Starting phenix.real_space_refine on Thu Jul 2 20:57:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jei_61418/07_2026/9jei_61418.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jei_61418/07_2026/9jei_61418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jei_61418/07_2026/9jei_61418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jei_61418/07_2026/9jei_61418.map" model { file = "/net/cci-nas-00/data/ceres_data/9jei_61418/07_2026/9jei_61418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jei_61418/07_2026/9jei_61418.cif" } resolution = 3.16 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= 0.037 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 70 5.16 5 C 6219 2.51 5 N 1669 2.21 5 O 1990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9956 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5698 Classifications: {'peptide': 737} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 703} Chain: "B" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3589 Classifications: {'peptide': 465} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 438} Chain breaks: 1 Chain: "C" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 371 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 2, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 14 Ad-hoc single atom residues: {' CA': 5} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 15 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' MG': 1, 'NAG': 1} Classifications: {'undetermined': 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.66, per 1000 atoms: 0.17 Number of scatterers: 9956 At special positions: 0 Unit cell: (78.02, 126.99, 151.89, 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 70 16.00 Mg 1 11.99 O 1990 8.00 N 1669 7.00 C 6219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, 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=2.04 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 2 " - pdb=" SG CYS C 11 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 32 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 37 " distance=2.09 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 39 " 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=1, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 6 " ALPHA1-4 " BMA F 4 " - " MAN F 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " BMA F 3 " - " BMA F 4 " NAG-ASN " NAG A1206 " - " ASN A 524 " " NAG B1004 " - " ASN B 99 " " NAG D 1 " - " ASN A 44 " " NAG E 1 " - " ASN A 260 " " NAG F 1 " - " ASN A 266 " " NAG G 1 " - " ASN A 458 " " NAG H 1 " - " ASN A 585 " " NAG J 1 " - " ASN B 320 " " NAG K 1 " - " ASN B 371 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 327.6 milliseconds 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 21 sheets defined 14.5% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 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 removed outlier: 3.574A pdb=" N ASP A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.554A 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: 4.187A pdb=" N SER B 20 " --> pdb=" O CYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 127 through 146 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 175 through 179 removed outlier: 4.380A 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: 3.624A 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: 3.784A pdb=" N ARG B 261 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.619A 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 281 through 286 removed outlier: 3.585A pdb=" N SER B 284 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 286 " --> pdb=" O ALA B 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 281 through 286' 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 436 through 441 Processing helix chain 'C' and resid 42 through 46 removed outlier: 4.731A pdb=" N GLY C 46 " --> pdb=" O PRO C 43 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.725A 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 164 removed outlier: 3.547A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.473A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.895A 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: 6.376A pdb=" N ILE A 344 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ALA A 361 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA A 359 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY A 348 " --> pdb=" O ASP A 357 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 511 through 513 removed outlier: 3.592A pdb=" N GLU A 536 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE A 477 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 