Starting phenix.real_space_refine on Thu Jul 2 23:42:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjf_60143/07_2026/8zjf_60143.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjf_60143/07_2026/8zjf_60143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zjf_60143/07_2026/8zjf_60143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjf_60143/07_2026/8zjf_60143.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zjf_60143/07_2026/8zjf_60143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjf_60143/07_2026/8zjf_60143.map" } resolution = 2.7 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= 0.001 sd= 0.027 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 2 9.91 5 Mg 1 5.21 5 S 73 5.16 5 C 6800 2.51 5 N 1931 2.21 5 O 2110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10917 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3882 Classifications: {'peptide': 510} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 478} Chain breaks: 1 Chain: "A" Number of atoms: 6993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 909, 6993 Classifications: {'peptide': 909} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 864} Chain breaks: 1 Chain: "C" 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: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 2.50, per 1000 atoms: 0.23 Number of scatterers: 10917 At special positions: 0 Unit cell: (87.69, 97.68, 172.05, 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 2 19.99 S 73 16.00 Mg 1 11.99 O 2110 8.00 N 1931 7.00 C 6800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS B 61 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 91 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 271 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 412 " - pdb=" SG CYS B 428 " distance=2.03 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 488 " - pdb=" SG CYS B 500 " distance=2.03 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 543 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 550 " - pdb=" SG CYS B 559 " distance=2.03 Simple disulfide: pdb=" SG CYS A 70 " - pdb=" SG CYS A 79 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 706 " - pdb=" SG CYS A 762 " distance=2.03 Simple disulfide: pdb=" SG CYS A 742 " - pdb=" SG CYS A 748 " distance=2.03 Simple disulfide: pdb=" SG CYS A 775 " - pdb=" SG CYS A 779 " distance=2.03 Simple disulfide: pdb=" SG CYS A 823 " - pdb=" SG CYS A 829 " distance=2.03 Simple disulfide: pdb=" SG CYS A 893 " - pdb=" SG CYS A 907 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN A 444 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 406.7 milliseconds 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2610 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 24 sheets defined 19.1% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'B' and resid 50 through 58 removed outlier: 3.736A pdb=" N HIS B 58 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 174 through 183 Processing helix chain 'B' and resid 208 through 214 Processing helix chain 'B' and resid 238 through 249 removed outlier: 3.964A pdb=" N PHE B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 271 removed outlier: 3.816A pdb=" N ALA B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 294 through 302 removed outlier: 4.155A pdb=" N GLY B 298 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 299 " --> pdb=" O GLY B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.560A pdb=" N SER B 322 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 319 through 323' Processing helix chain 'B' and resid 329 through 340 Processing helix chain 'B' and resid 352 through 362 removed outlier: 3.580A pdb=" N TYR B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 391 Processing helix chain 'B' and resid 515 through 520 removed outlier: 3.591A pdb=" N SER B 520 " --> pdb=" O ALA B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 3.528A pdb=" N SER B 525 " --> pdb=" O PRO B 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 214 through 236 Processing helix chain 'A' and resid 257 through 260 removed outlier: 3.818A pdb=" N GLN A 260 " --> pdb=" O ARG A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 260' Processing helix chain 'A' and resid 261 through 271 Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 294 through 298 removed outlier: 4.022A pdb=" N HIS A 297 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 327 removed outlier: 3.511A pdb=" N ILE A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.674A pdb=" N GLN A 332 " --> pdb=" O PRO A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 348 removed outlier: 3.925A pdb=" N LYS A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 358 removed outlier: 3.657A pdb=" N GLU A 353 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 374 through 385 removed outlier: 4.465A pdb=" N SER A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LYS A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 450 through 456 Processing helix chain 'A' and resid 482 through 486 Processing helix chain 'A' and resid 606 through 610 removed outlier: 3.895A pdb=" N GLY A 609 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 744 through 748 removed outlier: 3.502A pdb=" N SER A 747 " --> pdb=" O ASP A 744 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS A 748 " --> pdb=" O VAL A 745 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 744 through 748' Processing sheet with id=AA1, first strand: chain 'B' and resid 102 through 107 removed outlier: 7.022A pdb=" N ARG B 127 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL B 128 " --> pdb=" O GLU B 469 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N HIS B 471 