 39 outliers final: 20 residues processed: 114 average time/residue: 0.4318 time to fit residues: 54.4568 Evaluate side-chains 106 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 155 CYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 97 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 30 optimal weight: 0.0470 chunk 62 optimal weight: 40.0000 chunk 13 optimal weight: 0.0870 chunk 111 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.218992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.132353 restraints weight = 11474.236| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.23 r_work: 0.3636 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10302 Z= 0.124 Angle : 0.580 9.758 14001 Z= 0.287 Chirality : 0.046 0.250 1593 Planarity : 0.003 0.030 1808 Dihedral : 6.142 56.967 1818 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.34 % Allowed : 21.78 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.23), residues: 1260 helix: 0.69 (0.49), residues: 121 sheet: 0.29 (0.25), residues: 412 loop : -1.01 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 562 TYR 0.016 0.001 TYR B 178 PHE 0.015 0.001 PHE A 154 TRP 0.014 0.001 TRP A 179 HIS 0.002 0.000 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (10256) covalent geometry : angle 0.56625 / 0.28 (13887) SS BOND : bond 0.00100 / 0.05 ( 24) SS BOND : angle 0.97184 / 0.57 ( 48) hydrogen bonds : bond 0.03285 / 2.17 ( 299) hydrogen bonds : angle 6.18636 / 4.37 ( 783) link_ALPHA1-3 : bond 0.00959 / 0.50 ( 1) link_ALPHA1-3 : angle 1.80835 / 1.28 ( 3) link_ALPHA1-4 : bond 0.00449 / 0.24 ( 1) link_ALPHA1-4 : angle 2.49992 / 1.52 ( 3) link_BETA1-4 : bond 0.00380 / 0.20 ( 10) link_BETA1-4 : angle 2.10312 / 1.37 ( 30) link_BETA1-6 : bond 0.00306 / 0.16 ( 1) link_BETA1-6 : angle 1.56732 / 0.94 ( 3) link_NAG-ASN : bond 0.00241 / 0.12 ( 9) link_NAG-ASN : angle 1.23273 / 0.85 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 83 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7075 (p0) cc_final: 0.6623 (p0) REVERT: A 162 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7827 (t70) REVERT: A 275 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.8492 (m-80) REVERT: A 368 ASP cc_start: 0.7854 (m-30) cc_final: 0.7090 (t0) REVERT: A 394 GLN cc_start: 0.8165 (mm110) cc_final: 0.7905 (mm-40) REVERT: A 435 TYR cc_start: 0.8722 (m-80) cc_final: 0.8420 (m-80) REVERT: A 474 ASN cc_start: 0.7499 (m-40) cc_final: 0.6617 (p0) REVERT: A 476 ARG cc_start: 0.7419 (mtp85) cc_final: 0.7196 (mtp85) REVERT: A 533 MET cc_start: 0.7457 (mmt) cc_final: 0.7132 (mmt) REVERT: A 539 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7327 (mm) REVERT: A 612 SER cc_start: 0.4641 (OUTLIER) cc_final: 0.4262 (p) REVERT: A 709 THR cc_start: 0.5498 (OUTLIER) cc_final: 0.5094 (p) REVERT: B 122 TYR cc_start: 0.9101 (t80) cc_final: 0.8765 (t80) REVERT: B 173 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7872 (mm) REVERT: C 46 ARG cc_start: 0.7980 (ttp-170) cc_final: 0.7587 (ttp-110) outliers start: 36 outliers final: 19 residues processed: 112 average time/residue: 0.4339 time to fit residues: 53.7139 Evaluate side-chains 107 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 CYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 38 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 623 ASN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.216834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.129026 restraints weight = 11344.811| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.22 r_work: 0.3595 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10302 Z= 0.206 Angle : 0.630 10.022 14001 Z= 0.313 Chirality : 0.048 0.267 1593 Planarity : 0.004 0.032 1808 Dihedral : 6.001 57.679 1818 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.34 % Allowed : 22.15 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.23), residues: 1260 helix: 0.54 (0.49), residues: 121 sheet: 0.24 (0.25), residues: 416 loop : -1.07 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 562 TYR 0.017 0.002 TYR A 275 PHE 0.020 0.002 PHE A 154 TRP 0.012 0.002 TRP A 179 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (10256) covalent geometry : angle 0.61563 / 0.31 (13887) SS BOND : bond 0.00145 / 0.07 ( 24) SS BOND : angle 1.01837 / 0.61 ( 48) hydrogen bonds : bond 0.03842 / 2.55 ( 299) hydrogen bonds : angle 6.36916 / 4.47 ( 783) link_ALPHA1-3 : bond 0.00897 / 0.47 ( 1) link_ALPHA1-3 : angle 1.90800 / 1.34 ( 3) link_ALPHA1-4 : bond 0.00256 / 0.13 ( 1) link_ALPHA1-4 : angle 2.69541 / 1.62 ( 3) link_BETA1-4 : bond 0.00450 / 0.24 ( 10) link_BETA1-4 : angle 2.20235 / 1.45 ( 30) link_BETA1-6 : bond 0.00069 / 0.04 ( 1) link_BETA1-6 : angle 1.90313 / 1.21 ( 3) link_NAG-ASN : bond 0.00356 / 0.18 ( 9) link_NAG-ASN : angle 1.45997 / 1.01 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7049 (p0) cc_final: 0.6544 (p0) REVERT: A 162 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7898 (t70) REVERT: A 236 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7858 (mm) REVERT: A 368 ASP cc_start: 0.7889 (m-30) cc_final: 0.7153 (t0) REVERT: A 369 LYS cc_start: 0.7135 (mtpt) cc_final: 0.6822 (mmpt) REVERT: A 394 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7964 (mm-40) REVERT: A 435 TYR cc_start: 0.8747 (m-80) cc_final: 0.8435 (m-80) REVERT: A 474 ASN cc_start: 0.7546 (m-40) cc_final: 0.6669 (p0) REVERT: A 533 MET cc_start: 0.7472 (mmt) cc_final: 0.7227 (mmt) REVERT: A 539 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7374 (mm) REVERT: A 612 SER cc_start: 0.4630 (OUTLIER) cc_final: 0.4262 (p) REVERT: A 623 ASN cc_start: 0.4288 (OUTLIER) cc_final: 0.3698 (m110) REVERT: A 709 THR cc_start: 0.5586 (OUTLIER) cc_final: 0.5228 (p) REVERT: B 122 TYR cc_start: 0.9099 (t80) cc_final: 0.8729 (t80) REVERT: B 173 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7904 (mm) REVERT: B 387 MET cc_start: 0.8126 (mmm) cc_final: 0.7901 (mpp) REVERT: C 46 ARG cc_start: 0.7965 (ttp-170) cc_final: 0.7758 (ttp-110) outliers start: 36 outliers final: 19 residues processed: 107 average time/residue: 0.3824 time to fit residues: 45.2887 Evaluate side-chains 101 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 155 CYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 33 optimal weight: 0.0980 chunk 40 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 579 ASN A 623 ASN ** B 215 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 = 0.4551 r_free = 0.4551 target = 0.217289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.129644 restraints weight = 11394.266| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.22 r_work: 0.3604 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10302 Z= 0.170 Angle : 0.607 10.004 14001 Z= 0.303 Chirality : 0.047 0.263 1593 Planarity : 0.004 0.032 1808 Dihedral : 5.838 57.645 1818 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.24 % Allowed : 22.24 