Starting phenix.real_space_refine on Wed Mar 4 03:20:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lt3_63364/03_2026/9lt3_63364.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lt3_63364/03_2026/9lt3_63364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lt3_63364/03_2026/9lt3_63364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lt3_63364/03_2026/9lt3_63364.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lt3_63364/03_2026/9lt3_63364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lt3_63364/03_2026/9lt3_63364.map" } resolution = 2.79 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= 0.075 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 73 5.16 5 C 6283 2.51 5 N 1699 2.21 5 O 2012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10075 Number of models: 1 Model: "" Number of chains: 11 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: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 504 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} 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: "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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 33 Unusual residues: {' CA': 5, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: 2.43, per 1000 atoms: 0.24 Number of scatterers: 10075 At special positions: 0 Unit cell: (91.16, 131.44, 154.76, 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 73 16.00 Mg 1 11.99 O 2012 8.00 N 1699 7.00 C 6283 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=2.03 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 6 " - pdb=" SG CYS C 21 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 16 " distance=1.93 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 38 " distance=2.03 Simple disulfide: pdb=" SG CYS C 29 " - pdb=" SG CYS C 35 " distance=2.03 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 59 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 66 " 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 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 585 " " NAG A1207 " - " 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 J 1 " - " ASN B 320 " " NAG K 1 " - " ASN B 371 " Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 487.1 milliseconds 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2340 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 24 sheets defined 13.5% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 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: 3.602A 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: 4.193A 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 126 removed outlier: 4.294A pdb=" N ASP B 126 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 146 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 175 through 179 removed outlier: 4.211A pdb=" N ASP B 179 " --> pdb=" O PRO B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 221 through 232 removed outlier: 3.684A 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 258 through 262 removed outlier: 3.707A pdb=" N ARG B 261 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 262 " --> pdb=" O ASP B 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 262' 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 removed outlier: 3.574A pdb=" N ALA B 439 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 4.071A 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: 3.651A pdb=" N ALA A 22 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.748A 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 225 through 229 removed outlier: 3.914A pdb=" N SER A 225 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.748A 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: 6.293A pdb=" N ILE A 344 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ALA A 361 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ALA A 359 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 348 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.834A 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 511 through 513 Processing sheet with id=AB4, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB5, 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=AB6, 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=AB7, first strand: chain 'A' and resid 668 through 671 removed outlier: 3.600A 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=AB8, first strand: chain 'B' and resid 38 through 39 removed outlier: 3.589A pdb=" N TRP B 25 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 60 through 65 removed outlier: 3.583A pdb=" N GLU B 60 " --> pdb=" O ARG B 91 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 91 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG B 87 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE B 88 " --> pdb=" O GLN B 428 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR B 430 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 90 " --> pdb=" O THR B 430 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 415 " --> pdb=" O ARG B 360 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL B 355 " --> pdb=" O MET B 387 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N MET B 387 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU B 357 " --> pdb=" O SER B 385 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N SER B 385 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.617A pdb=" N SER B 396 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 190 through 197 removed outlier: 6.948A pdb=" N VAL B 193 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ALA B 155 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N THR B 195 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N PHE B 153 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N LEU B 245 " --> pdb=" O PRO B 111 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 113 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL B 247 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR B 115 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR B 249 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 117 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 250 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N THR B 329 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 306 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLY B 331 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N PHE B 308 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 454 through 456 Processing sheet with id=AC4, first strand: chain 'C' and resid 16 through 17 Processing sheet with id=AC5, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AC6, first strand: chain 'C' and resid 46 through 48 removed outlier: 3.581A pdb=" N ARG C 48 " --> pdb=" O ASP C 57 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 798 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 1.16 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: 2817 1.33 - 1.45: 1797 1.45 - 1.58: 5544 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 10256 Sorted by residual: bond pdb=" CA ASN C 69 " pdb=" C ASN C 69 " ideal model delta sigma weight residual 1.523 1.474 0.048 1.23e-02 6.61e+03 1.54e+01 bond pdb=" C LYS C 43 " pdb=" N ARG C 44 " ideal model delta sigma weight residual 1.332 1.386 -0.054 1.38e-02 5.25e+03 1.54e+01 bond pdb=" C ASN B 99 " pdb=" N PHE B 100 " ideal model delta sigma weight residual 1.331 1.378 -0.047 1.51e-02 4.39e+03 9.78e+00 bond pdb=" C CYS C 47 " pdb=" N ARG C 48 " ideal model delta sigma weight residual 1.332 1.296 0.036 1.26e-02 6.30e+03 8.06e+00 bond pdb=" CA LEU A 593 " pdb=" C LEU A 593 " ideal model delta sigma weight residual 1.524 1.490 0.034 1.29e-02 6.01e+03 6.93e+00 ... (remaining 10251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 13355 1.55 - 3.10: 409 3.10 - 4.65: 88 4.65 - 6.20: 23 6.20 - 7.75: 9 Bond angle restraints: 13884 Sorted by residual: angle pdb=" C ASN B 449 " pdb=" CA ASN B 449 " pdb=" CB ASN B 449 " ideal model delta sigma weight residual 115.79 109.96 5.83 1.19e+00 7.06e-01 2.40e+01 angle pdb=" C SER B 445 " pdb=" CA SER B 445 " pdb=" CB SER B 445 " ideal model delta sigma weight residual 116.34 110.07 6.27 1.40e+00 5.10e-01 2.01e+01 angle pdb=" CA ARG A 566 " pdb=" CB ARG A 566 " pdb=" CG ARG A 566 " ideal model delta sigma weight residual 114.10 121.85 -7.75 2.00e+00 2.50e-01 1.50e+01 angle pdb=" O ASN B 99 " pdb=" C ASN B 99 " pdb=" N PHE B 100 " ideal model delta sigma weight residual 123.21 127.42 -4.21 1.27e+00 6.20e-01 1.10e+01 angle pdb=" C ASP C 65 " pdb=" N CYS C 66 " pdb=" CA CYS C 66 " ideal model delta sigma weight residual 121.61 126.16 -4.55 1.39e+00 5.18e-01 1.07e+01 ... (remaining 13879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.55: 5784 21.55 - 43.10: 584 43.10 - 64.65: 113 64.65 - 86.20: 43 86.20 - 107.75: 32 Dihedral angle restraints: 6556 sinusoidal: 2909 harmonic: 3647 Sorted by residual: dihedral pdb=" CB CYS C 29 " pdb=" SG CYS C 29 " pdb=" SG CYS C 35 " pdb=" CB CYS C 35 " ideal model delta sinusoidal sigma weight residual -86.00 -23.83 -62.17 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 38 " pdb=" CB CYS C 38 " ideal model delta sinusoidal sigma weight residual -86.00 -134.50 48.50 1 1.00e+01 1.00e-02 3.24e+01 dihedral pdb=" CA TYR A 450 " pdb=" C TYR A 450 " pdb=" N PRO A 451 " pdb=" CA PRO A 451 " ideal model delta harmonic sigma weight residual -180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 6553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1289 0.058 - 0.115: 261 0.115 - 0.173: 31 0.173 - 0.231: 6 0.231 - 0.288: 4 Chirality restraints: 1591 Sorted by residual: 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 -2.56 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE A 147 " pdb=" CA ILE A 147 " pdb=" CG1 ILE A 147 " pdb=" CG2 ILE A 147 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1588 not shown) Planarity restraints: 1819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 438 " -0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C ARG A 438 " 0.079 2.00e-02 2.50e+03 pdb=" O ARG A 438 " -0.030 2.00e-02 2.50e+03 pdb=" N PRO A 439 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 68 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C ARG C 68 " 0.066 2.00e-02 2.50e+03 pdb=" O ARG C 68 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN C 69 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 438 " 0.049 5.00e-02 4.00e+02 7.54e-02 9.09e+00 pdb=" N PRO A 439 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 439 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 439 " 0.041 5.00e-02 4.00e+02 ... (remaining 1816 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 2 1.99 - 2.72: 468 2.72 - 3.45: 13834 3.45 - 4.17: 25395 4.17 - 4.90: 44761 Nonbonded interactions: 84460 Sorted by model distance: nonbonded pdb=" OG SER B 123 " pdb="MG MG B1001 " model vdw 1.263 2.170 nonbonded pdb=" OD1 ASP C 53 " pdb="MG MG B1001 " model vdw 1.838 2.170 nonbonded pdb=" OD1 ASN A 232 " pdb="CA CA A1202 " model vdw 2.066 2.510 nonbonded pdb=" ND2 ASN B 215 " pdb="CA CA B1003 " model vdw 2.079 2.590 nonbonded pdb=" OH TYR A 275 " pdb=" OD1 ASP B 259 " model vdw 2.167 3.040 ... (remaining 84455 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 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 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: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.160 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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 : 0.005 0.105 10301 Z= 0.231 Angle : 0.728 22.832 13995 Z= 0.369 Chirality : 0.049 0.288 1591 Planarity : 0.004 0.075 1810 Dihedral : 19.583 107.753 4144 Min Nonbonded Distance : 1.263 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.20 % Allowed : 24.63 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.23), residues: 1262 helix: 0.42 (0.49), residues: 127 sheet: 0.23 (0.25), residues: 428 loop : -1.20 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 562 TYR 0.016 0.001 TYR A 275 PHE 0.018 0.002 PHE A 154 TRP 0.012 0.002 TRP A 179 HIS 0.005 0.001 HIS B 446 Details of bonding type rmsd covalent geometry : bond 0.00443 (10256) covalent geometry : angle 0.69460 (13884) SS BOND : bond 0.02152 ( 24) SS BOND : angle 3.35705 ( 48) hydrogen bonds : bond 0.21164 ( 308) hydrogen bonds : angle 9.36190 ( 798) link_ALPHA1-3 : bond 0.00442 ( 1) link_ALPHA1-3 : angle 1.57775 ( 3) link_ALPHA1-4 : bond 0.00517 ( 1) link_ALPHA1-4 : angle 2.31737 ( 3) link_BETA1-4 : bond 0.00446 ( 9) link_BETA1-4 : angle 1.61405 ( 27) link_BETA1-6 : bond 0.01013 ( 1) link_BETA1-6 : angle 0.74166 ( 3) link_NAG-ASN : bond 0.00447 ( 9) link_NAG-ASN : angle 1.75671 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7401 (mmm-85) cc_final: 0.6930 (mtp-110) REVERT: A 248 ARG cc_start: 0.7612 (mtm-85) cc_final: 0.6422 (pmt170) REVERT: A 416 LYS cc_start: 0.7594 (mmtm) cc_final: 0.7292 (mmpt) REVERT: A 444 ASN cc_start: 0.7647 (m110) cc_final: 0.6992 (m-40) REVERT: A 529 ARG cc_start: 0.7222 (mtp85) cc_final: 0.6494 (mtm-85) REVERT: A 559 MET cc_start: 0.6679 (ttp) cc_final: 0.6240 (ttt) REVERT: A 687 MET cc_start: 0.6211 (ttt) cc_final: 0.5646 (ttp) REVERT: B 86 GLN cc_start: 0.5815 (OUTLIER) cc_final: 0.5346 (tm-30) REVERT: B 207 VAL cc_start: 0.8635 (t) cc_final: 0.8353 (t) outliers start: 13 outliers final: 4 residues processed: 149 average time/residue: 0.6008 time to fit residues: 96.0272 Evaluate side-chains 104 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 357 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 187 GLN A 394 GLN A 494 GLN A 589 GLN A 692 GLN B 141 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.223291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148422 restraints weight = 10375.641| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.57 r_work: 0.3501 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.095 10301 Z= 0.352 Angle : 0.829 11.042 13995 Z= 0.415 Chirality : 0.055 0.262 1591 Planarity : 0.006 0.058 1810 Dihedral : 11.871 85.999 1809 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.54 % Allowed : 22.22 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.23), residues: 1262 helix: 0.03 (0.48), residues: 127 sheet: 0.18 (0.24), residues: 420 loop : -1.20 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 