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 130 " --> pdb=" O HIS B 471 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS B 453 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AA3, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AA4, first strand: chain 'B' and resid 230 through 236 removed outlier: 5.246A pdb=" N HIS B 231 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER B 195 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU B 235 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE B 191 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B 152 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLY B 192 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 154 " --> pdb=" O GLY B 192 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLY B 194 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR B 156 " --> pdb=" O GLY B 194 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE B 196 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N MET B 158 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASP B 153 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL B 285 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TYR B 155 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N THR B 287 " --> pdb=" O TYR B 155 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU B 157 " --> pdb=" O THR B 287 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 543 through 544 Processing sheet with id=AA6, first strand: chain 'A' and resid 21 through 28 removed outlier: 4.585A pdb=" N ARG A 675 " --> pdb=" O ASP A 22 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALA A 24 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 10.924A pdb=" N VAL A 673 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 10.765A pdb=" N ALA A 671 " --> pdb=" O PRO A 26 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ASP A 662 " --> pdb=" O GLY A 652 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 652 " --> pdb=" O ASP A 662 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.629A pdb=" N SER A 39 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA9, first strand: chain 'A' and resid 95 through 100 Processing sheet with id=AB1, first strand: chain 'A' and resid 251 through 252 removed outlier: 4.311A pdb=" N GLN A 251 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 201 " --> pdb=" O ASN A 240 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ALA A 242 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE A 203 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N VAL A 244 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE A 205 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR A 246 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU A 207 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS A 305 " --> pdb=" O GLU A 335 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N PHE A 337 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N MET A 307 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A 339 " --> pdb=" O MET A 307 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 309 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N PHE A 367 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA A 338 " --> pdb=" O PHE A 367 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 404 through 410 removed outlier: 4.227A pdb=" N SER A 407 " --> pdb=" O GLY A 419 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 465 through 469 removed outlier: 11.942A pdb=" N LEU A 474 " --> pdb=" O LYS A 494 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LYS A 494 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N TYR A 476 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 489 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 500 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 518 through 521 removed outlier: 6.280A pdb=" N ARG A 552 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU A 562 " --> pdb=" O ARG A 552 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 518 through 521 removed outlier: 7.185A pdb=" N GLU A 545 " --> pdb=" O PHE A 577 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 580 through 583 removed outlier: 4.050A pdb=" N ALA A 580 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 631 " --> pdb=" O ILE A 617 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 679 through 680 Processing sheet with id=AB8, first strand: chain 'A' and resid 682 through 683 Processing sheet with id=AB9, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AC1, first strand: chain 'A' and resid 751 through 754 Processing sheet with id=AC2, first strand: chain 'A' and resid 729 through 731 Processing sheet with id=AC3, first strand: chain 'A' and resid 833 through 835 Processing sheet with id=AC4, first strand: chain 'A' and resid 838 through 839 removed outlier: 7.319A pdb=" N SER A 922 " --> pdb=" O MET A 883 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N MET A 883 " --> pdb=" O SER A 922 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N VAL A 924 " --> pdb=" O LYS A 881 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 881 " --> pdb=" O VAL A 924 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 868 through 869 Processing sheet with id=AC6, first strand: chain 'A' and resid 868 through 869 removed outlier: 3.654A pdb=" N GLU A 955 " --> pdb=" O VAL A 941 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 943 " --> pdb=" O ALA A 953 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A 953 " --> pdb=" O VAL A 943 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 873 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3741 1.34 - 1.46: 2390 1.46 - 1.58: 4908 1.58 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 