Starting phenix.real_space_refine on Wed Sep 17 18:36:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iuj_60907/09_2025/9iuj_60907.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iuj_60907/09_2025/9iuj_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 { model { file = "/net/cci-nas-00/data/ceres_data/9iuj_60907/09_2025/9iuj_60907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iuj_60907/09_2025/9iuj_60907.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iuj_60907/09_2025/9iuj_60907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iuj_60907/09_2025/9iuj_60907.map" } 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-2.0-5805/lib/python3.9/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, 19 Unusual residues: {' CA': 5, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 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, 17 Unusual residues: {' CA': 2, ' MG': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.23, 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: 0.83 Conformation dependent library (CDL) restraints added in 336.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.26 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: 2.04 Time building geometry restraints manager: 1.04 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 2.510 nonbonded pdb=" OD1 ASN A 232 " pdb="CA CA A1202 " model vdw 2.100 2.510 nonbonded pdb=" OD1 ASP A 415 " pdb="CA CA A1205 " model vdw 2.134 2.510 ... (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: 3.830 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.920 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 aren 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 covalent geometry : bond 0.00364 (10256) covalent geometry : angle 0.65796 (13887) SS BOND : bond 0.01790 ( 24) SS BOND : angle 1.13077 ( 48) hydrogen bonds : bond 0.20819 ( 299) hydrogen bonds : angle 8.95921 ( 783) link_ALPHA1-3 : bond 0.00477 ( 1) link_ALPHA1-3 : angle 1.43977 ( 3) link_ALPHA1-4 : bond 0.00617 ( 1) link_ALPHA1-4 : angle 2.14595 ( 3) link_BETA1-4 : bond 0.00662 ( 10) link_BETA1-4 : angle 1.98285 ( 30) link_BETA1-6 : bond 0.01030 ( 1) link_BETA1-6 : angle 0.74104 ( 3) link_NAG-ASN : bond 0.00221 ( 9) link_NAG-ASN : angle 1.14126 ( 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 : 0.353 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: 0.4458 time to fit residues: 60.0368 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 : 0.371 ------------------------------------------------------------------------------- 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: 0.4980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.219146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.131967 restraints weight = 11320.847| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.21 r_work: 0.3641 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10302 Z= 0.199 Angle : 0.690 9.821 14001 Z= 0.345 Chirality : 0.050 0.294 1593 Planarity : 0.004 0.041 1808 Dihedral : 11.533 81.499 1821 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.52 % Allowed : 21.78 % Favored : 74.70 % 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 aren not related in a simple way. whole: -0.59 (0.23), residues: 1260 helix: 0.73 (0.49), residues: 120 sheet: 0.34 (0.25), residues: 417 loop : -1.04 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 93 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 0.002 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00468 (10256) covalent geometry : angle 0.67102 (13887) SS BOND : bond 0.00284 ( 24) SS BOND : angle 1.46447 ( 48) hydrogen bonds : bond 0.04080 ( 299) hydrogen bonds : angle 6.96641 ( 783) link_ALPHA1-3 : bond 0.00708 ( 1) link_ALPHA1-3 : angle 2.74917 ( 3) link_ALPHA1-4 : bond 0.00135 ( 1) link_ALPHA1-4 : angle 2.55472 ( 3) link_BETA1-4 : bond 0.00500 ( 10) link_BETA1-4 : angle 2.55738 ( 30) link_BETA1-6 : bond 0.00167 ( 1) link_BETA1-6 : angle 1.97203 ( 3) link_NAG-ASN : bond 0.00330 ( 9) link_NAG-ASN : angle 1.39609 ( 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 132 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8278 (mttm) REVERT: A 275 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.8587 (m-80) REVERT: A 368 ASP cc_start: 0.7899 (m-30) cc_final: 0.7192 (t0) REVERT: A 394 GLN cc_start: 0.8214 (mm110) cc_final: 0.7992 (mm-40) REVERT: A 435 TYR cc_start: 0.8599 (m-80) cc_final: 0.8239 (m-80) REVERT: A 474 ASN cc_start: 0.7690 (m-40) cc_final: 0.6633 (p0) REVERT: A 498 LEU cc_start: 0.7297 (tp) cc_final: 0.6970 (tm) REVERT: A 536 GLU cc_start: 0.6850 (mp0) cc_final: 0.6637 (pm20) REVERT: A 539 ILE cc_start: 0.7277 (mm) cc_final: 0.7071 (mm) REVERT: A 612 SER cc_start: 0.4971 (OUTLIER) cc_final: 0.4547 (t) REVERT: B 10 VAL cc_start: -0.2302 (OUTLIER) cc_final: -0.2701 (p) REVERT: B 173 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7849 (mm) REVERT: B 174 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: C 46 ARG cc_start: 0.7959 (ttp-170) cc_final: 0.7689 (ttp-110) outliers start: 38 outliers final: 9 residues processed: 121 average time/residue: 0.4881 time to fit residues: 64.7704 Evaluate side-chains 101 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 CYS Chi-restraints excluded: chain A residue 194 LYS 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 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 249 THR 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: 0.9980 chunk 75 optimal weight: 9.9990 chunk 93 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 chunk 122 optimal weight: 8.9990 chunk 18 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 115 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4561 r_free = 0.4561 target = 0.218143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.130583 restraints weight = 11257.945| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.23 r_work: 0.3608 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10302 Z= 0.149 Angle : 0.622 9.795 14001 Z= 0.307 Chirality : 0.047 0.250 1593 Planarity : 0.004 0.053 1808 Dihedral : 9.341 72.171 1819 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.24 % Allowed : 20.85 % Favored : 75.90 % 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 aren not related in a simple way. whole: -0.61 (0.23), residues: 1260 helix: 0.72 (0.48), residues: 121 sheet: 0.29 (0.25), residues: 413 loop : -1.03 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 93 TYR 0.020 0.001 TYR B 178 PHE 0.015 0.002 PHE A 154 TRP 0.012 0.001 TRP A 179 HIS 0.001 0.000 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00348 (10256) covalent geometry : angle 0.60707 (13887) SS BOND : bond 0.00196 ( 24) SS BOND : angle 1.01874 ( 48) hydrogen bonds : bond 0.03785 ( 299) hydrogen bonds : angle 6.50339 ( 783) link_ALPHA1-3 : bond 0.01262 ( 1) link_ALPHA1-3 : angle 2.03304 ( 3) link_ALPHA1-4 : bond 0.00387 ( 1) link_ALPHA1-4 : angle 2.31723 ( 3) link_BETA1-4 : bond 0.00404 ( 10) link_BETA1-4 : angle 2.36627 ( 30) link_BETA1-6 : bond 0.00398 ( 1) link_BETA1-6 : angle 1.15928 ( 3) link_NAG-ASN : bond 0.00264 ( 9) link_NAG-ASN : angle 1.22197 ( 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 128 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7874 (m-30) cc_final: 0.7639 (m-30) REVERT: A 368 ASP cc_start: 0.7884 (m-30) cc_final: 0.7144 (t0) REVERT: A 380 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8516 (t) REVERT: A 394 GLN cc_start: 0.8177 (mm110) cc_final: 0.7922 (mm-40) REVERT: A 435 TYR cc_start: 0.8705 (m-80) cc_final: 0.8421 (m-80) REVERT: A 474 ASN cc_start: 0.7649 (m-40) cc_final: 0.6441 (p0) REVERT: A 476 ARG cc_start: 0.7552 (mtp85) cc_final: 0.6952 (mtp85) REVERT: A 498 LEU cc_start: 0.7203 (tp) cc_final: 0.6998 (tt) REVERT: A 533 MET cc_start: 0.7666 (mmt) cc_final: 0.7321 (mmt) REVERT: A 536 GLU cc_start: 0.6907 (mp0) cc_final: 0.6700 (pm20) REVERT: A 539 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.7035 (mm) REVERT: A 586 ILE cc_start: 0.8426 (pt) cc_final: 0.8174 (pp) REVERT: A 612 SER cc_start: 0.4979 (OUTLIER) cc_final: 0.4488 (t) REVERT: B 173 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7794 (mm) REVERT: C 46 ARG cc_start: 0.7911 (ttp-170) cc_final: 0.7620 (ttp-110) outliers start: 35 outliers final: 15 residues processed: 120 average time/residue: 0.4799 time to fit residues: 63.3484 Evaluate side-chains 105 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR 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 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 195 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 249 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 80 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN ** B 82 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 = 0.4539 r_free = 0.4539 target = 0.216032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.127859 restraints weight = 11255.771| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.20 r_work: 0.3576 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10302 Z= 0.207 Angle : 0.652 9.975 14001 Z= 0.323 Chirality : 0.049 0.261 1593 Planarity : 0.004 0.033 1808 Dihedral : 8.120 59.043 1818 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.61 % Allowed : 21.13 % 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 aren not related in a simple way. whole: -0.68 (0.23), residues: 1260 helix: 0.51 (0.48), residues: 121 sheet: 0.26 (0.25), residues: 412 loop : -1.06 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 476 TYR 0.017 0.002 TYR A 275 PHE 0.019 0.002 PHE A 154 TRP 0.013 0.002 TRP A 179 HIS 0.003 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00496 (10256) covalent geometry : angle 0.63647 (13887) SS BOND : bond 0.00156 ( 24) SS BOND : angle 1.00084 ( 48) hydrogen bonds : bond 0.03894 ( 299) hydrogen bonds : angle 6.49947 ( 783) link_ALPHA1-3 : bond 0.01083 ( 1) link_ALPHA1-3 : angle 2.02906 ( 3) link_ALPHA1-4 : bond 0.00197 ( 1) link_ALPHA1-4 : angle 2.50552 ( 3) link_BETA1-4 : bond 0.00360 ( 10) link_BETA1-4 : angle 2.43499 ( 30) link_BETA1-6 : bond 0.00025 ( 1) link_BETA1-6 : angle 1.79149 ( 3) link_NAG-ASN : bond 0.00292 ( 9) link_NAG-ASN : angle 1.36656 ( 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 127 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 88 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7022 (p0) cc_final: 0.6667 (p0) REVERT: A 60 ASP cc_start: 0.7977 (m-30) cc_final: 0.7773 (m-30) REVERT: A 162 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7940 (t70) REVERT: A 368 ASP cc_start: 0.7943 (m-30) cc_final: 0.7170 (t0) REVERT: A 394 GLN cc_start: 0.8263 (mm110) cc_final: 0.7970 (mm-40) REVERT: A 435 TYR cc_start: 0.8779 (m-80) cc_final: 0.8494 (m-80) REVERT: A 474 ASN cc_start: 0.7608 (m-40) cc_final: 0.6596 (p0) REVERT: A 533 MET cc_start: 0.7543 (mmt) cc_final: 0.7232 (mmt) REVERT: A 539 ILE cc_start: 0.7295 (mm) cc_final: 0.7064 (mm) REVERT: A 612 SER cc_start: 0.4907 (OUTLIER) cc_final: 0.4526 (p) REVERT: B 122 TYR cc_start: 0.9069 (t80) cc_final: 0.8831 (t80) REVERT: B 174 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7167 (pm20) REVERT: B 199 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7535 (mm-40) REVERT: C 46 ARG cc_start: 0.7865 (ttp-170) cc_final: 0.7490 (ttp-110) outliers start: 39 outliers final: 18 residues processed: 120 average time/residue: 0.4546 time to fit residues: 60.1958 Evaluate side-chains 105 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 249 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 423 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 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: 0.7980 chunk 11 optimal weight: 0.4980 chunk 120 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 101 optimal weight: 0.4980 chunk 97 optimal weight: 0.5980 chunk 