480 " --> pdb=" O ASN A 444 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 442 " --> pdb=" O ASP A 482 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 453 through 454 removed outlier: 3.639A pdb=" N GLN A 494 " --> pdb=" O ARG A 562 " (cutoff:3.500A) Processing sheet with id=AB4, 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: 3.604A 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: 6.112A pdb=" N PHE A 653 " --> pdb=" O SER A 700 " (cutoff:3.500A) Processing sheet with id=AB5, 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=AB6, 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=AB7, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AB8, first strand: chain 'B' and resid 60 through 65 removed outlier: 7.551A pdb=" N ARG B 87 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 92 " --> pdb=" O THR B 430 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR B 415 " --> pdb=" O ARG B 360 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL B 355 " --> pdb=" O MET B 387 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N MET B 387 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU B 357 " --> pdb=" O SER B 385 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER B 385 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.516A pdb=" N ASP B 96 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP B 393 " --> pdb=" O GLN B 106 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER B 396 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 194 through 197 removed outlier: 5.393A pdb=" N THR B 195 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N PHE B 153 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL B 112 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N GLY B 152 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 114 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N GLY B 154 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TYR B 116 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N PHE B 156 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N MET B 118 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ASP B 113 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL B 247 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR B 115 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N THR B 249 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU B 117 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR B 250 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N THR B 329 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 306 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLY B 331 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE B 308 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 455 through 456 Processing sheet with id=AC3, first strand: chain 'C' and resid 19 through 21 removed outlier: 7.104A pdb=" N ASP C 30 " --> pdb=" O CYS C 20 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 1.31 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: 2255 1.33 - 1.45: 2182 1.45 - 1.57: 5605 1.57 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 10138 Sorted by residual: bond pdb=" C LEU B 69 " pdb=" N SER B 70 " ideal model delta sigma weight residual 1.331 1.284 0.046 1.26e-02 6.30e+03 1.36e+01 bond pdb=" C THR B 296 " pdb=" N GLU B 297 " ideal model delta sigma weight residual 1.334 1.291 0.044 1.27e-02 6.20e+03 1.19e+01 bond pdb=" CA ILE B 351 " pdb=" C ILE B 351 " ideal model delta sigma weight residual 1.524 1.485 0.039 1.23e-02 6.61e+03 1.00e+01 bond pdb=" C MET B 295 " pdb=" N THR B 296 " ideal model delta sigma weight residual 1.334 1.372 -0.038 1.27e-02 6.20e+03 9.00e+00 bond pdb=" C SER B 70 " pdb=" N ASP B 71 " ideal model delta sigma weight residual 1.331 1.294 0.037 1.33e-02 5.65e+03 7.70e+00 ... (remaining 10133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 13252 1.78 - 3.57: 392 3.57 - 5.35: 59 5.35 - 7.13: 16 7.13 - 8.91: 7 Bond angle restraints: 13726 Sorted by residual: angle pdb=" N ILE B 351 " pdb=" CA ILE B 351 " pdb=" CB ILE B 351 " ideal model delta sigma weight residual 111.00 117.65 -6.65 1.14e+00 7.69e-01 3.41e+01 angle pdb=" C SER B 445 " pdb=" CA SER B 445 " pdb=" CB SER B 445 " ideal model delta sigma weight residual 116.34 110.00 6.34 1.40e+00 5.10e-01 2.05e+01 angle pdb=" N VAL B 112 " pdb=" CA VAL B 112 " pdb=" C VAL B 112 " ideal model delta sigma weight residual 108.45 114.33 -5.88 1.48e+00 4.57e-01 1.58e+01 angle pdb=" O LYS B 350 " pdb=" C LYS B 350 " pdb=" N ILE B 351 " ideal model delta sigma weight residual 122.06 127.02 -4.96 1.34e+00 5.57e-01 1.37e+01 angle pdb=" C ASN A 685 " pdb=" N PRO