11136 Sorted by residual: bond pdb=" CB CYS A 236 " pdb=" SG CYS A 236 " ideal model delta sigma weight residual 1.808 1.756 0.052 3.30e-02 9.18e+02 2.48e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.546 -0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" N PRO A 811 " pdb=" CA PRO A 811 " ideal model delta sigma weight residual 1.468 1.478 -0.011 7.90e-03 1.60e+04 1.80e+00 bond pdb=" N MET A 867 " pdb=" CA MET A 867 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.29e+00 bond pdb=" CB CYS A 239 " pdb=" SG CYS A 239 " ideal model delta sigma weight residual 1.808 1.771 0.037 3.30e-02 9.18e+02 1.26e+00 ... (remaining 11131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 14859 2.12 - 4.24: 203 4.24 - 6.35: 33 6.35 - 8.47: 3 8.47 - 10.59: 5 Bond angle restraints: 15103 Sorted by residual: angle pdb=" CA MET A 867 " pdb=" CB MET A 867 " pdb=" CG MET A 867 " ideal model delta sigma weight residual 114.10 122.82 -8.72 2.00e+00 2.50e-01 1.90e+01 angle pdb=" C THR A 936 " pdb=" N ALA A 937 " pdb=" CA ALA A 937 " ideal model delta sigma weight residual 121.54 128.44 -6.90 1.91e+00 2.74e-01 1.30e+01 angle pdb=" CB MET A 867 " pdb=" CG MET A 867 " pdb=" SD MET A 867 " ideal model delta sigma weight residual 112.70 123.29 -10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CB MET A 883 " pdb=" CG MET A 883 " pdb=" SD MET A 883 " ideal model delta sigma weight residual 112.70 123.08 -10.38 3.00e+00 1.11e-01 1.20e+01 angle pdb=" CB MET A 768 " pdb=" CG MET A 768 " pdb=" SD MET A 768 " ideal model delta sigma weight residual 112.70 121.84 -9.14 3.00e+00 1.11e-01 9.29e+00 ... (remaining 15098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 6132 21.43 - 42.86: 531 42.86 - 64.29: 119 64.29 - 85.72: 26 85.72 - 107.14: 8 Dihedral angle restraints: 6816 sinusoidal: 2759 harmonic: 4057 Sorted by residual: dihedral pdb=" CB CYS A 775 " pdb=" SG CYS A 775 " pdb=" SG CYS A 779 " pdb=" CB CYS A 779 " ideal model delta sinusoidal sigma weight residual 93.00 176.62 -83.62 1 1.00e+01 1.00e-02 8.53e+01 dihedral pdb=" CB CYS B 488 " pdb=" SG CYS B 488 " pdb=" SG CYS B 500 " pdb=" CB CYS B 500 " ideal model delta sinusoidal sigma weight residual -86.00 -9.12 -76.88 1 1.00e+01 1.00e-02 7.42e+01 dihedral pdb=" CB CYS B 527 " pdb=" SG CYS B 527 " pdb=" SG CYS B 543 " pdb=" CB CYS B 543 " ideal model delta sinusoidal sigma weight residual -86.00 -154.74 68.74 1 1.00e+01 1.00e-02 6.12e+01 ... (remaining 6813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1373 0.053 - 0.106: 282 0.106 - 0.159: 37 0.159 - 0.212: 3 0.212 - 0.265: 1 Chirality restraints: 1696 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.65e+00 chirality pdb=" CG LEU B 523 " pdb=" CB LEU B 523 " pdb=" CD1 LEU B 523 " pdb=" CD2 LEU B 523 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1693 not shown) Planarity restraints: 2003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 136 " 0.052 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO B 137 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 137 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 137 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 911 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO A 912 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 912 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 912 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 133 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO B 134 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 134 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 134 " -0.028 5.00e-02 4.00e+02 ... (remaining 2000 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 227 2.68 - 3.24: 10174 3.24 - 3.79: 17112 3.79 - 4.35: 23761 4.35 - 4.90: 38453 Nonbonded interactions: 89727 Sorted by model distance: nonbonded pdb=" OD2 ASP B 198 " pdb="CA CA B 902 " model vdw 2.127 3.250 nonbonded pdb=" OD1 ASP B 297 " pdb=" OH TYR A 513 " model vdw 2.141 3.040 nonbonded pdb=" OD1 ASP B 256 " pdb="CA CA B 902 " model vdw 2.162 3.250 nonbonded pdb=" O PRO B 258 " pdb="CA CA B 902 " model vdw 2.181 3.250 nonbonded pdb=" ND2 ASN B 254 " pdb="CA CA B 902 " model vdw 2.218 3.330 ... (remaining 89722 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 11.390 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 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 : 0.003 0.052 11158 Z= 0.138 Angle : 0.660 10.588 15150 Z= 0.341 Chirality : 0.044 0.265 1696 Planarity : 0.005 0.080 2002 Dihedral : 16.727 107.144 4149 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.50 % Allowed : 19.58 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.43 (0.22), residues: 1411 helix: 0.26 (0.39), residues: 203 sheet: -0.50 (0.26), residues: 413 loop : -1.55 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 753 TYR 0.012 0.001 TYR B 162 PHE 0.013 0.001 PHE A 688 TRP 0.012 0.001 TRP A 925 HIS 0.012 0.001 HIS B 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (11136) covalent geometry : angle 0.65191 / 0.34 (15103) SS BOND : bond 0.00177 / 0.11 ( 19) SS BOND : angle 2.08507 / 1.04 ( 38) hydrogen bonds : bond 0.21872 / 14.86 ( 308) hydrogen bonds : angle 8.81183 / 5.91 ( 873) link_BETA1-4 : bond 0.00507 / 0.24 ( 2) link_BETA1-4 : angle 1.49327 / 0.82 ( 6) link_NAG-ASN : bond 0.00231 / 0.12 ( 1) link_NAG-ASN : angle 1.60836 / 0.85 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 GLU cc_start: 0.7223 (tt0) cc_final: 0.7023 (tt0) REVERT: B 164 MET cc_start: 0.7521 (mmm) cc_final: 0.7030 (mmm) REVERT: B 314 ASP cc_start: 0.7108 (p0) cc_final: 0.6790 (p0) REVERT: B 326 ASP cc_start: 0.7203 (t0) cc_final: 0.6970 (t0) REVERT: B 383 MET cc_start: 0.8269 (mmm) cc_final: 0.8063 (mmm) REVERT: B 421 LYS cc_start: 0.6005 (ptpp) cc_final: 0.5675 (ttmt) REVERT: B 500 CYS cc_start: 0.4210 (m) cc_final: 0.3877 (m) REVERT: B 543 CYS cc_start: 0.3093 (OUTLIER) cc_final: 0.2542 (t) REVERT: A 76 GLU cc_start: 0.6026 (tp30) cc_final: 0.5344 (tm-30) REVERT: A 146 ASN cc_start: 0.8029 (m-40) cc_final: 0.7674 (m-40) REVERT: A 228 MET cc_start: 0.8809 (ttp) cc_final: 0.8014 (tpt) REVERT: A 574 ASN cc_start: 0.6992 (m-40) cc_final: 0.6696 (m110) REVERT: A 594 ASP cc_start: 0.7196 (p0) cc_final: 0.6723 (p0) REVERT: A 686 MET cc_start: 0.8310 (mmt) cc_final: 0.8063 (mmt) REVERT: A 870 MET cc_start: 0.5572 (tpt) cc_final: 0.5175 (mtm) outliers start: 30 outliers final: 16 residues processed: 154 average time/residue: 0.4171 time to fit residues: 70.7676 Evaluate side-chains 98 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 0.0170 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 183 GLN B 272 GLN B 274 GLN B 453 HIS ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 797 GLN A 802 GLN A 884 GLN A 945 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.243116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.166812 restraints weight = 10460.707| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.70 r_work: 0.3422 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11158 Z= 0.171 Angle : 0.667 9.211 15150 Z= 0.337 Chirality : 0.046 0.185 1696 Planarity : 0.005 0.055 2002 Dihedral : 7.106 57.787 1622 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.25 % Allowed : 19.92 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.33 (0.22), residues: 1411 helix: 0.49 (0.39), residues: 201 sheet: -0.42 (0.27), residues: 410 loop : -1.52 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 439 TYR 0.012 0.002 TYR A 433 PHE 0.013 0.002 PHE A 812 TRP 0.011 0.002 TRP B 277 HIS 0.007 0.001 HIS B 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (11136) covalent geometry : angle 0.66238 / 0.34 (15103) SS BOND : bond 0.00392 / 0.27 ( 19) SS BOND : angle 1.15103 / 0.71 ( 38) hydrogen bonds : bond 0.03839 / 2.55 ( 308) hydrogen bonds : angle 6.35715 / 4.22 ( 873) link_BETA1-4 : bond 0.00538 / 0.26 ( 2) link_BETA1-4 : angle 2.35391 / 1.28 ( 6) link_NAG-ASN : bond 0.00279 / 0.15 ( 1) link_NAG-ASN : angle 2.95268 / 1.52 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 93 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 245 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7763 (mm-30) REVERT: B 314 ASP cc_start: 0.7796 (p0) cc_final: 0.7547 (p0) REVERT: B 384 ASP cc_start: 0.7568 (m-30) cc_final: 0.7359 (m-30) REVERT: B 409 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7030 (mt-10) REVERT: A 76 GLU cc_start: 0.6496 (tp30) cc_final: 0.5821 (tm-30) REVERT: A 228 MET cc_start: 0.8788 (ttp) cc_final: 0.8113 (tpt) REVERT: A 229 MET cc_start: 0.7246 (ttp) cc_final: 0.6933 (ttm) REVERT: A 331 MET cc_start: 0.4844 (mpp) cc_final: 0.4620 (mpp) REVERT: A 513 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.8635 (m-80) REVERT: A 686 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8387 (mmt) REVERT: A 720 LEU cc_start: 0.2279 (OUTLIER) cc_final: 0.1833 (pp) outliers start: 51 outliers final: 22 residues processed: 136 average time/residue: 0.4582 time to fit residues: 68.3075 Evaluate side-chains 105 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 941 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 121 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 0.1980 chunk 94 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 139 optimal weight: 40.0000 chunk 110 optimal weight: 4.9990 chunk 133 optimal weight: 20.0000 chunk 75 optimal weight: 40.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 176 HIS B 187 HIS B 224 GLN B 274 GLN B 427 GLN B 453 HIS ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.238977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.155511 restraints weight = 10445.796| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.29 r_work: 0.3242 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11158 Z= 0.196 Angle : 0.689 9.103 15150 Z= 0.345 Chirality : 0.047 0.160 1696 Planarity : 0.005 0.047 2002 Dihedral : 6.539 56.446 1618 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.50 % Allowed : 20.58 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.41 (0.22), residues: 1411 helix: 0.45 (0.38), residues: 200 sheet: -0.45 (0.26), residues: 426 loop : -1.63 (0.20), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 677 TYR 0.018 0.002 TYR B 162 PHE 0.018 0.002 PHE A 406 TRP 0.017 0.002 TRP B 277 HIS 0.007 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (11136) covalent geometry : angle 0.68449 / 0.34 (15103) SS BOND : bond 0.00153 / 0.10 ( 19) SS BOND : angle 1.20066 / 0.78 ( 38) hydrogen bonds : bond 0.04555 / 3.09 ( 308) hydrogen bonds : angle 6.12317 / 4.06 ( 873) link_BETA1-4 : bond 0.00494 / 0.26 ( 2) link_BETA1-4 : angle 2.62610 / 1.26 ( 6) link_NAG-ASN : bond 0.00376 / 0.20 ( 1) link_NAG-ASN : angle 2.77835 / 1.