Starting phenix.real_space_refine on Wed Feb 4 10:41:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jei_61418/02_2026/9jei_61418.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jei_61418/02_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_61418/02_2026/9jei_61418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jei_61418/02_2026/9jei_61418.map" model { file = "/net/cci-nas-00/data/ceres_data/9jei_61418/02_2026/9jei_61418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jei_61418/02_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-2.0-5952/lib/python3.9/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, 19 Unusual residues: {' CA': 5, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 2, ' MG': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.39, per 1000 atoms: 0.24 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: 1.06 Conformation dependent library (CDL) restraints added in 550.9 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: 0.46 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: 1.99 Time building geometry restraints manager: 1.36 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 2.590 nonbonded pdb=" OD2 ASP B 158 " pdb="CA CA B1003 " model vdw 1.943 2.510 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 2.510 ... (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: 5.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.750 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 covalent geometry : bond 0.00470 (10138) covalent geometry : angle 0.72693 (13726) SS BOND : bond 0.01219 ( 22) SS BOND : angle 4.42816 ( 44) hydrogen bonds : bond 0.21886 ( 290) hydrogen bonds : angle 9.61483 ( 762) Misc. bond : bond 0.00107 ( 1) link_ALPHA1-3 : bond 0.00438 ( 1) link_ALPHA1-3 : angle 1.54708 ( 3) link_ALPHA1-4 : bond 0.00321 ( 1) link_ALPHA1-4 : angle 2.48996 ( 3) link_BETA1-4 : bond 0.00574 ( 10) link_BETA1-4 : angle 1.48030 ( 30) link_BETA1-6 : bond 0.00930 ( 1) link_BETA1-6 : angle 1.18070 ( 3) link_NAG-ASN : bond 0.00422 ( 9) link_NAG-ASN : angle 1.69344 ( 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 : 0.384 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 96 average time/residue: 0.0977 time to fit residues: 13.6135 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 : 0.248 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4467 r_free = 0.4467 target = 0.179473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.106598 restraints weight = 13807.135| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.66 r_work: 0.3428 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10183 Z= 0.242 Angle : 0.712 9.878 13836 Z= 0.348 Chirality : 0.048 0.237 1576 Planarity : 0.004 0.036 1784 Dihedral : 12.078 87.078 1799 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.81 % Allowed : 22.14 % Favored : 75.05 % 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: 0.37 (0.49), residues: 121 sheet: -0.26 (0.25), residues: 400 loop : -1.41 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 93 TYR 0.017 0.002 TYR A 112 PHE 0.017 0.002 PHE B 153 TRP 0.015 0.002 TRP A 114 HIS 0.007 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00577 (10138) covalent geometry : angle 0.69010 (13726) SS BOND : bond 0.00172 ( 22) SS BOND : angle 1.05755 ( 44) hydrogen bonds : bond 0.04240 ( 290) hydrogen bonds : angle 7.10355 ( 762) Misc. bond : bond 0.00070 ( 1) link_ALPHA1-3 : bond 0.00485 ( 1) link_ALPHA1-3 : angle 3.30931 ( 3) link_ALPHA1-4 : bond 0.00106 ( 1) link_ALPHA1-4 : angle 2.62107 ( 3) link_BETA1-4 : bond 0.00615 ( 10) link_BETA1-4 : angle 2.59281 ( 30) link_BETA1-6 : bond 0.00256 ( 1) link_BETA1-6 : angle 2.39641 ( 3) link_NAG-ASN : bond 0.00534 ( 9) link_NAG-ASN : angle 2.43220 ( 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 109 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.8411 (mmm) cc_final: 0.8079 (mtt) REVERT: A 275 TYR cc_start: 0.9010 (OUTLIER) cc_final: 0.8469 (t80) REVERT: A 707 MET cc_start: 0.2941 (OUTLIER) cc_final: 0.2538 (mmp) REVERT: B 318 TYR cc_start: 0.8304 (m-80) cc_final: 0.8045 (m-80) REVERT: B 419 VAL cc_start: 0.9089 (p) cc_final: 0.8807 (m) outliers start: 30 outliers final: 20 residues processed: 103 average time/residue: 0.0784 time to fit residues: 