A 686 " pdb=" CD PRO A 686 " ideal model delta sigma weight residual 120.60 128.25 -7.65 2.20e+00 2.07e-01 1.21e+01 ... (remaining 13721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.55: 5740 21.55 - 43.10: 575 43.10 - 64.65: 101 64.65 - 86.20: 35 86.20 - 107.75: 30 Dihedral angle restraints: 6481 sinusoidal: 2888 harmonic: 3593 Sorted by residual: dihedral pdb=" CB CYS B 406 " pdb=" SG CYS B 406 " pdb=" SG CYS B 433 " pdb=" CB CYS B 433 " ideal model delta sinusoidal sigma weight residual 93.00 38.90 54.10 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CB CYS C 7 " pdb=" SG CYS C 7 " pdb=" SG CYS C 32 " pdb=" CB CYS C 32 " ideal model delta sinusoidal sigma weight residual 93.00 44.20 48.80 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CB CYS B 462 " pdb=" SG CYS B 462 " pdb=" SG CYS B 471 " pdb=" CB CYS B 471 " ideal model delta sinusoidal sigma weight residual -86.00 -125.34 39.34 1 1.00e+01 1.00e-02 2.18e+01 ... (remaining 6478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1282 0.058 - 0.116: 253 0.116 - 0.173: 33 0.173 - 0.231: 4 0.231 - 0.289: 4 Chirality restraints: 1576 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 2.09e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.91e+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 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 1573 not shown) Planarity restraints: 1793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 591 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C HIS A 591 " -0.035 2.00e-02 2.50e+03 pdb=" O HIS A 591 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE A 592 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 478 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C CYS A 478 " 0.030 2.00e-02 2.50e+03 pdb=" O CYS A 478 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 479 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 42 " 0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO C 43 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " 0.021 5.00e-02 4.00e+02 ... (remaining 1790 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 55 2.45 - 3.06: 6467 3.06 - 3.68: 14703 3.68 - 4.29: 22303 4.29 - 4.90: 37978 Nonbonded interactions: 81506 Sorted by model distance: nonbonded pdb=" OG SER B 123 " pdb="MG MG B1001 " model vdw 1.841 2.170 nonbonded pdb=" ND2 ASN B 215 " pdb="CA CA B1003 " model vdw 1.909 3.330 nonbonded pdb=" OD2 ASP B 158 " pdb="CA CA B1003 " model vdw 1.943 3.250 nonbonded pdb=" OE2 GLU B 220 " pdb="MG MG B1001 " model vdw 1.962 2.170 nonbonded pdb=" OD1 ASP A 238 " pdb="CA CA A1202 " model vdw 2.018 3.250 ... (remaining 81501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.070 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: 0.180 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.260 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 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 0.057 10183 Z= 0.229 Angle : 0.774 27.841 13836 Z= 0.384 Chirality : 0.049 0.289 1576 Planarity : 0.004 0.039 1784 Dihedral : 19.156 107.750 4111 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.28 % Allowed : 23.83 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.23), residues: 1243 helix: 0.44 (0.48), residues: 120 sheet: -0.26 (0.25), residues: 411 loop : -1.37 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 216 TYR 0.018 0.002 TYR A 112 PHE 0.020 0.002 PHE B 414 TRP 0.009 0.001 TRP A 114 HIS 0.004 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.23 (10138) covalent geometry : angle 0.72693 / 0.37 (13726) SS BOND : bond 0.01219 / 0.99 ( 22) SS BOND : angle 4.42816 / 1.96 ( 44) hydrogen bonds : bond 0.21886 / 14.00 ( 290) hydrogen bonds : angle 9.61483 / 6.95 ( 762) Misc. bond : bond 0.00107 / 0.06 ( 1) link_ALPHA1-3 : bond 0.00438 / 0.23 ( 1) link_ALPHA1-3 : angle 1.54708 / 1.29 ( 3) link_ALPHA1-4 : bond 0.00321 / 0.17 ( 1) link_ALPHA1-4 : angle 2.48996 / 1.61 ( 3) link_BETA1-4 : bond 0.00574 / 0.27 ( 10) link_BETA1-4 : angle 1.48030 / 0.92 ( 30) link_BETA1-6 : bond 0.00930 / 0.49 ( 1) link_BETA1-6 : angle 1.18070 / 0.83 ( 3) link_NAG-ASN : bond 0.00422 / 0.19 ( 9) link_NAG-ASN : angle 1.69344 / 1.16 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.244 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 96 average time/residue: 0.0769 time to fit residues: 10.6737 Evaluate side-chains 74 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 30.