65 optimal weight: 30.0000 chunk 123 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.216651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.128984 restraints weight = 11339.183| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.22 r_work: 0.3586 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10302 Z= 0.168 Angle : 0.618 9.803 14001 Z= 0.305 Chirality : 0.047 0.258 1593 Planarity : 0.003 0.033 1808 Dihedral : 7.143 57.558 1818 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.15 % Allowed : 22.24 % Favored : 74.61 % 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 aren not related in a simple way. whole: -0.64 (0.23), residues: 1260 helix: 0.57 (0.48), residues: 121 sheet: 0.28 (0.25), residues: 412 loop : -1.03 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 562 TYR 0.014 0.001 TYR B 178 PHE 0.018 0.002 PHE A 477 TRP 0.014 0.002 TRP A 179 HIS 0.002 0.000 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00399 (10256) covalent geometry : angle 0.60383 (13887) SS BOND : bond 0.00165 ( 24) SS BOND : angle 0.96731 ( 48) hydrogen bonds : bond 0.03592 ( 299) hydrogen bonds : angle 6.37310 ( 783) link_ALPHA1-3 : bond 0.00978 ( 1) link_ALPHA1-3 : angle 1.88545 ( 3) link_ALPHA1-4 : bond 0.00291 ( 1) link_ALPHA1-4 : angle 2.56113 ( 3) link_BETA1-4 : bond 0.00401 ( 10) link_BETA1-4 : angle 2.22678 ( 30) link_BETA1-6 : bond 0.00244 ( 1) link_BETA1-6 : angle 1.61166 ( 3) link_NAG-ASN : bond 0.00284 ( 9) link_NAG-ASN : angle 1.28981 ( 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 115 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 81 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7007 (p0) cc_final: 0.6563 (p0) REVERT: A 162 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7889 (t70) REVERT: A 368 ASP cc_start: 0.7901 (m-30) cc_final: 0.7157 (t0) REVERT: A 369 LYS cc_start: 0.7111 (mtpt) cc_final: 0.6826 (mmpt) REVERT: A 394 GLN cc_start: 0.8253 (mm110) cc_final: 0.7984 (mm-40) REVERT: A 435 TYR cc_start: 0.8781 (m-80) cc_final: 0.8506 (m-80) REVERT: A 474 ASN cc_start: 0.7576 (m-40) cc_final: 0.6631 (p0) REVERT: A 533 MET cc_start: 0.7602 (mmt) cc_final: 0.7375 (mmt) REVERT: A 539 ILE cc_start: 0.7383 (mm) cc_final: 0.7115 (mm) REVERT: A 612 SER cc_start: 0.4658 (OUTLIER) cc_final: 0.4270 (p) REVERT: A 709 THR cc_start: 0.5414 (OUTLIER) cc_final: 0.4997 (p) REVERT: B 173 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7963 (mm) REVERT: C 46 ARG cc_start: 0.7960 (ttp-170) cc_final: 0.7569 (ttp-110) outliers start: 34 outliers final: 18 residues processed: 108 average time/residue: 0.4424 time to fit residues: 52.8501 Evaluate side-chains 101 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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 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 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: 0.9990 chunk 49 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.215419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.127223 restraints weight = 11308.478| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.21 r_work: 0.3561 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10302 Z= 0.215 Angle : 0.648 10.037 14001 Z= 0.322 Chirality : 0.048 0.264 1593 Planarity : 0.004 0.035 1808 Dihedral : 6.446 58.118 1818 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.71 % Allowed : 21.87 % Favored : 74.42 % 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 aren not related in a simple way. whole: -0.75 (0.23), residues: 1260 helix: 0.48 (0.48), residues: 121 sheet: 0.16 (0.24), residues: 417 loop : -1.08 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 562 TYR 0.019 0.002 TYR A 275 PHE 0.020 0.002 PHE A 154 TRP 0.014 0.002 TRP A 179 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00517 (10256) covalent geometry : angle 0.63307 (13887) SS BOND : bond 0.00160 ( 24) SS BOND : angle 1.03133 ( 48) hydrogen bonds : bond 0.03969 ( 299) hydrogen