12.4822 Evaluate side-chains 93 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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: 0.9990 chunk 113 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 104 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 106 optimal weight: 0.6980 chunk 121 optimal weight: 0.4980 chunk 60 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.177462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.109322 restraints weight = 13620.211| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.55 r_work: 0.3466 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1425 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= 0.153 Angle : 0.625 9.759 13836 Z= 0.305 Chirality : 0.046 0.246 1576 Planarity : 0.003 0.030 1784 Dihedral : 10.485 83.905 1799 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.35 % Allowed : 23.26 % Favored : 74.39 % 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: -1.09 (0.23), residues: 1243 helix: 0.53 (0.49), residues: 121 sheet: -0.15 (0.25), residues: 392 loop : -1.30 (0.22), residues: 730 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 0.001 PHE B 414 TRP 0.011 0.001 TRP A 114 HIS 0.002 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00357 (10138) covalent geometry : angle 0.60777 (13726) SS BOND : bond 0.00118 ( 22) SS BOND : angle 0.81288 ( 44) hydrogen bonds : bond 0.03723 ( 290) hydrogen bonds : angle 6.60355 ( 762) Misc. bond : bond 0.00068 ( 1) link_ALPHA1-3 : bond 0.00971 ( 1) link_ALPHA1-3 : angle 2.54948 ( 3) link_ALPHA1-4 : bond 0.00131 ( 1) link_ALPHA1-4 : angle 2.39889 ( 3) link_BETA1-4 : bond 0.00532 ( 10) link_BETA1-4 : angle 2.35238 ( 30) link_BETA1-6 : bond 0.00085 ( 1) link_BETA1-6 : angle 1.83225 ( 3) link_NAG-ASN : bond 0.00318 ( 9) link_NAG-ASN : angle 1.85278 ( 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 104 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.8384 (mmm) cc_final: 0.8089 (mtt) REVERT: A 275 TYR cc_start: 0.8921 (OUTLIER) cc_final: 0.8463 (t80) REVERT: A 707 MET cc_start: 0.3124 (OUTLIER) cc_final: 0.2734 (mmp) REVERT: B 318 TYR cc_start: 0.8228 (m-80) cc_final: 0.7872 (m-80) REVERT: B 419 VAL cc_start: 0.9126 (p) cc_final: 0.8872 (m) REVERT: C 33 ASN cc_start: 0.8034 (p0) cc_final: 0.7704 (p0) outliers start: 25 outliers final: 15 residues processed: 97 average time/residue: 0.0871 time to fit residues: 12.8230 Evaluate side-chains 89 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 707 MET Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 118 MET 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: 0.9980 chunk 83 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 48 optimal weight: 0.0270 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4477 r_free = 0.4477 target = 0.180573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.112448 restraints weight = 13800.609| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.11 r_work: 0.3439 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10183 Z= 0.146 Angle : 0.608 9.845 13836 Z= 0.296 Chirality : 0.046 0.262 1576 Planarity : 0.003 0.031 1784 Dihedral : 9.071 76.618 1799 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.19 % Allowed : 21.95 % 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: -1.07 (0.23), residues: 1243 helix: 0.65 (0.49), residues: 122 sheet: -0.24 (0.25), residues: 412 loop : -1.25 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 566 TYR 0.015 0.001 TYR A 112 PHE 0.012 0.001 PHE B 370 TRP 0.009 0.001 TRP A 114 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00344 (10138) covalent geometry : angle 0.59152 (13726) SS BOND : bond 0.00112 ( 22) SS BOND : angle 0.73478 ( 44) hydrogen bonds : bond 0.03307 ( 290) hydrogen bonds : angle 6.21985 ( 762) Misc. bond : bond 0.00046 ( 1) link_ALPHA1-3 : bond 0.00994 ( 1) link_ALPHA1-3 : angle 2.55676 ( 3) link_ALPHA1-4 : bond 0.00137 ( 1) link_ALPHA1-4 : angle 2.44395 ( 3) link_BETA1-4 : bond 0.00541 ( 10) link_BETA1-4 : angle 2.29818 ( 30) link_BETA1-6 : bond 0.00002 ( 1) link_BETA1-6 : angle 1.83169 ( 3) link_NAG-ASN : bond 0.00300 ( 9) link_NAG-ASN : angle 1.74535 ( 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 107 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 275 