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.23), residues: 1260 helix: 0.58 (0.49), residues: 121 sheet: 0.26 (0.25), residues: 414 loop : -1.08 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 562 TYR 0.017 0.002 TYR B 178 PHE 0.018 0.002 PHE A 154 TRP 0.013 0.002 TRP A 179 HIS 0.002 0.000 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (10256) covalent geometry : angle 0.59378 / 0.30 (13887) SS BOND : bond 0.00134 / 0.07 ( 24) SS BOND : angle 0.97980 / 0.58 ( 48) hydrogen bonds : bond 0.03621 / 2.41 ( 299) hydrogen bonds : angle 6.28234 / 4.40 ( 783) link_ALPHA1-3 : bond 0.00823 / 0.43 ( 1) link_ALPHA1-3 : angle 1.83358 / 1.31 ( 3) link_ALPHA1-4 : bond 0.00358 / 0.19 ( 1) link_ALPHA1-4 : angle 2.65537 / 1.58 ( 3) link_BETA1-4 : bond 0.00405 / 0.21 ( 10) link_BETA1-4 : angle 2.08017 / 1.35 ( 30) link_BETA1-6 : bond 0.00150 / 0.08 ( 1) link_BETA1-6 : angle 1.69092 / 1.05 ( 3) link_NAG-ASN : bond 0.00312 / 0.16 ( 9) link_NAG-ASN : angle 1.40805 / 0.97 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 78 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7045 (p0) cc_final: 0.6579 (p0) REVERT: A 162 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7860 (t70) REVERT: A 236 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7854 (mm) REVERT: A 368 ASP cc_start: 0.7880 (m-30) cc_final: 0.7129 (t0) REVERT: A 394 GLN cc_start: 0.8199 (mm110) cc_final: 0.7953 (mm-40) REVERT: A 435 TYR cc_start: 0.8738 (m-80) cc_final: 0.8398 (m-80) REVERT: A 474 ASN cc_start: 0.7526 (m-40) cc_final: 0.6657 (p0) REVERT: A 476 ARG cc_start: 0.7601 (mtp85) cc_final: 0.7397 (mtp85) REVERT: A 533 MET cc_start: 0.7456 (mmt) cc_final: 0.7253 (mmt) REVERT: A 539 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7351 (mm) REVERT: A 612 SER cc_start: 0.4727 (OUTLIER) cc_final: 0.4350 (p) REVERT: A 623 ASN cc_start: 0.3879 (OUTLIER) cc_final: 0.3174 (m110) REVERT: B 10 VAL cc_start: -0.2058 (OUTLIER) cc_final: -0.2466 (p) REVERT: B 122 TYR cc_start: 0.9110 (t80) cc_final: 0.8734 (t80) REVERT: B 173 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7908 (mm) REVERT: B 387 MET cc_start: 0.8086 (mmm) cc_final: 0.7863 (mpp) REVERT: C 46 ARG cc_start: 0.7948 (ttp-170) cc_final: 0.7642 (ttp-170) outliers start: 35 outliers final: 20 residues processed: 105 average time/residue: 0.3706 time to fit residues: 43.0154 Evaluate side-chains 104 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 155 CYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.0870 chunk 80 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 579 ASN A 623 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 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 = 0.4550 r_free = 0.4550 target = 0.217191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.129673 restraints weight = 11418.870| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.22 r_work: 0.3604 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10302 Z= 0.176 Angle : 0.608 10.030 14001 Z= 0.303 Chirality : 0.047 0.266 1593 Planarity : 0.004 0.033 1808 Dihedral : 5.794 57.675 1818 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.06 % Allowed : 22.43 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.23), residues: 1260 helix: 0.59 (0.49), residues: 121 sheet: 0.22 (0.25), residues: 415 loop : -1.06 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 562 TYR 0.019 0.002 TYR B 178 PHE 0.018 0.002 PHE A 154 TRP 0.013 0.002 TRP A 179 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (10256) covalent