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 80 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 GLN cc_start: 0.8152 (tt0) cc_final: 0.7942 (tt0) REVERT: B 290 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.7796 (t0) REVERT: B 316 ASN cc_start: 0.8211 (m-40) cc_final: 0.7927 (m-40) REVERT: B 387 ASN cc_start: 0.8141 (t0) cc_final: 0.7578 (m110) REVERT: B 444 GLN cc_start: 0.7199 (tp40) cc_final: 0.6770 (tp40) REVERT: A 76 GLU cc_start: 0.6778 (tp30) cc_final: 0.6517 (tp30) REVERT: A 113 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7839 (ttm170) REVERT: A 228 MET cc_start: 0.8816 (ttp) cc_final: 0.8143 (tpt) REVERT: A 238 GLU cc_start: 0.7327 (pt0) cc_final: 0.7097 (mt-10) REVERT: A 498 GLU cc_start: 0.6132 (mm-30) cc_final: 0.5640 (mp0) REVERT: A 513 TYR cc_start: 0.9346 (OUTLIER) cc_final: 0.8945 (m-80) REVERT: A 584 MET cc_start: 0.9011 (mmm) cc_final: 0.8590 (mmm) REVERT: A 622 TRP cc_start: 0.6616 (m100) cc_final: 0.6363 (m100) REVERT: A 720 LEU cc_start: 0.3003 (OUTLIER) cc_final: 0.2444 (pp) REVERT: A 790 GLN cc_start: 0.8784 (tt0) cc_final: 0.8451 (tt0) outliers start: 54 outliers final: 26 residues processed: 128 average time/residue: 0.4853 time to fit residues: 68.0601 Evaluate side-chains 106 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 3 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 chunk 102 optimal weight: 0.0370 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 40.0000 chunk 138 optimal weight: 0.0070 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 overall best weight: 1.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 176 HIS ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN ** B 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 842 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.239076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.156659 restraints weight = 10347.307| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.40 r_work: 0.3230 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 11158 Z= 0.166 Angle : 0.654 12.588 15150 Z= 0.326 Chirality : 0.046 0.221 1696 Planarity : 0.005 0.050 2002 Dihedral : 6.439 59.593 1618 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.50 % Allowed : 20.42 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.28 (0.22), residues: 1411 helix: 0.56 (0.38), residues: 202 sheet: -0.36 (0.26), residues: 435 loop : -1.55 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 482 TYR 0.013 0.002 TYR B 162 PHE 0.020 0.002 PHE A 812 TRP 0.015 0.002 TRP B 277 HIS 0.007 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (11136) covalent geometry : angle 0.64110 / 0.32 (15103) SS BOND : bond 0.00526 / 0.22 ( 19) SS BOND : angle 2.41135 / 2.09 ( 38) hydrogen bonds : bond 0.03685 / 2.48 ( 308) hydrogen bonds : angle 5.80660 / 3.83 ( 873) link_BETA1-4 : bond 0.00567 / 0.28 ( 2) link_BETA1-4 : angle 2.34248 / 1.21 ( 6) link_NAG-ASN : bond 0.00408 / 0.21 ( 1) link_NAG-ASN : angle 2.67409 / 1.37 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 81 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.7768 (t0) REVERT: B 387 ASN cc_start: 0.8095 (t0) cc_final: 0.7538 (m110) REVERT: B 444 GLN cc_start: 0.7469 (tp40) cc_final: 0.7078 (tp40) REVERT: A 72 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8666 (mp) REVERT: A 76 GLU cc_start: 0.6717 (tp30) cc_final: 0.6499 (tp30) REVERT: A 99 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8413 (ppp-140) REVERT: A 228 MET cc_start: 0.8785 (ttp) cc_final: 0.8089 (tpt) REVERT: A 285 MET cc_start: 0.6673 (OUTLIER) cc_final: 0.6352 (mmm) REVERT: A 468 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8745 (mp) REVERT: A 498 GLU cc_start: 0.6056 (mm-30) cc_final: 0.5281 (tp30) REVERT: A 513 TYR cc_start: 0.9371 (OUTLIER) cc_final: 0.8856 (m-80) REVERT: A 584 MET cc_start: 0.9021 (mmm) cc_final: 0.8582 (mmm) REVERT: A 622 TRP cc_start: 0.6563 (m100) cc_final: 0.6350 (m100) REVERT: A 720 LEU cc_start: 0.3026 (OUTLIER) cc_final: 0.2627 (pp) REVERT: A 791 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7592 (mp) REVERT: A 842 GLN cc_start: 0.3345 (OUTLIER) cc_final: 0.2771 (pp30) outliers start: 54 outliers final: 24 residues processed: 129 average time/residue: 0.5056 time to fit residues: 71.3325 Evaluate side-chains 107 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 842 GLN Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 941 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 66 optimal weight: 30.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 141 GLN B 176 HIS B 274 GLN ** B 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.237956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.155150 restraints weight = 10323.465| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.20 r_work: 0.3231 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11158 Z= 0.185 Angle : 0.670 11.572 15150 Z= 0.331 Chirality : 0.046 0.190 1696 Planarity : 0.005 0.057 2002 Dihedral : 6.389 59.448 1617 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.42 % Allowed : 21.08 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.30 (0.22), residues: 1411 helix: 0.40 (0.38), residues: 208 sheet: -0.35 (0.26), residues: 436 loop : -1.55 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 753 TYR 0.013 0.002 TYR B 162 PHE 0.016 0.002 PHE A 812 TRP 0.016 0.002 TRP B 277 HIS 0.006 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.18 (11136) covalent geometry : angle 0.66306 / 0.33 (15103) SS BOND : bond 0.00292 / 0.13 ( 19) SS BOND : angle 1.63401 / 1.34 ( 38) hydrogen bonds : bond 0.03726 / 2.53 ( 308) hydrogen bonds : angle 5.70136 / 3.77 ( 873) link_BETA1-4 : bond 0.00497 / 0.25 ( 2) link_BETA1-4 : angle 2.26356 / 1.17 ( 6) link_NAG-ASN : bond 0.00381 / 0.20 ( 1) link_NAG-ASN : angle 2.77929 / 1.