66 TYR 0.022 0.003 TYR B 318 PHE 0.039 0.003 PHE A 154 TRP 0.018 0.003 TRP A 179 HIS 0.006 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00852 (10256) covalent geometry : angle 0.81578 (13884) SS BOND : bond 0.00301 ( 24) SS BOND : angle 0.97458 ( 48) hydrogen bonds : bond 0.05492 ( 308) hydrogen bonds : angle 7.28941 ( 798) link_ALPHA1-3 : bond 0.00571 ( 1) link_ALPHA1-3 : angle 2.17419 ( 3) link_ALPHA1-4 : bond 0.00800 ( 1) link_ALPHA1-4 : angle 3.10085 ( 3) link_BETA1-4 : bond 0.00520 ( 9) link_BETA1-4 : angle 2.58917 ( 27) link_BETA1-6 : bond 0.00336 ( 1) link_BETA1-6 : angle 2.53584 ( 3) link_NAG-ASN : bond 0.00587 ( 9) link_NAG-ASN : angle 1.90729 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 98 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7868 (mmm-85) cc_final: 0.7382 (mtp-110) REVERT: A 46 THR cc_start: 0.7531 (OUTLIER) cc_final: 0.7127 (p) REVERT: A 186 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.7879 (t70) REVERT: A 248 ARG cc_start: 0.8174 (mtm-85) cc_final: 0.7392 (ptt90) REVERT: A 249 THR cc_start: 0.9129 (t) cc_final: 0.8639 (m) REVERT: A 331 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8549 (tt) REVERT: A 416 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8115 (mmpt) REVERT: A 444 ASN cc_start: 0.7815 (m110) cc_final: 0.7514 (m-40) REVERT: A 529 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7757 (mtm110) REVERT: A 580 GLN cc_start: 0.6180 (pt0) cc_final: 0.5934 (mt0) REVERT: B 62 ARG cc_start: 0.5305 (OUTLIER) cc_final: 0.5026 (pmt170) REVERT: B 180 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8453 (ptp) REVERT: B 356 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6377 (tp30) outliers start: 49 outliers final: 19 residues processed: 134 average time/residue: 0.6096 time to fit residues: 87.4614 Evaluate side-chains 120 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 529 ARG Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 357 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 122 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 74 optimal weight: 20.0000 chunk 115 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 GLN ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.225745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147288 restraints weight = 10335.511| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.89 r_work: 0.3605 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10301 Z= 0.170 Angle : 0.642 9.749 13995 Z= 0.320 Chirality : 0.047 0.241 1591 Planarity : 0.004 0.039 1810 Dihedral : 8.946 75.524 1804 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.70 % Allowed : 23.98 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.23), residues: 1262 helix: 0.37 (0.49), residues: 121 sheet: 0.30 (0.25), residues: 413 loop : -1.04 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 62 TYR 0.014 0.001 TYR B 318 PHE 0.025 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 0.00395 (10256) covalent geometry : angle 0.62965 (13884) SS BOND : bond 0.00165 ( 24) SS BOND : angle 0.65164 ( 48) hydrogen bonds : bond 0.03955 ( 308) hydrogen bonds : angle 6.58458 ( 798) link_ALPHA1-3 : bond 0.00920 ( 1) link_ALPHA1-3 : angle 2.02276 ( 3) link_ALPHA1-4 : bond 0.00140 ( 1) link_ALPHA1-4 : angle 2.78326 ( 3) link_BETA1-4 : bond 0.00341 ( 9) link_BETA1-4 : angle 2.28586 ( 27) link_BETA1-6 : bond 0.00039 ( 1) link_BETA1-6 : angle 1.82343 ( 3) link_NAG-ASN : bond 0.00347 ( 9) link_NAG-ASN : angle 1.49669 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 95 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7772 (mmm-85) cc_final: 0.7327 (mtp-110) REVERT: A 46 THR cc_start: 0.7517 (m) cc_final: 0.7285 (p) REVERT: A 249 THR cc_start: 0.9153 (t) cc_final: 0.8699 (m) REVERT: A 327 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8303 (mm-40) REVERT: A 416 LYS cc_start: 0.8461 (mmtm) cc_final: 0.8247 (mmpt) REVERT: A 444 ASN cc_start: 0.7784 (m110) cc_final: 0.7548 (m110) REVERT: A 510 ARG cc_start: 0.5038 (OUTLIER) cc_final: 0.4715 (mtt180) REVERT: A 571 THR cc_start: 0.6129 (p) cc_final: 0.5870 (t) REVERT: B 62 ARG cc_start: 0.5179 (ptt-90) cc_final: 0.4884 (pmt170) REVERT: B 180 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8364 (ptp) REVERT: B 356 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6216 (tp30) REVERT: B 387 MET cc_start: 0.7292 (tpt) cc_final: 0.7062 (tmm) outliers start: 40 outliers final: 17 residues processed: 125 average time/residue: 0.6315 time to fit residues: 84.2263 Evaluate side-chains 112 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 510 ARG Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 356 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 40 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 