bonds : angle 6.46640 ( 783) link_ALPHA1-3 : bond 0.00945 ( 1) link_ALPHA1-3 : angle 1.94606 ( 3) link_ALPHA1-4 : bond 0.00155 ( 1) link_ALPHA1-4 : angle 2.76684 ( 3) link_BETA1-4 : bond 0.00458 ( 10) link_BETA1-4 : angle 2.28590 ( 30) link_BETA1-6 : bond 0.00005 ( 1) link_BETA1-6 : angle 1.94677 ( 3) link_NAG-ASN : bond 0.00393 ( 9) link_NAG-ASN : angle 1.50169 ( 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: 40 poor density : 79 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7058 (p0) cc_final: 0.6626 (p0) REVERT: A 162 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7889 (t70) REVERT: A 368 ASP cc_start: 0.7861 (m-30) cc_final: 0.7097 (t0) REVERT: A 394 GLN cc_start: 0.8256 (mm110) cc_final: 0.8002 (mm-40) REVERT: A 435 TYR cc_start: 0.8768 (m-80) cc_final: 0.8467 (m-80) REVERT: A 474 ASN cc_start: 0.7634 (m-40) cc_final: 0.6784 (p0) REVERT: A 539 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7148 (mm) REVERT: A 612 SER cc_start: 0.4730 (OUTLIER) cc_final: 0.4356 (p) REVERT: A 709 THR cc_start: 0.5572 (OUTLIER) cc_final: 0.5207 (p) REVERT: B 122 TYR cc_start: 0.9043 (t80) cc_final: 0.8797 (t80) REVERT: B 173 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8007 (mm) REVERT: C 46 ARG cc_start: 0.7979 (ttp-170) cc_final: 0.7776 (ttp-110) outliers start: 40 outliers final: 20 residues processed: 112 average time/residue: 0.4531 time to fit residues: 55.7444 Evaluate side-chains 98 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 249 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 285 ILE 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 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: 0.8980 chunk 77 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 102 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 ASN ** 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 = 0.4526 r_free = 0.4526 target = 0.214670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126268 restraints weight = 11228.363| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.20 r_work: 0.3555 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10302 Z= 0.260 Angle : 0.677 10.227 14001 Z= 0.337 Chirality : 0.049 0.271 1593 Planarity : 0.004 0.039 1808 Dihedral : 6.334 58.961 1818 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.52 % Allowed : 22.06 % Favored : 74.42 % 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 aren not related in a simple way. whole: -0.80 (0.23), residues: 1260 helix: 0.40 (0.49), residues: 121 sheet: 0.14 (0.24), residues: 415 loop : -1.11 (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 A 275 PHE 0.023 0.002 PHE A 154 TRP 0.016 0.002 TRP A 179 HIS 0.004 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00629 (10256) covalent geometry : angle 0.66269 (13887) SS BOND : bond 0.00190 ( 24) SS BOND : angle 1.02144 ( 48) hydrogen bonds : bond 0.04168 ( 299) hydrogen bonds : angle 6.53105 ( 783) link_ALPHA1-3 : bond 0.00854 ( 1) link_ALPHA1-3 : angle 2.07766 ( 3) link_ALPHA1-4 : bond 0.00128 ( 1) link_ALPHA1-4 : angle 2.94056 ( 3) link_BETA1-4 : bond 0.00469 ( 10) link_BETA1-4 : angle 2.29444 ( 30) link_BETA1-6 : bond 0.00076 ( 1) link_BETA1-6 : angle 2.10237 ( 3) link_NAG-ASN : bond 0.00447 ( 9) link_NAG-ASN : angle 1.58071 ( 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 116 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 78 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7091 (p0) cc_final: 0.6656 (p0) REVERT: A 60 ASP cc_start: 0.7986 (m-30) cc_final: 0.7753 (m-30) REVERT: A 162 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7920 (t70) REVERT: A 368 ASP cc_start: 0.7885 (m-30) cc_final: 0.7169 (t0) REVERT: A 369 LYS cc_start: 0.7205 (mtpt) cc_final: 0.6879 (mmpt) REVERT: A 394 GLN cc_start: 0.8249 (mm110) cc_final: 0.8023 (mm-40) REVERT: A 435 TYR cc_start: 0.8774 (m-80) cc_final: 0.8479 (m-80) REVERT: A 474 ASN cc_start: 0.7649 (m-40) cc_final: 0.6783 (p0) REVERT: A 539 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7380 (mm) REVERT: A 612 SER cc_start: 0.4646 (OUTLIER) cc_final: 0.4280 (p) REVERT: A 623 ASN cc_start: 0.4250 (OUTLIER) cc_final: 0.3629 (m110) REVERT: A 709 THR cc_start: 0.5567 (OUTLIER) cc_final: 0.5213 (p) REVERT: B 199 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7444 (mm-40) outliers start: 38 outliers final: 24 residues processed: 110 average time/residue: 0.4456 time to fit residues: 54.0346 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 : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR 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 285 ILE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 510 ARG 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 63 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 66 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 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 = 0.4538 r_free = 0.4538 target = 0.216020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.128491 restraints weight = 11269.849| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.20 r_work: 0.3578 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10302 Z= 0.163 Angle : 0.625 10.060 14001 Z= 0.310 Chirality : 0.047 0.268 1593 Planarity : 0.004 0.036 1808 Dihedral : 5.989 58.119 1818 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % 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 aren not related in a simple way. whole: -0.76 (0.23), residues: 1260 helix: 0.51 (0.49), residues: 121 sheet: 0.13 (0.24), residues: 413 loop : -1.07 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 562 TYR 0.018 0.001 TYR B 178 PHE 0.018 0.002 PHE A 154 TRP 0.015 0.002 TRP A 179 HIS 0.002 0.000 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00388 (10256) covalent geometry : angle 0.61132 (13887) SS BOND : bond 0.00134 ( 24) SS BOND : angle 0.98191 ( 48) hydrogen bonds : bond 0.03674 ( 299) hydrogen bonds : angle 6.33245 ( 783) link_ALPHA1-3 : bond 0.00877 ( 1) link_ALPHA1-3 : angle 1.84110 ( 3) link_ALPHA1-4 : bond 0.00349 ( 1) link_ALPHA1-4 : angle 2.75327 ( 3) link_BETA1-4 : bond 0.00417 ( 10) link_BETA1-4 : angle 2.10764 ( 30) link_BETA1-6 : bond 0.00213 ( 1) link_BETA1-6 : angle 1.80876 ( 3) link_NAG-ASN : bond 0.00294 ( 9) link_NAG-ASN : angle 1.46359 ( 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 111 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7039 (p0) cc_final: 0.6582 (p0) REVERT: A 162 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7864 (t70) REVERT: A 368 ASP cc_start: 0.7869 (m-30) cc_final: 0.7138 (t0) REVERT: A 394 GLN cc_start: 0.8206 (mm110) cc_final: 0.7956 (mm-40) REVERT: A 435 TYR cc_start: 0.8772 (m-80) cc_final: 0.8471 (m-80) REVERT: A 474 ASN cc_start: 0.7624 (m-40) cc_final: 0.6768 (p0) REVERT: A 539 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7341 (mm) REVERT: A 612 SER cc_start: 0.4641 (OUTLIER) cc_final: 0.4281 (p) REVERT: A 709 THR cc_start: 0.5592 (OUTLIER) cc_final: 0.5239 (p) REVERT: B 10 VAL cc_start: -0.2189 (OUTLIER) cc_final: -0.2608 (p) REVERT: B 173 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7951 (mm) REVERT: B 174 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7231 (pm20) REVERT: B 387 MET cc_start: 0.8115 (mmm) cc_final: 0.7810 (mpp) outliers start: 34 outliers final: 19 residues processed: 104 average time/residue: 0.4362 time to fit residues: 49.8771 Evaluate side-chains 103 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 252 MET Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 285 ILE 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 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 174 GLU Chi-restraints excluded: chain B residue 179 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 80 optimal weight: 0.0870 chunk 43 optimal weight: 0.8980 chunk 105 optimal weight: 0.0170 chunk 46 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 