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 623 ASN A 716 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.179439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.110213 restraints weight = 13810.543| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.19 r_work: 0.3417 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10183 Z= 0.245 Angle : 0.713 9.893 13836 Z= 0.350 Chirality : 0.049 0.243 1576 Planarity : 0.004 0.036 1784 Dihedral : 12.334 87.263 1799 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.91 % Allowed : 22.23 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.23), residues: 1243 helix: 0.36 (0.49), residues: 121 sheet: -0.36 (0.25), residues: 410 loop : -1.42 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 566 TYR 0.017 0.002 TYR A 112 PHE 0.017 0.002 PHE B 153 TRP 0.016 0.002 TRP A 114 HIS 0.007 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.24 (10138) covalent geometry : angle 0.69187 / 0.35 (13726) SS BOND : bond 0.00201 / 0.14 ( 22) SS BOND : angle 1.02729 / 0.63 ( 44) hydrogen bonds : bond 0.04183 / 2.82 ( 290) hydrogen bonds : angle 7.13540 / 5.00 ( 762) Misc. bond : bond 0.00081 / 0.04 ( 1) link_ALPHA1-3 : bond 0.00557 / 0.29 ( 1) link_ALPHA1-3 : angle 3.20123 / 1.86 ( 3) link_ALPHA1-4 : bond 0.00018 / 0.01 ( 1) link_ALPHA1-4 : angle 2.57200 / 1.80 ( 3) link_BETA1-4 : bond 0.00462 / 0.21 ( 10) link_BETA1-4 : angle 2.50083 / 1.66 ( 30) link_BETA1-6 : bond 0.00252 / 0.13 ( 1) link_BETA1-6 : angle 2.56405 / 2.05 ( 3) link_NAG-ASN : bond 0.00498 / 0.25 ( 9) link_NAG-ASN : angle 2.37681 / 1.65 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.8476 (mmm) cc_final: 0.8159 (mtt) REVERT: A 275 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.8478 (t80) REVERT: A 707 MET cc_start: 0.2937 (OUTLIER) cc_final: 0.2534 (mmp) REVERT: B 318 TYR cc_start: 0.8335 (m-80) cc_final: 0.8079 (m-80) REVERT: B 419 VAL cc_start: 0.9066 (p) cc_final: 0.8774 (m) outliers start: 31 outliers final: 20 residues processed: 103 average time/residue: 0.0661 time to fit residues: 10.6436 Evaluate side-chains 94 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 340 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 5 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 104 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.181021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.112234 restraints weight = 13826.733| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.96 r_work: 0.3435 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10183 Z= 0.166 Angle : 0.632 9.758 13836 Z= 0.310 Chirality : 0.047 0.246 1576 Planarity : 0.003 0.031 1784 Dihedral : 10.444 83.674 1799 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.63 % Allowed : 22.61 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.23), residues: 1243 helix: 0.51 (0.49), residues: 121 sheet: -0.14 (0.26), residues: 389 loop : -1.35 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 566 TYR 0.016 0.001 TYR A 112 PHE 0.012 0.002 PHE B 414 TRP 0.011 0.001 TRP A 114 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (10138) covalent geometry : angle 0.61526 / 0.31 (13726) SS BOND : bond 0.00118 / 0.07 ( 22) SS BOND : angle 0.83921 / 0.53 ( 44) hydrogen bonds : bond 0.03780 / 2.56 ( 290) hydrogen bonds : angle 6.59577 / 4.60 ( 762) Misc. bond : bond 0.00067 / 0.04 ( 1) link_ALPHA1-3 : bond 0.00997 / 0.52 ( 1) link_ALPHA1-3 : angle 2.48549 / 1.47 ( 3) link_ALPHA1-4 : bond 0.00122 / 0.06 ( 1) link_ALPHA1-4 : angle 2.43475 / 1.60 ( 3) link_BETA1-4 : bond 0.00513 / 0.25 ( 10) link_BETA1-4 : angle 2.33125 / 1.54 ( 30) link_BETA1-6 : bond 0.00123 / 0.06 ( 1) link_BETA1-6 : angle 1.84463 / 1.38 ( 3) link_NAG-ASN : bond 0.00328 / 0.16 ( 9) link_NAG-ASN : angle 1.84122 / 1.28 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.8446 (mmm) cc_final: 0.8159 (mtt) REVERT: A 275 TYR cc_start: 0.8956 (OUTLIER) cc_final: 0.8499 (t80) REVERT: A 580 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7282 (pt0) REVERT: A 707 MET cc_start: 0.3137 (OUTLIER) cc_final: 0.2787 (mmp) REVERT: B 318 TYR cc_start: 0.8282 (m-80) cc_final: 0.7925 (m-80) REVERT: B 419 VAL cc_start: 0.9133 (p) cc_final: 0.8878 (m) REVERT: C 33 ASN cc_start: 0.8113 (p0) cc_final: 0.7809 (p0) outliers start: 28 outliers final: 14 residues processed: 99 average time/residue: 0.0710 time to fit residues: 10.7414 Evaluate side-chains 88 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 291 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 77 optimal weight: 40.0000 chunk 119 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 444 ASN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.178750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.110088 restraints weight = 13857.395| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.87 r_work: 0.3409 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10183 Z= 