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 73 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.7734 (t0) REVERT: B 387 ASN cc_start: 0.8020 (t0) cc_final: 0.7526 (m110) REVERT: B 444 GLN cc_start: 0.7581 (tp40) cc_final: 0.7274 (tp-100) REVERT: A 72 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8717 (mp) REVERT: A 99 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8379 (ppp-140) REVERT: A 113 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7947 (ttm170) REVERT: A 228 MET cc_start: 0.8812 (ttp) cc_final: 0.8097 (tpt) REVERT: A 260 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.6768 (mp10) REVERT: A 285 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6509 (mmm) REVERT: A 331 MET cc_start: 0.4625 (mpp) cc_final: 0.4402 (mpp) REVERT: A 468 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8780 (mp) REVERT: A 498 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5300 (tp30) REVERT: A 584 MET cc_start: 0.8991 (mmm) cc_final: 0.8655 (mmm) REVERT: A 622 TRP cc_start: 0.6659 (m100) cc_final: 0.6436 (m100) REVERT: A 708 GLU cc_start: 0.8105 (tt0) cc_final: 0.7539 (tt0) REVERT: A 720 LEU cc_start: 0.3120 (OUTLIER) cc_final: 0.2812 (pp) REVERT: A 798 THR cc_start: 0.7477 (OUTLIER) cc_final: 0.7207 (p) outliers start: 53 outliers final: 28 residues processed: 121 average time/residue: 0.4733 time to fit residues: 63.0161 Evaluate side-chains 107 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 69 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 941 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 18 optimal weight: 0.1980 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 274 GLN ** B 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.238888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.156883 restraints weight = 10393.097| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.38 r_work: 0.3235 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11158 Z= 0.136 Angle : 0.611 10.319 15150 Z= 0.303 Chirality : 0.044 0.160 1696 Planarity : 0.005 0.054 2002 Dihedral : 5.897 59.431 1615 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.17 % Allowed : 21.67 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.22), residues: 1411 helix: 0.62 (0.38), residues: 204 sheet: -0.35 (0.26), residues: 424 loop : -1.44 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 753 TYR 0.011 0.002 TYR A 458 PHE 0.016 0.002 PHE A 812 TRP 0.012 0.002 TRP B 277 HIS 0.005 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (11136) covalent geometry : angle 0.60661 / 0.30 (15103) SS BOND : bond 0.00218 / 0.11 ( 19) SS BOND : angle 1.24601 / 0.98 ( 38) hydrogen bonds : bond 0.03323 / 2.24 ( 308) hydrogen bonds : angle 5.49964 / 3.63 ( 873) link_BETA1-4 : bond 0.00496 / 0.24 ( 2) link_BETA1-4 : angle 1.94099 / 1.02 ( 6) link_NAG-ASN : bond 0.00235 / 0.12 ( 1) link_NAG-ASN : angle 2.44980 / 1.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 70 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7250 (mm) REVERT: B 387 ASN cc_start: 0.8011 (t0) cc_final: 0.7518 (m110) REVERT: B 444 GLN cc_start: 0.7507 (tp40) cc_final: 0.6798 (tp40) REVERT: A 72 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8763 (mt) REVERT: A 99 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8433 (ppp-140) REVERT: A 113 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7911 (ttm170) REVERT: A 228 MET cc_start: 0.8824 (ttp) cc_final: 0.8093 (tpt) REVERT: A 260 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6785 (mp10) REVERT: A 498 GLU cc_start: 0.6024 (mm-30) cc_final: 0.5264 (tp30) REVERT: A 513 TYR cc_start: 0.9351 (OUTLIER) cc_final: 0.8943 (m-80) REVERT: A 584 MET cc_start: 0.9014 (mmm) cc_final: 0.8712 (mmm) REVERT: A 622 TRP cc_start: 0.6704 (m100) cc_final: 0.6492 (m100) REVERT: A 708 GLU cc_start: 0.8135 (tt0) cc_final: 0.7532 (tt0) outliers start: 50 outliers final: 31 residues processed: 116 average time/residue: 0.4723 time to fit residues: 59.9763 Evaluate side-chains 105 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 68 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 941 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 6 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 74 optimal weight: 0.0670 overall best weight: 1.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN ** B 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 802 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.238326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.154213 restraints weight = 10379.883| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.30 r_work: 0.3213 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11158 Z= 0.149 Angle : 0.621 10.565 15150 Z= 0.307 Chirality : 0.044 0.164 1696 Planarity : 0.005 0.047 2002 Dihedral : 5.902 58.500 1615 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.33 % Allowed : 21.25 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.17 (0.22), residues: 1411 helix: 0.64 (0.38), residues: 204 sheet: -0.31 (0.26), residues: 419 loop : -1.46 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 753 TYR 0.012 0.002 TYR A 458 PHE 0.014 0.002 PHE A 812 TRP 0.013 0.002 TRP B 277 HIS 0.006 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (11136) covalent geometry : angle 0.61718 / 0.31 (15103) SS BOND : bond 0.00195 / 0.11 ( 19) SS BOND : angle 1.14118 / 0.87 ( 38) hydrogen bonds : bond 0.03356 / 2.29 ( 308) hydrogen bonds : angle 5.42795 / 3.58 ( 873) link_BETA1-4 : bond 0.00476 / 0.23 ( 2) link_BETA1-4 : angle 1.95759 / 1.03 ( 6) link_NAG-ASN : bond 0.00328 / 0.17 ( 1) link_NAG-ASN : angle 2.52148 / 1.