90 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN B 438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.217301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.130582 restraints weight = 11295.163| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.20 r_work: 0.3608 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3644 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= 0.129 Angle : 0.585 9.996 14001 Z= 0.291 Chirality : 0.046 0.265 1593 Planarity : 0.003 0.040 1808 Dihedral : 5.568 58.638 1818 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.97 % Allowed : 22.80 % Favored : 74.24 % 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 aren not related in a simple way. whole: -0.59 (0.23), residues: 1260 helix: 0.69 (0.49), residues: 121 sheet: 0.21 (0.25), residues: 411 loop : -0.94 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 562 TYR 0.021 0.001 TYR B 178 PHE 0.014 0.001 PHE A 154 TRP 0.014 0.001 TRP A 179 HIS 0.002 0.000 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00305 (10256) covalent geometry : angle 0.57254 (13887) SS BOND : bond 0.00108 ( 24) SS BOND : angle 0.97769 ( 48) hydrogen bonds : bond 0.03343 ( 299) hydrogen bonds : angle 6.09280 ( 783) link_ALPHA1-3 : bond 0.00781 ( 1) link_ALPHA1-3 : angle 1.66186 ( 3) link_ALPHA1-4 : bond 0.00493 ( 1) link_ALPHA1-4 : angle 2.55273 ( 3) link_BETA1-4 : bond 0.00401 ( 10) link_BETA1-4 : angle 1.86675 ( 30) link_BETA1-6 : bond 0.00359 ( 1) link_BETA1-6 : angle 1.26315 ( 3) link_NAG-ASN : bond 0.00223 ( 9) link_NAG-ASN : angle 1.41241 ( 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 111 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7019 (p0) cc_final: 0.6550 (p0) REVERT: A 162 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7843 (t70) REVERT: A 275 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8494 (m-80) REVERT: A 368 ASP cc_start: 0.7858 (m-30) cc_final: 0.7150 (t0) REVERT: A 394 GLN cc_start: 0.8116 (mm110) cc_final: 0.7887 (mm-40) REVERT: A 435 TYR cc_start: 0.8737 (m-80) cc_final: 0.8452 (m-80) REVERT: A 474 ASN cc_start: 0.7609 (m-40) cc_final: 0.6789 (p0) REVERT: A 539 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7372 (mm) REVERT: A 709 THR cc_start: 0.5414 (OUTLIER) cc_final: 0.5074 (p) REVERT: B 10 VAL cc_start: -0.2200 (OUTLIER) cc_final: -0.2615 (p) REVERT: B 173 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7960 (mm) REVERT: B 174 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7190 (pm20) outliers start: 32 outliers final: 19 residues processed: 105 average time/residue: 0.4684 time to fit residues: 53.8043 Evaluate side-chains 104 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 252 MET Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 510 ARG 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 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 174 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 101 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 0.0470 chunk 117 optimal weight: 9.9990 chunk 36 optimal weight: 0.0030 chunk 1 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 overall best weight: 0.5088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN A 623 ASN B 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.216548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129428 restraints weight = 11158.447| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.19 r_work: 0.3595 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10302 Z= 0.150 Angle : 0.599 10.019 14001 Z= 0.298 Chirality : 0.046 0.263 1593 Planarity : 0.004 0.043 1808 Dihedral : 5.436 57.211 1818 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.97 % Allowed : 23.26 % Favored : 73.77 % 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 aren not related in a simple way. whole: -0.61 (0.23), residues: 1260 helix: 0.65 (0.49), residues: 121 sheet: 0.18 (0.25), residues: 413 loop : -0.94 