0.219 Angle : 0.663 9.969 13836 Z= 0.324 Chirality : 0.047 0.260 1576 Planarity : 0.004 0.036 1784 Dihedral : 9.193 76.709 1799 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.03 % Allowed : 22.05 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.23), residues: 1243 helix: 0.39 (0.48), residues: 122 sheet: -0.34 (0.25), residues: 412 loop : -1.37 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 566 TYR 0.016 0.002 TYR A 112 PHE 0.015 0.002 PHE A 326 TRP 0.012 0.001 TRP A 114 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (10138) covalent geometry : angle 0.64525 / 0.32 (13726) SS BOND : bond 0.00139 / 0.08 ( 22) SS BOND : angle 0.86169 / 0.55 ( 44) hydrogen bonds : bond 0.03646 / 2.50 ( 290) hydrogen bonds : angle 6.37788 / 4.45 ( 762) Misc. bond : bond 0.00064 / 0.03 ( 1) link_ALPHA1-3 : bond 0.00855 / 0.45 ( 1) link_ALPHA1-3 : angle 2.71149 / 1.60 ( 3) link_ALPHA1-4 : bond 0.00062 / 0.03 ( 1) link_ALPHA1-4 : angle 2.74879 / 1.77 ( 3) link_BETA1-4 : bond 0.00563 / 0.27 ( 10) link_BETA1-4 : angle 2.33369 / 1.52 ( 30) link_BETA1-6 : bond 0.00278 / 0.15 ( 1) link_BETA1-6 : angle 2.22229 / 1.53 ( 3) link_NAG-ASN : bond 0.00471 / 0.24 ( 9) link_NAG-ASN : angle 2.00639 / 1.34 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 71 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 275 TYR cc_start: 0.9024 (OUTLIER) cc_final: 0.8396 (t80) REVERT: A 707 MET cc_start: 0.3251 (OUTLIER) cc_final: 0.2875 (mmp) REVERT: B 262 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8760 (mp) REVERT: B 318 TYR cc_start: 0.8300 (m-80) cc_final: 0.8030 (m-80) REVERT: B 419 VAL cc_start: 0.9150 (p) cc_final: 0.8880 (m) REVERT: C 33 ASN cc_start: 0.8229 (p0) cc_final: 0.7889 (p0) outliers start: 43 outliers final: 27 residues processed: 105 average time/residue: 0.0840 time to fit residues: 13.2810 Evaluate side-chains 102 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 360 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 101 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.180114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.111620 restraints weight = 13819.502| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.96 r_work: 0.3426 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10183 Z= 0.164 Angle : 0.628 9.974 13836 Z= 0.305 Chirality : 0.046 0.247 1576 Planarity : 0.003 0.033 1784 Dihedral : 8.452 71.810 1799 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.38 % Allowed : 22.51 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.23), residues: 1243 helix: 0.55 (0.49), residues: 122 sheet: -0.30 (0.25), residues: 410 loop : -1.31 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 566 TYR 0.015 0.001 TYR A 112 PHE 0.011 0.001 PHE A 326 TRP 0.010 0.001 TRP A 114 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (10138) covalent geometry : angle 0.61053 / 0.30 (13726) SS BOND : bond 0.00128 / 0.08 ( 22) SS BOND : angle 1.21097 / 0.74 ( 44) hydrogen bonds : bond 0.03360 / 2.29 ( 290) hydrogen bonds : angle 6.17219 / 4.30 ( 762) Misc. bond : bond 0.00034 / 0.02 ( 1) link_ALPHA1-3 : bond 0.01033 / 0.54 ( 1) link_ALPHA1-3 : angle 2.43313 / 1.47 ( 3) link_ALPHA1-4 : bond 0.00101 / 0.05 ( 1) link_ALPHA1-4 : angle 2.61285 / 1.66 ( 3) link_BETA1-4 : bond 0.00579 / 0.28 ( 10) link_BETA1-4 : angle 2.21092 / 1.43 ( 30) link_BETA1-6 : bond 0.00047 / 0.02 ( 1) link_BETA1-6 : angle 2.14840 / 1.38 ( 3) link_NAG-ASN : bond 0.00362 / 0.17 ( 9) link_NAG-ASN : angle 1.75682 / 1.17 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.8503 (t80) REVERT: A 707 MET cc_start: 0.3148 (OUTLIER) cc_final: 0.2776 (mmp) REVERT: B 124 MET cc_start: 0.8550 (tpp) cc_final: 0.8163 (mtp) REVERT: B 262 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8719 (mp) REVERT: B 314 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8357 (m) REVERT: B 318 TYR cc_start: 0.8285 (m-80) cc_final: 0.8015 (m-80) REVERT: B 419 VAL cc_start: 0.9109 (p) cc_final: 0.8838 (m) REVERT: C 33 ASN cc_start: 0.8238 (p0) cc_final: 0.7867 (p0) outliers start: 36 outliers final: 24 residues processed: 104 average time/residue: 0.0937 time to fit residues: 14.3044 Evaluate side-chains 98 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 360 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 42 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.0270 chunk 85 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.180731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.109818 restraints weight = 13880.967| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.67 r_work: 0.3469 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10183 Z= 0.144 Angle : 0.613 9.875 13836 