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8444 (t80) REVERT: A 707 MET cc_start: 0.3225 (OUTLIER) cc_final: 0.2865 (mmp) REVERT: B 124 MET cc_start: 0.8476 (tpp) cc_final: 0.8008 (mtp) REVERT: B 314 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8334 (m) REVERT: B 318 TYR cc_start: 0.8223 (m-80) cc_final: 0.7901 (m-80) REVERT: B 419 VAL cc_start: 0.9101 (p) cc_final: 0.8839 (m) REVERT: C 33 ASN cc_start: 0.8175 (p0) cc_final: 0.7824 (p0) outliers start: 34 outliers final: 21 residues processed: 98 average time/residue: 0.0994 time to fit residues: 14.3900 Evaluate side-chains 93 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 101 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.179341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.112248 restraints weight = 13830.086| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.16 r_work: 0.3421 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10183 Z= 0.186 Angle : 0.633 9.909 13836 Z= 0.308 Chirality : 0.046 0.248 1576 Planarity : 0.003 0.034 1784 Dihedral : 8.393 71.276 1799 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.47 % Allowed : 22.42 % 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: -1.11 (0.23), residues: 1243 helix: 0.59 (0.49), residues: 122 sheet: -0.32 (0.25), residues: 414 loop : -1.23 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 566 TYR 0.016 0.001 TYR A 112 PHE 0.013 0.002 PHE A 326 TRP 0.010 0.001 TRP A 114 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00445 (10138) covalent geometry : angle 0.61604 (13726) SS BOND : bond 0.00155 ( 22) SS BOND : angle 1.06991 ( 44) hydrogen bonds : bond 0.03408 ( 290) hydrogen bonds : angle 6.13650 ( 762) Misc. bond : bond 0.00049 ( 1) link_ALPHA1-3 : bond 0.00907 ( 1) link_ALPHA1-3 : angle 2.38214 ( 3) link_ALPHA1-4 : bond 0.00057 ( 1) link_ALPHA1-4 : angle 2.59861 ( 3) link_BETA1-4 : bond 0.00569 ( 10) link_BETA1-4 : angle 2.23617 ( 30) link_BETA1-6 : bond 0.00091 ( 1) link_BETA1-6 : angle 2.22767 ( 3) link_NAG-ASN : bond 0.00376 ( 9) link_NAG-ASN : angle 1.79911 ( 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 110 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 73 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.8514 (t80) REVERT: A 707 MET cc_start: 0.3147 (OUTLIER) cc_final: 0.2780 (mmp) REVERT: B 262 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8736 (mp) REVERT: B 314 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8382 (m) REVERT: B 318 TYR cc_start: 0.8271 (m-80) cc_final: 0.8000 (m-80) REVERT: B 419 VAL cc_start: 0.9102 (p) cc_final: 0.8833 (m) REVERT: C 33 ASN cc_start: 0.8210 (p0) cc_final: 0.7849 (p0) outliers start: 37 outliers final: 26 residues processed: 104 average time/residue: 0.1001 time to fit residues: 15.3939 Evaluate side-chains 99 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 69 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 42 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.0770 chunk 85 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.181133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.114822 restraints weight = 13836.979| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.12 r_work: 0.3455 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10183 Z= 0.129 Angle : 0.601 9.972 13836 Z= 0.290 Chirality : 0.045 0.255 1576 Planarity : 0.003 0.030 1784 Dihedral : 7.655 65.581 1799 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.10 % Allowed : 22.23 % Favored : 74.67 % 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: -0.99 (0.23), residues: 1243 helix: 0.72 (0.49), residues: 122 sheet: -0.24 (0.25), residues: 408 loop : -1.16 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 566 TYR 0.016 0.001 TYR A 112 PHE 0.011 0.001 PHE B 370 TRP 0.007 0.001 TRP A 114 HIS 0.001 0.000 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00302 (10138) covalent geometry : angle 0.58518 (13726) SS BOND : bond 0.00113 ( 22) SS BOND : angle 0.97419 ( 44) hydrogen bonds : bond 0.03111 ( 290) hydrogen bonds : angle 5.95538 ( 762) Misc. bond : bond 0.00034 ( 1) link_ALPHA1-3 : bond 0.00875 ( 1) link_ALPHA1-3 : angle 2.06353 ( 3) link_ALPHA1-4 : bond 0.00284 ( 1) link_ALPHA1-4 : angle 2.45023 ( 3) link_BETA1-4 : bond 0.00536 ( 10) link_BETA1-4 : angle 2.18673 ( 30) link_BETA1-6 : bond 0.00075 ( 1) link_BETA1-6 : angle 1.84471 ( 3) link_NAG-ASN : bond 0.00304 ( 9) link_NAG-ASN : angle 1.59617 ( 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 107 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 ASP cc_start: 0.7776 (t70) cc_final: 0.7525 (m-30) REVERT: A 657 VAL cc_start: 0.7506 (OUTLIER) cc_final: 0.7184 (p) REVERT: A 707 MET cc_start: 0.3134 (OUTLIER) cc_final: 0.2791 (mmp) REVERT: B 262 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8704 (mp) REVERT: B 314 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8336 (m) REVERT: B 318 TYR cc_start: 0.8222 (m-80) cc_final: 0.7855 (m-80) REVERT: B 360 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.7058 (ptp90) REVERT: B 419 VAL cc_start: 0.9110 (p) cc_final: 0.8862 (m) REVERT: C 33 ASN cc_start: 0.8131 (p0) cc_final: 0.7754 (p0) outliers start: 33 outliers final: 22 residues processed: 101 average time/residue: 0.1048 time to fit residues: 15.4251 Evaluate side-chains 99 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 216 ILE 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 538 LEU 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 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 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: 1.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4456 r_free = 0.4456 target = 0.177750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.109360 restraints weight = 13838.731| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.06 r_work: 0.3397 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 10183 Z= 0.256 Angle : 0.679 9.983 13836 Z= 0.330 Chirality : 0.047 0.248 1576 Planarity : 0.004 0.036 1784 Dihedral : 7.460 60.316 1799 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.75 % Allowed : 21.58 % Favored : 74.67 % 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: -1.12 (0.23), residues: 1243 helix: 0.37 (0.49), residues: 122 sheet: -0.34 (0.25), residues: 408 loop : -1.19 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 566 TYR 0.016 0.002 TYR A 112 PHE 0.018 0.002 PHE A 19 TRP 0.012 0.001 TRP A 114 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00615 (10138) covalent geometry : angle 0.66333 (13726) SS BOND : bond 0.00143 ( 22) SS BOND : angle 0.96802 ( 44) hydrogen bonds : bond 0.03565 ( 290) hydrogen bonds : angle 6.11453 ( 762) Misc. bond : bond 0.00052 ( 1) link_ALPHA1-3 : bond 0.00732 ( 1) link_ALPHA1-3 : angle 2.33363 ( 3) link_ALPHA1-4 : bond 0.00004 ( 1) link_ALPHA1-4 : angle 2.76543 ( 3) link_BETA1-4 : bond 0.00610 ( 10) link_BETA1-4 : angle 2.23592 ( 30) link_BETA1-6 : bond 0.00238 ( 1) link_BETA1-6 : angle 2.35502 ( 3) link_NAG-ASN : bond 0.00500 ( 9) link_NAG-ASN : angle 1.87599 ( 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 111 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 71 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.8337 (mmm) cc_final: 0.7982 (mtt) REVERT: A 657 VAL cc_start: 0.7600 (OUTLIER) cc_final: 0.7282 (p) REVERT: A 707 MET cc_start: 0.3135 (OUTLIER) cc_final: 0.2788 (mmp) REVERT: B 124 MET cc_start: 0.8681 (tpp) cc_final: 0.8390 (tpp) REVERT: B 262 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8732 (mp) REVERT: B 318 TYR cc_start: 0.8296 (m-80) cc_final: 0.8075 (m-80) REVERT: B 419 VAL cc_start: 0.9078 (p) cc_final: 0.8814 (m) REVERT: C 33 ASN cc_start: 0.8241 (p0) cc_final: 0.7897 (p0) outliers start: 40 outliers final: 28 residues processed: 104 average time/residue: 0.0936 time to fit residues: 14.6768 Evaluate side-chains 103 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 16 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 119 optimal weight: 0.0570 chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.181225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.110577 restraints weight = 13744.518| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.62 r_work: 0.3473 rms_B_bonded: 2.82 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: 0.8249 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10183 Z= 0.120 Angle : 0.594 9.787 13836 Z= 0.287 Chirality : 0.044 0.245 1576 Planarity : 0.003 0.030 1784 Dihedral : 6.620 55.508 1799 