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 562 TYR 0.021 0.002 TYR B 178 PHE 0.015 0.002 PHE A 154 TRP 0.015 0.002 TRP A 179 HIS 0.002 0.000 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00358 (10256) covalent geometry : angle 0.58749 (13887) SS BOND : bond 0.00120 ( 24) SS BOND : angle 0.98772 ( 48) hydrogen bonds : bond 0.03501 ( 299) hydrogen bonds : angle 6.11818 ( 783) link_ALPHA1-3 : bond 0.00650 ( 1) link_ALPHA1-3 : angle 1.72178 ( 3) link_ALPHA1-4 : bond 0.00416 ( 1) link_ALPHA1-4 : angle 2.56084 ( 3) link_BETA1-4 : bond 0.00406 ( 10) link_BETA1-4 : angle 1.81383 ( 30) link_BETA1-6 : bond 0.00271 ( 1) link_BETA1-6 : angle 1.36201 ( 3) link_NAG-ASN : bond 0.00281 ( 9) link_NAG-ASN : angle 1.46865 ( 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 111 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7043 (p0) cc_final: 0.6562 (p0) REVERT: A 162 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7833 (t70) REVERT: A 368 ASP cc_start: 0.7894 (m-30) cc_final: 0.7189 (t0) REVERT: A 394 GLN cc_start: 0.8197 (mm110) cc_final: 0.7954 (mm-40) REVERT: A 435 TYR cc_start: 0.8809 (m-80) cc_final: 0.8522 (m-80) REVERT: A 474 ASN cc_start: 0.7618 (m-40) cc_final: 0.6822 (p0) REVERT: A 476 ARG cc_start: 0.7911 (mtp85) cc_final: 0.7502 (mtp85) REVERT: A 539 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7371 (mm) REVERT: A 612 SER cc_start: 0.4618 (OUTLIER) cc_final: 0.4253 (p) REVERT: A 623 ASN cc_start: 0.4479 (OUTLIER) cc_final: 0.3757 (m-40) REVERT: B 10 VAL cc_start: -0.2196 (OUTLIER) cc_final: -0.2614 (p) REVERT: B 173 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7943 (mm) REVERT: B 174 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7209 (pm20) outliers start: 32 outliers final: 19 residues processed: 106 average time/residue: 0.4918 time to fit residues: 56.8067 Evaluate side-chains 104 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 252 MET 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 174 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 54 optimal weight: 5.9990 chunk 4 optimal weight: 0.4980 chunk 65 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 103 optimal weight: 0.0970 chunk 70 optimal weight: 20.0000 chunk 93 optimal weight: 0.1980 chunk 79 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN A 623 ASN B 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.216685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.129580 restraints weight = 11281.260| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.20 r_work: 0.3597 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 10302 Z= 0.191 Angle : 0.912 59.200 14001 Z= 0.527 Chirality : 0.047 0.309 1593 Planarity : 0.004 0.050 1808 Dihedral : 5.464 57.190 1818 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.41 % Allowed : 23.63 % Favored : 73.96 % Cbeta Deviations : 0.09 % 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 aren not related in a simple way. whole: -0.61 (0.23), residues: 1260 helix: 0.65 (0.49), residues: 121 sheet: 0.18 (0.25), residues: 413 loop : -0.94 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 562 TYR 0.020 0.001 TYR B 178 PHE 0.014 0.002 PHE A 154 TRP 0.014 0.002 TRP A 179 HIS 0.001 0.000 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00414 (10256) covalent geometry : angle 0.90655 (13887) SS BOND : bond 0.00110 ( 24) SS BOND : angle 0.97934 ( 48) hydrogen bonds : bond 0.03492 ( 299) hydrogen bonds : angle 6.11877 ( 783) link_ALPHA1-3 : bond 0.00613 ( 1) link_ALPHA1-3 : angle 1.78746 ( 3) link_ALPHA1-4 : bond 0.00428 ( 1) link_ALPHA1-4 : angle 2.55511 ( 3) link_BETA1-4 : bond 0.00431 ( 10) link_BETA1-4 : angle 1.83192 ( 30) link_BETA1-6 : bond 0.00256 ( 1) link_BETA1-6 : angle 1.36119 ( 3) link_NAG-ASN : bond 0.00277 ( 9) link_NAG-ASN : angle 1.47368 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4767.88 seconds wall clock time: 81 minutes 50.13 seconds (4910.13 seconds total)