Z= 0.297 Chirality : 0.045 0.252 1576 Planarity : 0.003 0.032 1784 Dihedral : 7.630 65.363 1799 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.38 % Allowed : 22.61 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.23), residues: 1243 helix: 0.60 (0.49), residues: 122 sheet: -0.19 (0.25), residues: 411 loop : -1.26 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 566 TYR 0.015 0.001 TYR B 318 PHE 0.010 0.001 PHE A 326 TRP 0.008 0.001 TRP A 114 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (10138) covalent geometry : angle 0.59691 / 0.29 (13726) SS BOND : bond 0.00119 / 0.07 ( 22) SS BOND : angle 0.97345 / 0.60 ( 44) hydrogen bonds : bond 0.03170 / 2.17 ( 290) hydrogen bonds : angle 5.97717 / 4.16 ( 762) Misc. bond : bond 0.00056 / 0.03 ( 1) link_ALPHA1-3 : bond 0.00964 / 0.51 ( 1) link_ALPHA1-3 : angle 2.16717 / 1.35 ( 3) link_ALPHA1-4 : bond 0.00195 / 0.10 ( 1) link_ALPHA1-4 : angle 2.53870 / 1.62 ( 3) link_BETA1-4 : bond 0.00580 / 0.28 ( 10) link_BETA1-4 : angle 2.18183 / 1.41 ( 30) link_BETA1-6 : bond 0.00080 / 0.04 ( 1) link_BETA1-6 : angle 1.93171 / 1.21 ( 3) link_NAG-ASN : bond 0.00314 / 0.15 ( 9) link_NAG-ASN : angle 1.62231 / 1.08 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7317 (pt0) REVERT: A 707 MET cc_start: 0.3107 (OUTLIER) cc_final: 0.2751 (mmp) REVERT: B 314 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8381 (m) REVERT: B 318 TYR cc_start: 0.8255 (m-80) cc_final: 0.7937 (m-80) REVERT: B 360 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7053 (ptp90) REVERT: B 419 VAL cc_start: 0.9116 (p) cc_final: 0.8869 (m) REVERT: C 33 ASN cc_start: 0.8152 (p0) cc_final: 0.7767 (p0) outliers start: 36 outliers final: 26 residues processed: 104 average time/residue: 0.0763 time to fit residues: 11.7472 Evaluate side-chains 105 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 657 VAL 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 40 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 360 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 56 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 GLN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.177435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.107988 restraints weight = 13820.337| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.98 r_work: 0.3399 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10183 Z= 0.257 Angle : 0.688 10.040 13836 Z= 0.335 Chirality : 0.047 0.249 1576 Planarity : 0.004 0.040 1784 Dihedral : 7.418 59.106 1799 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.75 % Allowed : 22.05 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.23), residues: 1243 helix: 0.27 (0.48), residues: 122 sheet: -0.38 (0.25), residues: 410 loop : -1.27 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 566 TYR 0.016 0.002 TYR B 318 PHE 0.018 0.002 PHE A 19 TRP 0.012 0.001 TRP A 114 HIS 0.006 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.26 (10138) covalent geometry : angle 0.67170 / 0.33 (13726) SS BOND : bond 0.00144 / 0.09 ( 22) SS BOND : angle 0.98456 / 0.61 ( 44) hydrogen bonds : bond 0.03605 / 2.48 ( 290) hydrogen bonds : angle 6.15957 / 4.28 ( 762) Misc. bond : bond 0.00051 / 0.03 ( 1) link_ALPHA1-3 : bond 0.00735 / 0.39 ( 1) link_ALPHA1-3 : angle 2.39371 / 1.48 ( 3) link_ALPHA1-4 : bond 0.00058 / 0.03 ( 1) link_ALPHA1-4 : angle 2.84595 / 1.80 ( 3) link_BETA1-4 : bond 0.00583 / 0.28 ( 10) link_BETA1-4 : angle 2.22319 / 1.43 ( 30) link_BETA1-6 : bond 0.00217 / 0.11 ( 1) link_BETA1-6 : angle 2.28254 / 1.48 ( 3) link_NAG-ASN : bond 0.00506 / 0.25 ( 9) link_NAG-ASN : angle 1.92801 / 1.26 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 76 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.8354 (mmm) cc_final: 0.8039 (mtt) REVERT: A 275 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.8442 (t80) REVERT: A 657 VAL cc_start: 0.7607 (OUTLIER) cc_final: 0.7294 (p) REVERT: A 707 MET cc_start: 0.3221 (OUTLIER) cc_final: 0.2875 (mmp) REVERT: B 262 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8756 (mp) REVERT: B 318 TYR cc_start: 0.8304 (m-80) cc_final: 0.8063 (m-80) REVERT: B 419 VAL cc_start: 0.9103 (p) cc_final: 0.8849 (m) REVERT: C 33 ASN cc_start: 0.8254 (p0) cc_final: 0.7909 (p0) outliers start: 40 outliers final: 29 residues processed: 109 average time/residue: 0.0777 time to fit residues: 12.5934 Evaluate side-chains 107 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 657 VAL 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 40 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 360 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 119 optimal weight: 8.9990 chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 17 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.181422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.115177 restraints weight = 13755.631| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.96 r_work: 0.3470 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10183 Z= 0.125 Angle : 0.597 9.827 13836 Z= 0.290 Chirality : 0.045 0.244 1576 Planarity : 0.003 0.033 1784 Dihedral : 6.455 55.159 1799 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.81 % Allowed : 22.89 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.23), residues: 1243 helix: 0.62 (0.49), residues: 122 sheet: -0.26 (0.25), residues: 403 loop : -1.20 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 566 TYR 0.016 0.001 TYR A 112 PHE 0.010 0.001 PHE A 154 TRP 0.007 0.001 TRP B 238 HIS 0.002 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (10138) covalent geometry : angle 0.58298 / 0.29 (13726) SS BOND : bond 0.00122 / 0.08 ( 22) SS BOND : angle 0.84362 / 0.53 ( 44) hydrogen bonds : bond 0.03039 / 2.09 ( 290) hydrogen bonds : angle 5.87245 / 4.07 ( 762) Misc. bond : bond 0.00010 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00635 / 0.33 ( 1) link_ALPHA1-3 : angle 1.58750 / 1.09 ( 3) link_ALPHA1-4 : bond 0.00567 / 0.30 ( 1) link_ALPHA1-4 : angle 2.43294 / 1.59 ( 3) link_BETA1-4 : bond 0.00642 / 0.32 ( 10) link_BETA1-4 : angle 2.17565 / 1.39 ( 30) link_BETA1-6 : bond 0.00264 / 0.14 ( 1) link_BETA1-6 : angle 1.35675 / 0.98 ( 3) link_NAG-ASN : bond 0.00281 / 0.13 ( 9) link_NAG-ASN : angle 1.54111 / 1.01 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.8294 (mmm) cc_final: 0.7981 (mtt) REVERT: A 482 ASP cc_start: 0.7792 (t70) cc_final: 0.7543 (m-30) REVERT: A 657 VAL cc_start: 0.7603 (OUTLIER) cc_final: 0.7289 (p) REVERT: A 707 MET cc_start: 0.3356 (OUTLIER) cc_final: 0.2996 (mmp) REVERT: B 314 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8362 (m) REVERT: B 318 TYR cc_start: 0.8225 (m-80) cc_final: 0.7864 (m-80) REVERT: B 360 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.7032 (ptp90) REVERT: B 419 VAL cc_start: 0.9045 (p) cc_final: 0.8795 (m) REVERT: C 18 THR cc_start: 0.8907 (m) cc_final: 0.8656 (p) REVERT: C 33 ASN cc_start: 0.8198 (p0) cc_final: 0.7860 (p0) outliers start: 30 outliers final: 24 residues processed: 102 average time/residue: 0.0931 time to fit residues: 14.1468 Evaluate side-chains 106 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 360 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 92 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 114 optimal weight: 0.0980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.177327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.109761 restraints weight = 13801.419| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.12 r_work: 0.3385 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10183 Z= 0.247 Angle : 0.670 10.074 13836 Z= 0.327 Chirality : 0.047 0.249 1576 Planarity : 0.004 0.037 1784 Dihedral : 6.256 56.574 1799 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.81 % Allowed : 23.08 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.23), residues: 1243 helix: 0.34 (0.48), residues: 122 sheet: -0.40 (0.25), residues: 410 loop : -1.25 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 566 TYR 0.017 0.002 TYR B 318 PHE 0.018 0.002 PHE A 19 TRP 0.011 0.001 TRP A 114 HIS 0.006 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.25 (10138) covalent geometry : angle 0.65468 / 0.32 (13726) SS BOND : bond 0.00141 / 0.09 ( 22) SS BOND : angle 0.91861 / 0.57 ( 44) hydrogen bonds : bond 0.03512 / 2.42 ( 290) hydrogen bonds : angle 6.06698 / 4.20 ( 762) Misc. bond : bond 0.00050 / 0.03 ( 1) link_ALPHA1-3 : bond 0.00565 / 0.30 ( 1) link_ALPHA1-3 : angle 2.09633 / 1.37 ( 3) link_ALPHA1-4 : bond 0.00030 / 0.02 ( 1) link_ALPHA1-4 : angle 2.76261 / 1.72 ( 3) link_BETA1-4 : bond 0.00620 / 0.31 ( 10) link_BETA1-4 : angle 2.28182 / 1.46 ( 30) link_BETA1-6 : bond 0.00136 / 0.07 ( 1) link_BETA1-6 : angle 1.75875 / 1.32 ( 3) link_NAG-ASN : bond 0.00510 / 0.25 ( 9) link_NAG-ASN : angle 1.86480 / 1.21 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.8163 (mmm) cc_final: 0.7959 (mtt) REVERT: A 482 ASP cc_start: 0.7718 (t70) cc_final: 0.7509 (m-30) REVERT: A 580 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7347 (pt0) REVERT: A 657 VAL cc_start: 0.7659 (OUTLIER) cc_final: 0.7374 (p) REVERT: A 707 MET cc_start: 0.3416 (OUTLIER) cc_final: 0.3032 (mmp) REVERT: B 318 TYR cc_start: 0.8206 (m-80) cc_final: 0.7964 (m-80) REVERT: B 419 VAL cc_start: 0.9047 (p) cc_final: 0.8809 (m) REVERT: C 18 THR cc_start: 0.8897 (m) cc_final: 0.8618 (p) REVERT: C 33 ASN cc_start: 0.8238 (p0) cc_final: 0.7899 (p0) outliers start: 30 outliers final: 24 residues processed: 100 average time/residue: 0.0912 time to fit residues: 13.6535 Evaluate side-chains 100 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 360 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 93 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 103 optimal weight: 0.4980 chunk 95 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.180490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.109218 restraints weight = 13695.650| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.71 r_work: 0.3475 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10183 Z= 0.131 Angle : 0.628 14.040 13836 Z= 0.305 Chirality : 0.045 0.243 1576 Planarity : 0.003 0.033 1784 Dihedral : 5.758 55.340 1799 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.44 % Allowed : 23.36 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.23), residues: 1243 helix: 0.30 (0.48), residues: 128 sheet: -0.25 (0.25), residues: 402 loop : -1.26 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 566 TYR 0.016 0.001 TYR A 112 PHE 0.010 0.001 PHE A 72 TRP 0.007 0.001 TRP B 238 HIS 0.004 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (10138) covalent geometry : angle 0.60965 / 0.30 (13726) SS BOND : bond 0.00245 / 0.12 ( 22) SS BOND : angle 1.53856 / 0.94 ( 44) hydrogen bonds : bond 0.03035 / 2.09 ( 290) hydrogen bonds : angle 5.87435 / 4.06 ( 762) Misc. bond : bond 0.00014 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00674 / 0.35 ( 1) link_ALPHA1-3 : angle 1.71764 / 1.21 ( 3) link_ALPHA1-4 : bond 0.00302 / 0.16 ( 1) link_ALPHA1-4 : angle 2.42985 / 1.51 ( 3) link_BETA1-4 : bond 0.00663 / 0.33 ( 10) link_BETA1-4 : angle 2.23310 / 1.42 ( 30) link_BETA1-6 : bond 0.00285 / 0.15 ( 1) link_BETA1-6 : angle 1.37756 / 1.08 ( 3) link_NAG-ASN : bond 0.00294 / 0.13 ( 9) link_NAG-ASN : angle 1.53472 / 0.99 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.8285 (mmm) cc_final: 0.8060 (mtt) REVERT: A 482 ASP cc_start: 0.7800 (t70) cc_final: 0.7557 (m-30) REVERT: A 517 ARG cc_start: 0.8026 (mtp180) cc_final: 0.7561 (tpt-90) REVERT: A 657 VAL cc_start: 0.7646 (OUTLIER) cc_final: 0.7347 (p) REVERT: A 687 MET cc_start: 0.6442 (ttp) cc_final: 0.6185 (ttm) REVERT: A 707 MET cc_start: 0.3497 (OUTLIER) cc_final: 0.3106 (mmp) REVERT: B 318 TYR cc_start: 0.8209 (m-80) cc_final: 0.7871 (m-80) REVERT: B 360 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.7084 (ptp90) REVERT: B 417 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7541 (tttp) REVERT: B 419 VAL cc_start: 0.9039 (p) cc_final: 0.8802 (m) REVERT: C 18 THR cc_start: 0.8893 (m) cc_final: 0.8644 (p) REVERT: C 33 ASN cc_start: 0.8240 (p0) cc_final: 0.7898 (p0) outliers start: 26 outliers final: 20 residues processed: 97 average time/residue: 0.0985 time to fit residues: 14.1237 Evaluate side-chains 97 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 417 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 63 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.179127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.107361 restraints weight = 13885.512| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.69 r_work: 0.3446 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10183 Z= 0.183 Angle : 0.644 11.824 13836 Z= 0.313 Chirality : 0.046 0.248 1576 Planarity : 0.004 0.034 1784 Dihedral : 5.597 55.994 1799 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.53 % Allowed : 22.98 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.23), residues: 1243 helix: 0.21 (0.48), residues: 128 sheet: -0.34 (0.25), residues: 410 loop : -1.24 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 566 TYR 0.016 0.001 TYR A 112 PHE 0.013 0.002 PHE A 326 TRP 0.009 0.001 TRP A 114 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (10138) covalent geometry : angle 0.62719 / 0.31 (13726) SS BOND : bond 0.00258 / 0.13 ( 22) SS BOND : angle 1.28718 / 0.81 ( 44) hydrogen bonds : bond 0.03269 / 2.25 ( 290) hydrogen bonds : angle 5.90255 / 4.08 ( 762) Misc. bond : bond 0.00029 / 0.02 ( 1) link_ALPHA1-3 : bond 0.00558 / 0.29 ( 1) link_ALPHA1-3 : angle 1.87336 / 1.28 ( 3) link_ALPHA1-4 : bond 0.00194 / 0.10 ( 1) link_ALPHA1-4 : angle 2.54736 / 1.60 ( 3) link_BETA1-4 : bond 0.00655 / 0.33 ( 10) link_BETA1-4 : angle 2.27627 / 1.44 ( 30) link_BETA1-6 : bond 0.00044 / 0.02 ( 1) link_BETA1-6 : angle 1.61573 / 1.22 ( 3) link_NAG-ASN : bond 0.00376 / 0.18 ( 9) link_NAG-ASN : angle 1.64544 / 1.05 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3110.57 seconds wall clock time: 53 minutes 50.12 seconds (3230.12 seconds total)