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.16 % Allowed : 23.17 % Favored : 74.67 % 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: -0.99 (0.23), residues: 1243 helix: 0.68 (0.49), residues: 122 sheet: -0.20 (0.25), residues: 403 loop : -1.18 (0.23), residues: 718 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 B 370 TRP 0.007 0.001 TRP B 238 HIS 0.002 0.000 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00281 (10138) covalent geometry : angle 0.57952 (13726) SS BOND : bond 0.00128 ( 22) SS BOND : angle 0.84110 ( 44) hydrogen bonds : bond 0.03020 ( 290) hydrogen bonds : angle 5.85027 ( 762) Misc. bond : bond 0.00021 ( 1) link_ALPHA1-3 : bond 0.00850 ( 1) link_ALPHA1-3 : angle 1.75637 ( 3) link_ALPHA1-4 : bond 0.00292 ( 1) link_ALPHA1-4 : angle 2.40488 ( 3) link_BETA1-4 : bond 0.00640 ( 10) link_BETA1-4 : angle 2.18595 ( 30) link_BETA1-6 : bond 0.00271 ( 1) link_BETA1-6 : angle 1.31522 ( 3) link_NAG-ASN : bond 0.00281 ( 9) link_NAG-ASN : angle 1.51704 ( 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 100 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.8276 (mmm) cc_final: 0.7957 (mtt) REVERT: A 482 ASP cc_start: 0.7735 (t70) cc_final: 0.7500 (m-30) REVERT: A 657 VAL cc_start: 0.7499 (OUTLIER) cc_final: 0.7182 (p) REVERT: A 707 MET cc_start: 0.3230 (OUTLIER) cc_final: 0.2865 (mmp) REVERT: B 318 TYR cc_start: 0.8208 (m-80) cc_final: 0.7806 (m-80) REVERT: B 360 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6776 (ptp90) REVERT: B 419 VAL cc_start: 0.9078 (p) cc_final: 0.8839 (m) REVERT: C 18 THR cc_start: 0.8909 (m) cc_final: 0.8656 (p) REVERT: C 33 ASN cc_start: 0.8175 (p0) cc_final: 0.7839 (p0) outliers start: 23 outliers final: 20 residues processed: 93 average time/residue: 0.0973 time to fit residues: 13.2587 Evaluate side-chains 99 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.178785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.110391 restraints weight = 13802.977| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.87 r_work: 0.3413 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10183 Z= 0.190 Angle : 0.626 9.977 13836 Z= 0.303 Chirality : 0.046 0.246 1576 Planarity : 0.004 0.039 1784 Dihedral : 6.227 56.447 1799 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % 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: -1.03 (0.23), residues: 1243 helix: 0.56 (0.49), residues: 122 sheet: -0.32 (0.25), residues: 408 loop : -1.12 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 566 TYR 0.015 0.002 TYR A 112 PHE 0.013 0.002 PHE A 326 TRP 0.010 0.001 TRP A 114 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00455 (10138) covalent geometry : angle 0.61124 (13726) SS BOND : bond 0.00123 ( 22) SS BOND : angle 0.85214 ( 44) hydrogen bonds : bond 0.03245 ( 290) hydrogen bonds : angle 5.92091 ( 762) Misc. bond : bond 0.00043 ( 1) link_ALPHA1-3 : bond 0.00613 ( 1) link_ALPHA1-3 : angle 1.89889 ( 3) link_ALPHA1-4 : bond 0.00148 ( 1) link_ALPHA1-4 : angle 2.56828 ( 3) link_BETA1-4 : bond 0.00628 ( 10) link_BETA1-4 : angle 2.24852 ( 30) link_BETA1-6 : bond 0.00052 ( 1) link_BETA1-6 : angle 1.52388 ( 3) link_NAG-ASN : bond 0.00351 ( 9) link_NAG-ASN : angle 1.67950 ( 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 103 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.8325 (mmm) cc_final: 0.8107 (mtt) REVERT: A 482 ASP cc_start: 0.7831 (t70) cc_final: 0.7570 (m-30) REVERT: A 657 VAL cc_start: 0.7546 (OUTLIER) cc_final: 0.7214 (p) REVERT: A 707 MET cc_start: 0.3437 (OUTLIER) cc_final: 0.3073 (mmp) REVERT: B 262 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8709 (mp) REVERT: B 314 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8390 (m) REVERT: B 318 TYR cc_start: 0.8270 (m-80) cc_final: 0.7998 (m-80) REVERT: B 360 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.7018 (ptp90) REVERT: B 419 VAL cc_start: 0.9019 (p) cc_final: 0.8764 (m) REVERT: C 18 THR cc_start: 0.8839 (m) cc_final: 0.8546 (p) REVERT: C 33 ASN cc_start: 0.8244 (p0) cc_final: 0.7902 (p0) outliers start: 27 outliers final: 22 residues processed: 96 average time/residue: 0.0961 time to fit residues: 13.4032 Evaluate side-chains 101 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 93 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 