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 67 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7079 (mm) REVERT: B 290 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.7830 (t0) REVERT: B 321 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8139 (ptm-80) REVERT: B 387 ASN cc_start: 0.8006 (t0) cc_final: 0.7526 (m110) REVERT: B 444 GLN cc_start: 0.7573 (tp40) cc_final: 0.6877 (tp40) REVERT: A 72 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8773 (mt) REVERT: A 99 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8440 (ppp-140) REVERT: A 113 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7916 (ttm170) REVERT: A 121 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7949 (mt-10) REVERT: A 228 MET cc_start: 0.8841 (ttp) cc_final: 0.8047 (tpt) REVERT: A 260 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6735 (mp10) REVERT: A 285 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6571 (mpt) REVERT: A 498 GLU cc_start: 0.6019 (OUTLIER) cc_final: 0.5353 (tp30) REVERT: A 584 MET cc_start: 0.9012 (mmm) cc_final: 0.8722 (mmm) REVERT: A 622 TRP cc_start: 0.6739 (m100) cc_final: 0.6477 (m100) REVERT: A 708 GLU cc_start: 0.8065 (tt0) cc_final: 0.7482 (tt0) REVERT: A 720 LEU cc_start: 0.3369 (OUTLIER) cc_final: 0.2932 (pp) REVERT: A 768 MET cc_start: 0.4683 (tpp) cc_final: 0.4448 (mmm) outliers start: 52 outliers final: 28 residues processed: 115 average time/residue: 0.5204 time to fit residues: 65.2699 Evaluate side-chains 104 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 66 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 941 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 2 optimal weight: 20.0000 chunk 9 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 46 optimal weight: 0.0980 chunk 108 optimal weight: 0.0030 chunk 76 optimal weight: 30.0000 chunk 78 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 176 HIS B 187 HIS B 274 GLN B 453 HIS ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.240797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.159690 restraints weight = 10334.224| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.42 r_work: 0.3258 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11158 Z= 0.092 Angle : 0.564 10.934 15150 Z= 0.278 Chirality : 0.043 0.164 1696 Planarity : 0.004 0.054 2002 Dihedral : 5.212 58.018 1609 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.50 % Allowed : 22.08 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.22), residues: 1411 helix: 0.74 (0.38), residues: 204 sheet: -0.21 (0.26), residues: 422 loop : -1.38 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 753 TYR 0.013 0.001 TYR A 789 PHE 0.016 0.001 PHE A 812 TRP 0.009 0.001 TRP A 925 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (11136) covalent geometry : angle 0.56140 / 0.28 (15103) SS BOND : bond 0.00181 / 0.11 ( 19) SS BOND : angle 0.94742 / 0.73 ( 38) hydrogen bonds : bond 0.02779 / 1.89 ( 308) hydrogen bonds : angle 5.17585 / 3.40 ( 873) link_BETA1-4 : bond 0.00536 / 0.26 ( 2) link_BETA1-4 : angle 1.63998 / 0.87 ( 6) link_NAG-ASN : bond 0.00042 / 0.02 ( 1) link_NAG-ASN : angle 1.56265 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 71 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.6974 (mm) REVERT: B 290 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.7879 (t0) REVERT: B 321 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8209 (ptm-80) REVERT: B 387 ASN cc_start: 0.8003 (t0) cc_final: 0.7529 (m110) REVERT: B 444 GLN cc_start: 0.7620 (tp40) cc_final: 0.6958 (tp40) REVERT: A 72 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8698 (mt) REVERT: A 99 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8443 (ppp-140) REVERT: A 113 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7860 (ttm170) REVERT: A 228 MET cc_start: 0.8827 (ttp) cc_final: 0.8068 (tpt) REVERT: A 285 MET cc_start: 0.6738 (OUTLIER) cc_final: 0.6514 (mpt) REVERT: A 474 LEU cc_start: 0.7784 (mp) cc_final: 0.7491 (mt) REVERT: A 498 GLU cc_start: 0.5900 (OUTLIER) cc_final: 0.5229 (tp30) REVERT: A 513 TYR cc_start: 0.9293 (OUTLIER) cc_final: 0.8929 (m-80) REVERT: A 584 MET cc_start: 0.9002 (mmm) cc_final: 0.8619 (mmm) REVERT: A 622 TRP cc_start: 0.6783 (m100) cc_final: 0.6535 (m100) REVERT: A 708 GLU cc_start: 0.7984 (tt0) cc_final: 0.7378 (tt0) REVERT: A 720 LEU cc_start: 0.3136 (OUTLIER) cc_final: 0.2732 (pp) REVERT: A 753 ARG cc_start: 0.7470 (ttm-80) cc_final: 0.6985 (mtt-85) outliers start: 42 outliers final: 22 residues processed: 109 average time/residue: 0.4658 time to fit residues: 55.3211 Evaluate side-chains 96 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 941 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 92 optimal weight: 0.5980 chunk 128 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 32 optimal weight: 0.0000 chunk 13 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 176 HIS B 187 HIS B 274 GLN B 341 ASN B 453 HIS ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.239574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.160604 restraints weight = 10214.165| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 8.15 r_work: 0.3150 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11158 Z= 0.106 Angle : 0.580 11.142 15150 Z= 0.284 Chirality : 0.043 0.166 1696 Planarity : 0.004 0.051 2002 Dihedral : 5.190 57.641 1606 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.08 % Allowed : 22.58 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.04 (0.22), residues: 1411 helix: 0.75 (0.38), residues: 204 sheet: -0.20 (0.26), residues: 422 loop : -1.39 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 753 TYR 0.015 0.001 TYR A 789 PHE 0.016 0.001 PHE A 812 TRP 0.009 0.001 TRP B 277 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (11136) covalent geometry : angle 0.57714 / 0.28 (15103) SS BOND : bond 0.00179 / 0.11 ( 19) SS BOND : angle 0.95112 / 0.72 ( 38) hydrogen bonds : bond 0.02871 / 1.96 ( 308) hydrogen bonds : angle 5.12855 / 3.38 ( 873) link_BETA1-4 : bond 0.00531 / 0.26 ( 2) link_BETA1-4 : angle 1.64410 / 0.88 ( 6) link_NAG-ASN : bond 0.00114 / 0.06 ( 1) link_NAG-ASN : angle 1.84150 / 0.94 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 69 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.7970 (t0) REVERT: B 321 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8239 (ptm-80) REVERT: B 387 ASN cc_start: 0.8136 (t0) cc_final: 0.7689 (m110) REVERT: B 444 GLN cc_start: 0.7692 (tp40) cc_final: 