geometry : angle 0.59426 / 0.30 (13887) SS BOND : bond 0.00143 / 0.07 ( 24) SS BOND : angle 0.97716 / 0.58 ( 48) hydrogen bonds : bond 0.03643 / 2.42 ( 299) hydrogen bonds : angle 6.27506 / 4.40 ( 783) link_ALPHA1-3 : bond 0.00745 / 0.39 ( 1) link_ALPHA1-3 : angle 1.78813 / 1.28 ( 3) link_ALPHA1-4 : bond 0.00348 / 0.18 ( 1) link_ALPHA1-4 : angle 2.64694 / 1.58 ( 3) link_BETA1-4 : bond 0.00409 / 0.22 ( 10) link_BETA1-4 : angle 2.03340 / 1.32 ( 30) link_BETA1-6 : bond 0.00139 / 0.07 ( 1) link_BETA1-6 : angle 1.66063 / 1.05 ( 3) link_NAG-ASN : bond 0.00322 / 0.16 ( 9) link_NAG-ASN : angle 1.43422 / 0.99 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 76 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7069 (p0) cc_final: 0.6589 (p0) REVERT: A 162 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7855 (t70) REVERT: A 236 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7862 (mm) REVERT: A 368 ASP cc_start: 0.7882 (m-30) cc_final: 0.7142 (t0) REVERT: A 394 GLN cc_start: 0.8191 (mm110) cc_final: 0.7946 (mm-40) REVERT: A 435 TYR cc_start: 0.8743 (m-80) cc_final: 0.8405 (m-80) REVERT: A 474 ASN cc_start: 0.7537 (m-40) cc_final: 0.6654 (p0) REVERT: A 476 ARG cc_start: 0.7719 (mtp85) cc_final: 0.7275 (mtp85) REVERT: A 539 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7355 (mm) REVERT: A 612 SER cc_start: 0.4624 (OUTLIER) cc_final: 0.4262 (p) REVERT: A 623 ASN cc_start: 0.4043 (OUTLIER) cc_final: 0.3226 (m-40) REVERT: A 709 THR cc_start: 0.5489 (OUTLIER) cc_final: 0.5144 (p) REVERT: B 10 VAL cc_start: -0.2173 (OUTLIER) cc_final: -0.2578 (p) REVERT: B 122 TYR cc_start: 0.9117 (t80) cc_final: 0.8739 (t80) REVERT: B 173 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7922 (mm) REVERT: C 46 ARG cc_start: 0.7931 (ttp-170) cc_final: 0.7724 (ttp-110) outliers start: 33 outliers final: 22 residues processed: 103 average time/residue: 0.3660 time to fit residues: 41.9403 Evaluate side-chains 104 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 155 CYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 101 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 68 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 117 optimal weight: 0.0470 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 579 ASN B 86 GLN ** B 215 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 = 0.4556 r_free = 0.4556 target = 0.217820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.130925 restraints weight = 11299.875| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.20 r_work: 0.3617 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10302 Z= 0.144 Angle : 0.592 9.990 14001 Z= 0.295 Chirality : 0.046 0.263 1593 Planarity : 0.004 0.035 1808 Dihedral : 5.625 57.611 1818 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.15 % Allowed : 22.71 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.23), residues: 1260 helix: 0.64 (0.49), residues: 121 sheet: 0.23 (0.25), residues: 416 loop : -1.01 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 562 TYR 0.022 0.001 TYR B 178 PHE 0.016 0.002 PHE A 154 TRP 0.013 0.002 TRP A 179 HIS 0.002 0.000 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (10256) covalent geometry : angle 0.57984 / 0.29 (13887) SS BOND : bond 0.00115 / 0.06 ( 24) SS BOND : angle 0.98682 / 0.58 ( 48) hydrogen bonds : bond 0.03461 / 2.29 ( 299) hydrogen bonds : angle 6.15804 / 4.32 ( 783) link_ALPHA1-3 : bond 0.00701 / 0.37 ( 