94 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 28 optimal weight: 0.0980 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 0.0770 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.181725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.111371 restraints weight = 13694.731| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.70 r_work: 0.3491 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 10183 Z= 0.107 Angle : 0.605 13.312 13836 Z= 0.293 Chirality : 0.044 0.242 1576 Planarity : 0.003 0.036 1784 Dihedral : 5.666 55.322 1799 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.16 % Allowed : 23.36 % 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: -0.96 (0.23), residues: 1243 helix: 0.43 (0.48), residues: 128 sheet: -0.13 (0.25), residues: 399 loop : -1.14 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 566 TYR 0.016 0.001 TYR A 112 PHE 0.010 0.001 PHE B 370 TRP 0.006 0.001 TRP B 238 HIS 0.002 0.000 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00248 (10138) covalent geometry : angle 0.58628 (13726) SS BOND : bond 0.00278 ( 22) SS BOND : angle 1.57088 ( 44) hydrogen bonds : bond 0.02867 ( 290) hydrogen bonds : angle 5.73507 ( 762) Misc. bond : bond 0.00022 ( 1) link_ALPHA1-3 : bond 0.00796 ( 1) link_ALPHA1-3 : angle 1.63191 ( 3) link_ALPHA1-4 : bond 0.00368 ( 1) link_ALPHA1-4 : angle 2.28514 ( 3) link_BETA1-4 : bond 0.00659 ( 10) link_BETA1-4 : angle 2.22698 ( 30) link_BETA1-6 : bond 0.00436 ( 1) link_BETA1-6 : angle 1.25080 ( 3) link_NAG-ASN : bond 0.00282 ( 9) link_NAG-ASN : angle 1.41615 ( 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 103 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 ASP cc_start: 0.7705 (t70) cc_final: 0.7477 (m-30) REVERT: A 657 VAL cc_start: 0.7558 (OUTLIER) cc_final: 0.7236 (p) REVERT: A 707 MET cc_start: 0.3382 (OUTLIER) cc_final: 0.3015 (mmp) REVERT: B 124 MET cc_start: 0.8348 (tpp) cc_final: 0.8126 (mtp) REVERT: B 314 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8365 (m) REVERT: B 318 TYR cc_start: 0.8156 (m-80) cc_final: 0.7782 (m-80) REVERT: B 360 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6805 (ptp90) REVERT: B 419 VAL cc_start: 0.9013 (p) cc_final: 0.8796 (m) REVERT: C 18 THR cc_start: 0.8881 (m) cc_final: 0.8641 (p) REVERT: C 33 ASN cc_start: 0.8193 (p0) cc_final: 0.7835 (p0) outliers start: 23 outliers final: 17 residues processed: 96 average time/residue: 0.1013 time to fit residues: 14.2294 Evaluate side-chains 97 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 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 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 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 63 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.180117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.112538 restraints weight = 13913.187| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.17 r_work: 0.3437 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10183 Z= 0.152 Angle : 0.617 11.966 13836 Z= 0.299 Chirality : 0.045 0.245 1576 Planarity : 0.003 0.035 1784 Dihedral : 5.494 55.970 1799 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.06 % Allowed : 23.36 % Favored : 74.58 % 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: -0.99 (0.23), residues: 1243 helix: 0.33 (0.47), residues: 128 sheet: -0.22 (0.25), residues: 409 loop : -1.11 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 566 TYR 0.015 0.001 TYR B 318 PHE 0.011 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 covalent geometry : bond 0.00361 (10138) covalent geometry : angle 0.59998 (13726) SS BOND : bond 0.00237 ( 22) SS BOND : angle 1.31315 ( 44) hydrogen bonds : bond 0.03074 ( 290) hydrogen bonds : angle 5.75564 ( 762) Misc. bond : bond 0.00074 ( 1) link_ALPHA1-3 : bond 0.00577 ( 1) link_ALPHA1-3 : angle 1.72962 ( 3) link_ALPHA1-4 : bond 0.00238 ( 1) link_ALPHA1-4 : angle 2.41509 ( 3) link_BETA1-4 : bond 0.00665 ( 10) link_BETA1-4 : angle 2.26290 ( 30) link_BETA1-6 : bond 0.00155 ( 1) link_BETA1-6 : angle 1.47563 ( 3) link_NAG-ASN : bond 0.00319 ( 9) link_NAG-ASN : angle 1.51945 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3705.95 seconds wall clock time: 64 minutes 2.77 seconds (3842.77 seconds total)