121 optimal weight: 0.0030 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.225015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.147004 restraints weight = 10444.731| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.76 r_work: 0.3604 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10301 Z= 0.174 Angle : 0.641 9.901 13995 Z= 0.318 Chirality : 0.047 0.254 1591 Planarity : 0.004 0.032 1810 Dihedral : 7.743 62.994 1802 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.70 % Allowed : 24.35 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.23), residues: 1262 helix: 0.52 (0.49), residues: 121 sheet: 0.30 (0.25), residues: 411 loop : -1.00 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 476 TYR 0.016 0.002 TYR B 318 PHE 0.024 0.002 PHE A 154 TRP 0.013 0.002 TRP A 179 HIS 0.002 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00410 (10256) covalent geometry : angle 0.62886 (13884) SS BOND : bond 0.00150 ( 24) SS BOND : angle 0.58116 ( 48) hydrogen bonds : bond 0.03708 ( 308) hydrogen bonds : angle 6.38379 ( 798) link_ALPHA1-3 : bond 0.00749 ( 1) link_ALPHA1-3 : angle 2.00226 ( 3) link_ALPHA1-4 : bond 0.00272 ( 1) link_ALPHA1-4 : angle 2.81239 ( 3) link_BETA1-4 : bond 0.00387 ( 9) link_BETA1-4 : angle 2.12697 ( 27) link_BETA1-6 : bond 0.00082 ( 1) link_BETA1-6 : angle 1.88758 ( 3) link_NAG-ASN : bond 0.00420 ( 9) link_NAG-ASN : angle 1.57802 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7771 (mmm-85) cc_final: 0.7319 (mtp-110) REVERT: A 118 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.6998 (mtp) REVERT: A 259 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8457 (mtpp) REVERT: A 327 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8253 (mm-40) REVERT: A 444 ASN cc_start: 0.7716 (m110) cc_final: 0.7456 (m110) REVERT: B 62 ARG cc_start: 0.5264 (ptt-90) cc_final: 0.4919 (pmt170) REVERT: B 356 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6232 (tp30) outliers start: 40 outliers final: 23 residues processed: 120 average time/residue: 0.6012 time to fit residues: 77.2141 Evaluate side-chains 112 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 356 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 0.1980 chunk 10 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 111 optimal weight: 0.0170 chunk 11 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.2218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 205 ASN A 591 HIS ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.227332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.150224 restraints weight = 10477.036| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.78 r_work: 0.3663 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10301 Z= 0.108 Angle : 0.581 9.735 13995 Z= 0.290 Chirality : 0.045 0.259 1591 Planarity : 0.003 0.030 1810 Dihedral : 6.872 56.079 1802 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.78 % Allowed : 25.37 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.23), residues: 1262 helix: 0.75 (0.49), residues: 121 sheet: 0.50 (0.25), residues: 401 loop : -0.93 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 476 TYR 0.013 0.001 TYR B 318 PHE 0.019 0.001 PHE B 397 TRP 0.010 0.001 TRP A 179 HIS 0.005 0.000 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00240 (10256) covalent geometry : angle 0.57120 (13884) SS BOND : bond 0.00126 ( 24) SS BOND : angle 0.47965 ( 48) hydrogen bonds : bond 0.03016 ( 308) hydrogen bonds : angle 6.08261 ( 798) link_ALPHA1-3 : bond 0.01004 ( 1) link_ALPHA1-3 : angle 1.92930 ( 3) link_ALPHA1-4 : bond 0.00198 ( 1) link_ALPHA1-4 : angle 2.44306 ( 3) link_BETA1-4 : bond 0.00377 ( 9) link_BETA1-4 : angle 1.91214 ( 27) link_BETA1-6 : bond 0.00329 ( 1) link_BETA1-6 : angle 1.67095 ( 3) link_NAG-ASN : bond 0.00291 ( 9) link_NAG-ASN : angle 1.39318 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7727 (mmm-85) cc_final: 0.7285 (mtp-110) REVERT: A 66 ARG cc_start: 0.7401 (ppt90) cc_final: 0.7190 (ppt90) REVERT: A 259 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8244 (mtpp) REVERT: A 327 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8232 (mm-40) REVERT: A 444 ASN cc_start: 0.7728 (m110) cc_final: 0.7456 (m110) REVERT: A 494 GLN cc_start: 0.7659 (tp40) cc_final: 0.7038 (tm-30) REVERT: A 571 THR cc_start: 0.6063 (p) cc_final: 0.5861 (t) REVERT: A 707 MET cc_start: 0.2414 (OUTLIER) cc_final: 0.1651 (pmm) REVERT: B 62 ARG cc_start: 0.5447 (ptt-90) cc_final: 0.5061 (pmt170) outliers start: 30 outliers final: 16 residues processed: 115 average time/residue: 0.5541 time to fit residues: 68.9115 Evaluate side-chains 109 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 454 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 101 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 