0.7055 (tp40) REVERT: A 99 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8591 (ppp-140) REVERT: A 113 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7902 (ttm170) REVERT: A 228 MET cc_start: 0.8817 (ttp) cc_final: 0.8068 (tpt) REVERT: A 260 GLN cc_start: 0.6988 (OUTLIER) cc_final: 0.6705 (mp10) REVERT: A 285 MET cc_start: 0.6663 (OUTLIER) cc_final: 0.6462 (mpt) REVERT: A 498 GLU cc_start: 0.6026 (OUTLIER) cc_final: 0.5348 (tp30) REVERT: A 513 TYR cc_start: 0.9283 (OUTLIER) cc_final: 0.8883 (m-80) REVERT: A 584 MET cc_start: 0.9002 (mmm) cc_final: 0.8616 (mmm) REVERT: A 622 TRP cc_start: 0.6933 (m100) cc_final: 0.6681 (m100) REVERT: A 708 GLU cc_start: 0.8136 (tt0) cc_final: 0.7560 (tt0) REVERT: A 720 LEU cc_start: 0.3411 (OUTLIER) cc_final: 0.2975 (pp) outliers start: 37 outliers final: 22 residues processed: 102 average time/residue: 0.4637 time to fit residues: 51.5986 Evaluate side-chains 99 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 68 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 941 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 82 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 chunk 52 optimal weight: 0.0770 chunk 116 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 81 optimal weight: 50.0000 chunk 49 optimal weight: 0.0870 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 176 HIS B 187 HIS B 274 GLN B 453 HIS ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.240679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.161756 restraints weight = 10342.767| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 8.44 r_work: 0.3159 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11158 Z= 0.095 Angle : 0.569 12.012 15150 Z= 0.278 Chirality : 0.043 0.172 1696 Planarity : 0.004 0.051 2002 Dihedral : 5.063 57.269 1606 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.92 % Allowed : 22.92 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.22), residues: 1411 helix: 0.78 (0.38), residues: 204 sheet: -0.15 (0.26), residues: 422 loop : -1.33 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 439 TYR 0.016 0.001 TYR A 789 PHE 0.016 0.001 PHE A 812 TRP 0.008 0.001 TRP A 27 HIS 0.004 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (11136) covalent geometry : angle 0.56707 / 0.28 (15103) SS BOND : bond 0.00212 / 0.12 ( 19) SS BOND : angle 0.94681 / 0.68 ( 38) hydrogen bonds : bond 0.02687 / 1.83 ( 308) hydrogen bonds : angle 5.04634 / 3.31 ( 873) link_BETA1-4 : bond 0.00577 / 0.28 ( 2) link_BETA1-4 : angle 1.58915 / 0.85 ( 6) link_NAG-ASN : bond 0.00016 / 0.01 ( 1) link_NAG-ASN : angle 1.43012 / 0.73 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 68 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: B 290 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.7986 (t0) REVERT: B 321 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8215 (ptm-80) REVERT: B 387 ASN cc_start: 0.8140 (t0) cc_final: 0.7686 (m110) REVERT: B 444 GLN cc_start: 0.7703 (tp40) cc_final: 0.7107 (tp40) REVERT: A 99 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8513 (ppp-140) REVERT: A 113 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7876 (ttm170) REVERT: A 228 MET cc_start: 0.8837 (ttp) cc_final: 0.8083 (tpt) REVERT: A 260 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6704 (mp10) REVERT: A 285 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6522 (mpt) REVERT: A 474 LEU cc_start: 0.7809 (mp) cc_final: 0.7531 (mt) REVERT: A 498 GLU cc_start: 0.6052 (OUTLIER) cc_final: 0.5370 (tp30) REVERT: A 513 TYR cc_start: 0.9254 (OUTLIER) cc_final: 0.8884 (m-80) REVERT: A 584 MET cc_start: 0.8986 (mmm) cc_final: 0.8652 (mmm) REVERT: A 622 TRP cc_start: 0.6946 (m100) cc_final: 0.6699 (m100) REVERT: A 708 GLU cc_start: 0.8154 (tt0) cc_final: 0.7585 (tt0) REVERT: A 753 ARG cc_start: 0.7322 (ttm-80) cc_final: 0.6930 (mtt-85) outliers start: 35 outliers final: 22 residues processed: 99 average time/residue: 0.5422 time to fit residues: 57.9153 Evaluate side-chains 96 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 49 optimal weight: 0.0470 chunk 55 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 81 optimal weight: 50.0000 chunk 78 optimal weight: 0.0470 chunk 104 optimal weight: 0.0570 chunk 107 optimal weight: 3.9990 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 176 HIS B 187 HIS B 274 GLN B 453 HIS ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.241303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.163112 restraints weight = 10415.418| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 8.20 r_work: 0.3182 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11158 Z= 0.090 Angle : 0.566 11.505 15150 Z= 0.276 Chirality : 0.042 0.171 1696 Planarity : 0.004 0.050 2002 Dihedral : 5.003 57.021 1606 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.58 % Allowed : 23.25 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.93 (0.22), residues: 1411 helix: 0.83 (0.38), residues: 204 sheet: -0.16 (0.26), residues: 413 loop : -1.28 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 753 TYR 0.015 0.001 TYR A 789 PHE 0.017 0.001 PHE A 812 TRP 0.008 0.001 TRP A 925 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (11136) covalent geometry : angle 0.56323 / 0.28 (15103) SS BOND : bond 0.00204 / 0.11 ( 19) SS BOND : angle 1.08200 / 0.76 ( 38) hydrogen bonds : bond 0.02609 / 1.78 ( 308) hydrogen bonds : angle 5.03511 / 3.30 ( 873) link_BETA1-4 : bond 0.00576 / 0.28 ( 2) link_BETA1-4 : angle 1.51106 / 0.82 ( 6) link_NAG-ASN : bond 0.00032 / 0.02 ( 1) link_NAG-ASN : angle 1.26235 / 0.64 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4074.44 seconds wall clock time: 69 minutes 57.18 seconds (4197.18 seconds total)