1) link_ALPHA1-3 : angle 1.68282 / 1.24 ( 3) link_ALPHA1-4 : bond 0.00417 / 0.22 ( 1) link_ALPHA1-4 : angle 2.56134 / 1.54 ( 3) link_BETA1-4 : bond 0.00403 / 0.22 ( 10) link_BETA1-4 : angle 1.90881 / 1.23 ( 30) link_BETA1-6 : bond 0.00268 / 0.14 ( 1) link_BETA1-6 : angle 1.41110 / 0.89 ( 3) link_NAG-ASN : bond 0.00249 / 0.12 ( 9) link_NAG-ASN : angle 1.40325 / 0.98 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7053 (p0) cc_final: 0.6552 (p0) REVERT: A 162 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7842 (t70) REVERT: A 236 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7855 (mm) REVERT: A 368 ASP cc_start: 0.7875 (m-30) cc_final: 0.7124 (t0) REVERT: A 394 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7911 (mm-40) REVERT: A 435 TYR cc_start: 0.8728 (m-80) cc_final: 0.8372 (m-80) REVERT: A 474 ASN cc_start: 0.7545 (m-40) cc_final: 0.6653 (p0) REVERT: A 476 ARG cc_start: 0.7622 (mtp85) cc_final: 0.7352 (mtp85) REVERT: A 539 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7340 (mm) REVERT: A 612 SER cc_start: 0.4614 (OUTLIER) cc_final: 0.4250 (p) REVERT: A 709 THR cc_start: 0.5440 (OUTLIER) cc_final: 0.5071 (p) REVERT: B 10 VAL cc_start: -0.2307 (OUTLIER) cc_final: -0.2722 (p) REVERT: B 122 TYR cc_start: 0.9100 (t80) cc_final: 0.8715 (t80) REVERT: B 173 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7906 (mm) outliers start: 34 outliers final: 22 residues processed: 105 average time/residue: 0.3813 time to fit residues: 44.2381 Evaluate side-chains 106 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 155 CYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 54 optimal weight: 5.9990 chunk 4 optimal weight: 0.0870 chunk 65 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 70 optimal weight: 0.0770 chunk 93 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 579 ASN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.217880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.130891 restraints weight = 11436.290| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.22 r_work: 0.3617 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10302 Z= 0.146 Angle : 0.585 9.956 14001 Z= 0.292 Chirality : 0.046 0.264 1593 Planarity : 0.003 0.032 1808 Dihedral : 5.311 57.220 1818 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.15 % Allowed : 22.71 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.23), residues: 1260 helix: 0.67 (0.49), residues: 121 sheet: 0.27 (0.25), residues: 412 loop : -0.97 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 562 TYR 0.022 0.001 TYR B 178 PHE 0.016 0.002 PHE A 154 TRP 0.013 0.002 TRP A 179 HIS 0.002 0.000 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (10256) covalent geometry : angle 0.57389 / 0.29 (13887) SS BOND : bond 0.00125 / 0.07 ( 24) SS BOND : angle 0.96786 / 0.57 ( 48) hydrogen bonds : bond 0.03463 / 2.28 ( 299) hydrogen bonds : angle 6.11112 / 4.29 ( 783) link_ALPHA1-3 : bond 0.00687 / 0.36 ( 1) link_ALPHA1-3 : angle 1.64025 / 1.22 ( 3) link_ALPHA1-4 : bond 0.00383 / 0.20 ( 1) link_ALPHA1-4 : angle 2.50564 / 1.52 ( 3) link_BETA1-4 : bond 0.00407 / 0.22 ( 10) link_BETA1-4 : angle 1.76846 / 1.15 ( 30) link_BETA1-6 : bond 0.00317 / 0.17 ( 1) link_BETA1-6 : angle 1.16493 / 0.79 ( 3) link_NAG-ASN : bond 0.00255 / 0.13 ( 9) link_NAG-ASN : angle 1.43247 / 1.00 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4157.68 seconds wall clock time: 71 minutes 33.56 seconds (4293.56 seconds total)