116 optimal weight: 50.0000 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN A 352 GLN B 106 GLN ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.224824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148683 restraints weight = 10483.292| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.72 r_work: 0.3517 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10301 Z= 0.186 Angle : 0.643 9.940 13995 Z= 0.319 Chirality : 0.048 0.258 1591 Planarity : 0.004 0.032 1810 Dihedral : 6.787 58.476 1802 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.70 % Allowed : 25.19 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.23), residues: 1262 helix: 0.70 (0.50), residues: 121 sheet: 0.44 (0.25), residues: 400 loop : -0.99 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 476 TYR 0.017 0.002 TYR B 318 PHE 0.023 0.002 PHE A 154 TRP 0.013 0.002 TRP A 179 HIS 0.002 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00440 (10256) covalent geometry : angle 0.63187 (13884) SS BOND : bond 0.00161 ( 24) SS BOND : angle 0.53037 ( 48) hydrogen bonds : bond 0.03680 ( 308) hydrogen bonds : angle 6.20833 ( 798) link_ALPHA1-3 : bond 0.00633 ( 1) link_ALPHA1-3 : angle 2.11937 ( 3) link_ALPHA1-4 : bond 0.00174 ( 1) link_ALPHA1-4 : angle 2.67139 ( 3) link_BETA1-4 : bond 0.00409 ( 9) link_BETA1-4 : angle 1.99513 ( 27) link_BETA1-6 : bond 0.00165 ( 1) link_BETA1-6 : angle 2.20229 ( 3) link_NAG-ASN : bond 0.00489 ( 9) link_NAG-ASN : angle 1.58161 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 91 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7878 (mmm-85) cc_final: 0.7353 (mtp-110) REVERT: A 118 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7009 (mtp) REVERT: A 259 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8384 (mtpp) REVERT: A 327 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8310 (mm-40) REVERT: A 707 MET cc_start: 0.2432 (OUTLIER) cc_final: 0.1878 (pmm) REVERT: B 14 GLN cc_start: 0.6365 (OUTLIER) cc_final: 0.6110 (pp30) REVERT: B 62 ARG cc_start: 0.5328 (ptt-90) cc_final: 0.4917 (pmt170) REVERT: B 373 THR cc_start: 0.7217 (m) cc_final: 0.6994 (t) REVERT: B 417 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6459 (tttp) outliers start: 40 outliers final: 20 residues processed: 116 average time/residue: 0.6176 time to fit residues: 76.7926 Evaluate side-chains 113 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 454 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 75 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 623 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.225328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.150300 restraints weight = 10395.794| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.82 r_work: 0.3571 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10301 Z= 0.157 Angle : 0.619 9.917 13995 Z= 0.307 Chirality : 0.047 0.258 1591 Planarity : 0.004 0.030 1810 Dihedral : 6.519 57.877 1802 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.43 % Allowed : 25.56 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.23), residues: 1262 helix: 0.75 (0.50), residues: 121 sheet: 0.42 (0.25), residues: 401 loop : -0.97 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 476 TYR 0.015 0.001 TYR B 318 PHE 0.024 0.002 PHE B 397 TRP 0.012 0.002 TRP A 179 HIS 0.001 0.000 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00367 (10256) covalent geometry : angle 0.60434 (13884) SS BOND : bond 0.00142 ( 24) SS BOND : angle 0.48276 ( 48) hydrogen bonds : bond 0.03407 ( 308) hydrogen bonds : angle 6.10872 ( 798) link_ALPHA1-3 : bond 0.00639 ( 1) link_ALPHA1-3 : angle 1.95325 ( 3) link_ALPHA1-4 : bond 0.00020 ( 1) link_ALPHA1-4 : angle 2.55085 ( 3) link_BETA1-4 : bond 0.00381 ( 9) link_BETA1-4 : angle 1.92139 ( 27) link_BETA1-6 : bond 0.00015 ( 1) link_BETA1-6 : angle 2.07548 ( 3) link_NAG-ASN : bond 0.00340 ( 9) link_NAG-ASN : angle 2.23770 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 87 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7822 (mmm-85) cc_final: 0.7341 (mtp-110) REVERT: A 68 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7647 (mm-40) REVERT: A 249 THR cc_start: 0.9099 (t) cc_final: 0.8692 (m) REVERT: A 259 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8413 (mtpp) REVERT: A 327 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8267 (mm-40) REVERT: A 496 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6668 (tp30) REVERT: A 707 MET cc_start: 0.2293 (OUTLIER) cc_final: 0.1873 (pmm) REVERT: B 14 GLN cc_start: 0.6342 (OUTLIER) cc_final: 0.6081 (pp30) REVERT: B 62 ARG cc_start: 0.5363 (ptt-90) cc_final: 0.4998 (pmt170) REVERT: B 86 GLN cc_start: 0.6767 (mp10) cc_final: 0.6392 (mp10) REVERT: B 417 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6556 (tttp) outliers start: 37 outliers final: 20 residues processed: 110 average time/residue: 0.6133 time to fit residues: 72.3512 Evaluate side-chains 112 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 454 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 101 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 105 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 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 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.225387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.152310 restraints weight = 10386.800| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.51 r_work: 0.3610 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10301 Z= 0.149 Angle : 0.606 9.933 13995 Z= 0.301 Chirality : 0.046 0.259 1591 Planarity : 0.004 0.031 1810 Dihedral : 6.300 57.704 1802 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.06 % Allowed : 25.83 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.23), residues: 1262 helix: 0.79 (0.50), residues: 121 sheet: 0.38 (0.25), residues: 402 loop : -0.93 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 66 TYR 0.015 0.001 TYR B 318 PHE 0.028 0.002 PHE B 397 TRP 0.012 0.001 TRP A 179 HIS 0.002 0.000 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00351 (10256) covalent geometry : angle 0.59400 (13884) SS BOND : bond 0.00142 ( 24) SS BOND : angle 0.49025 ( 48) hydrogen bonds : bond 0.03317 ( 308) hydrogen bonds : angle 6.05129 ( 798) link_ALPHA1-3 : bond 0.00620 ( 1) link_ALPHA1-3 : angle 1.87764 ( 3) link_ALPHA1-4 : bond 0.00064 ( 1) link_ALPHA1-4 : angle 2.50570 ( 3) link_BETA1-4 : bond 0.00389 ( 9) link_BETA1-4 : angle 1.87342 ( 27) link_BETA1-6 : bond 0.00043 ( 1) link_BETA1-6 : angle 2.00231 ( 3) link_NAG-ASN : bond 0.00333 ( 9) link_NAG-ASN : angle 1.87977 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7785 (mmm-85) cc_final: 0.7343 (mtp-110) REVERT: A 249 THR cc_start: 0.9109 (t) cc_final: 0.8683 (m) REVERT: A 259 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8399 (mtpp) REVERT: A 264 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8221 (mp) REVERT: A 327 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8221 (mm-40) REVERT: A 496 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6688 (tp30) REVERT: A 707 MET cc_start: 0.2208 (OUTLIER) cc_final: 0.1840 (pmm) REVERT: B 14 GLN cc_start: 0.6281 (OUTLIER) cc_final: 0.6021 (pp30) REVERT: B 62 ARG cc_start: 0.5579 (ptt-90) cc_final: 0.5305 (pmt170) REVERT: B 86 GLN cc_start: 0.6689 (mp10) cc_final: 0.6457 (mp10) REVERT: B 417 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6601 (tttp) outliers start: 33 outliers final: 22 residues processed: 107 average time/residue: 0.6027 time to fit residues: 69.1859 Evaluate side-chains 114 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain C residue 49 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.225436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.150100 restraints weight = 10375.534| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.57 r_work: 0.3614 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10301 Z= 0.152 Angle : 0.602 9.952 13995 Z= 0.301 Chirality : 0.046 0.261 1591 Planarity : 0.004 0.030 1810 Dihedral : 6.159 57.740 1802 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.06 % Allowed : 26.20 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.23), residues: 1262 helix: 0.81 (0.50), residues: 121 sheet: 0.32 (0.25), residues: 401 loop : -0.85 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 48 TYR 0.015 0.001 TYR B 318 PHE 0.027 0.002 PHE B 397 TRP 0.012 0.002 TRP A 179 HIS 0.002 0.000 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00359 (10256) covalent geometry : angle 0.59161 (13884) SS BOND : bond 0.00137 ( 24) SS BOND : angle 0.50582 ( 48) hydrogen bonds : bond 0.03389 ( 308) hydrogen bonds : angle 6.03396 ( 798) link_ALPHA1-3 : bond 0.00542 ( 1) link_ALPHA1-3 : angle 1.83601 ( 3) link_ALPHA1-4 : bond 0.00035 ( 1) link_ALPHA1-4 : angle 2.47419 ( 3) link_BETA1-4 : bond 0.00378 ( 9) link_BETA1-4 : angle 1.83119 ( 27) link_BETA1-6 : bond 0.00107 ( 1) link_BETA1-6 : angle 1.96761 ( 3) link_NAG-ASN : bond 0.00329 ( 9) link_NAG-ASN : angle 1.61180 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7322 (mtp-110) REVERT: A 259 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8421 (mtpp) REVERT: A 264 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8221 (mp) REVERT: A 316 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8278 (m) REVERT: A 327 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8216 (mm-40) REVERT: A 496 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6647 (tp30) REVERT: A 707 MET cc_start: 0.2161 (OUTLIER) cc_final: 0.1852 (pmm) REVERT: B 62 ARG cc_start: 0.5591 (ptt-90) cc_final: 0.5364 (pmt170) REVERT: B 390 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7778 (mtpp) REVERT: B 417 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6529 (tttp) outliers start: 33 outliers final: 22 residues processed: 111 average time/residue: 0.6212 time to fit residues: 73.9414 Evaluate side-chains 115 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 454 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 25 optimal weight: 0.9990 chunk 96 optimal weight: 0.0770 chunk 91 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 chunk 81 optimal weight: 0.6980 chunk 24 optimal weight: 0.0980 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 ASN B 14 GLN ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.226281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.152912 restraints weight = 10411.187| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.63 r_work: 0.3580 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10301 Z= 0.131 Angle : 0.602 9.905 13995 Z= 0.303 Chirality : 0.046 0.258 1591 Planarity : 0.003 0.029 1810 Dihedral : 5.891 57.237 1802 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.87 % Allowed : 26.39 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.23), residues: 1262 helix: 0.87 (0.51), residues: 121 sheet: 0.38 (0.26), residues: 398 loop : -0.82 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 476 TYR 0.014 0.001 TYR B 318 PHE 0.035 0.002 PHE B 397 TRP 0.012 0.001 TRP A 179 HIS 0.002 0.000 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00304 (10256) covalent geometry : angle 0.59270 (13884) SS BOND : bond 0.00141 ( 24) SS BOND : angle 0.50666 ( 48) hydrogen bonds : bond 0.03152 ( 308) hydrogen bonds : angle 5.95848 ( 798) link_ALPHA1-3 : bond 0.00594 ( 1) link_ALPHA1-3 : angle 1.70699 ( 3) link_ALPHA1-4 : bond 0.00219 ( 1) link_ALPHA1-4 : angle 2.37512 ( 3) link_BETA1-4 : bond 0.00378 ( 9) link_BETA1-4 : angle 1.75797 ( 27) link_BETA1-6 : bond 0.00260 ( 1) link_BETA1-6 : angle 1.77115 ( 3) link_NAG-ASN : bond 0.00286 ( 9) link_NAG-ASN : angle 1.50278 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7863 (mmm-85) cc_final: 0.7379 (mtp-110) REVERT: A 249 THR cc_start: 0.9093 (t) cc_final: 0.8694 (m) REVERT: A 259 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8422 (mtpp) REVERT: A 264 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8347 (mt) REVERT: A 327 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8267 (mm-40) REVERT: A 430 ASP cc_start: 0.8427 (m-30) cc_final: 0.8178 (m-30) REVERT: A 496 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6737 (tp30) REVERT: A 707 MET cc_start: 0.2294 (OUTLIER) cc_final: 0.1899 (pmm) REVERT: B 62 ARG cc_start: 0.5612 (ptt-90) cc_final: 0.5399 (pmt170) REVERT: B 417 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6519 (tttp) outliers start: 31 outliers final: 18 residues processed: 106 average time/residue: 0.5700 time to fit residues: 65.1150 Evaluate side-chains 109 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 454 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 28 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 109 optimal weight: 0.0770 chunk 110 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN 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 = 0.224903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.147047 restraints weight = 10468.636| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.71 r_work: 0.3606 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10301 Z= 0.171 Angle : 0.638 10.029 13995 Z= 0.320 Chirality : 0.047 0.265 1591 Planarity : 0.004 0.031 1810 Dihedral : 5.925 58.320 1802 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.69 % Allowed : 26.57 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.23), residues: 1262 helix: 0.84 (0.51), residues: 121 sheet: 0.28 (0.26), residues: 400 loop : -0.82 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 476 TYR 0.016 0.002 TYR B 318 PHE 0.036 0.002 PHE B 397 TRP 0.014 0.002 TRP A 179 HIS 0.002 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00406 (10256) covalent geometry : angle 0.62801 (13884) SS BOND : bond 0.00158 ( 24) SS BOND : angle 0.53508 ( 48) hydrogen bonds : bond 0.03458 ( 308) hydrogen bonds : angle 6.07061 ( 798) link_ALPHA1-3 : bond 0.00407 ( 1) link_ALPHA1-3 : angle 1.83472 ( 3) link_ALPHA1-4 : bond 0.00020 ( 1) link_ALPHA1-4 : angle 2.50214 ( 3) link_BETA1-4 : bond 0.00384 ( 9) link_BETA1-4 : angle 1.82214 ( 27) link_BETA1-6 : bond 0.00087 ( 1) link_BETA1-6 : angle 2.28898 ( 3) link_NAG-ASN : bond 0.00342 ( 9) link_NAG-ASN : angle 1.57145 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4654.69 seconds wall clock time: 79 minutes 38.63 seconds (4778.63 seconds total)