Starting phenix.real_space_refine on Wed Sep 17 19:59:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjf_60143/09_2025/8zjf_60143.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjf_60143/09_2025/8zjf_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_60143/09_2025/8zjf_60143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjf_60143/09_2025/8zjf_60143.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zjf_60143/09_2025/8zjf_60143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjf_60143/09_2025/8zjf_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-2.0-5805/lib/python3.9/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, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.74, per 1000 atoms: 0.25 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: 0.96 Conformation dependent library (CDL) restraints added in 514.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.52 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: 2.30 Time building geometry restraints manager: 1.42 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 2.510 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 2.510 nonbonded pdb=" O PRO B 258 " pdb="CA CA B 902 " model vdw 2.181 2.510 nonbonded pdb=" ND2 ASN B 254 " pdb="CA CA B 902 " model vdw 2.218 2.590 ... (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: 0.610 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.470 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 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 aren 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 covalent geometry : bond 0.00292 (11136) covalent geometry : angle 0.65191 (15103) SS BOND : bond 0.00177 ( 19) SS BOND : angle 2.08507 ( 38) hydrogen bonds : bond 0.21872 ( 308) hydrogen bonds : angle 8.81183 ( 873) link_BETA1-4 : bond 0.00507 ( 2) link_BETA1-4 : angle 1.49327 ( 6) link_NAG-ASN : bond 0.00231 ( 1) link_NAG-ASN : angle 1.60836 ( 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 : 0.487 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: 0.7204 (t0) cc_final: 0.6969 (t0) REVERT: B 383 MET cc_start: 0.8268 (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: 0.8311 (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: 0.4513 time to fit residues: 76.3235 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 : 0.397 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 842 GLN A 884 GLN A 945 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.242655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.164272 restraints weight = 10470.437| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.73 r_work: 0.3389 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11158 Z= 0.166 Angle : 0.667 9.090 15150 Z= 0.338 Chirality : 0.046 0.188 1696 Planarity : 0.005 0.059 2002 Dihedral : 7.024 57.913 1622 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.42 % Allowed : 19.33 % Favored : 76.25 % 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 aren not related in a simple way. whole: -1.34 (0.22), residues: 1411 helix: 0.46 (0.39), residues: 201 sheet: -0.47 (0.26), residues: 419 loop : -1.51 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 439 TYR 0.013 0.002 TYR A 433 PHE 0.016 0.002 PHE A 812 TRP 0.010 0.002 TRP B 277 HIS 0.012 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00365 (11136) covalent geometry : angle 0.66228 (15103) SS BOND : bond 0.00349 ( 19) SS BOND : angle 1.16094 ( 38) hydrogen bonds : bond 0.04209 ( 308) hydrogen bonds : angle 6.40258 ( 873) link_BETA1-4 : bond 0.01091 ( 2) link_BETA1-4 : angle 2.34453 ( 6) link_NAG-ASN : bond 0.00062 ( 1) link_NAG-ASN : angle 2.99100 ( 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 140 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 87 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 245 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7753 (mm-30) REVERT: B 314 ASP cc_start: 0.7805 (p0) cc_final: 0.7545 (p0) REVERT: B 384 ASP cc_start: 0.7620 (m-30) cc_final: 0.7394 (m-30) REVERT: B 409 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: A 76 GLU cc_start: 0.6529 (tp30) cc_final: 0.5866 (tm-30) REVERT: A 228 MET cc_start: 0.8827 (ttp) cc_final: 0.8169 (tpt) REVERT: A 229 MET cc_start: 0.7388 (ttp) cc_final: 0.7067 (ttm) REVERT: A 468 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8639 (mp) REVERT: A 513 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.8561 (m-80) REVERT: A 720 LEU cc_start: 0.2316 (OUTLIER) cc_final: 0.1875 (pp) REVERT: A 842 GLN cc_start: 0.3486 (OUTLIER) cc_final: 0.2841 (pp30) outliers start: 53 outliers final: 22 residues processed: 132 average time/residue: 0.5342 time to fit residues: 77.2936 Evaluate side-chains 101 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 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 562 LEU 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 842 GLN 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: 7.9990 chunk 125 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 139 optimal weight: 30.0000 chunk 110 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 75 optimal weight: 40.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.237978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.156036 restraints weight = 10426.716| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.25 r_work: 0.3219 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11158 Z= 0.225 Angle : 0.717 8.558 15150 Z= 0.358 Chirality : 0.048 0.160 1696 Planarity : 0.005 0.048 2002 Dihedral : 6.696 57.730 1618 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.67 % Allowed : 19.92 % Favored : 75.42 % 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 aren not related in a simple way. whole: -1.47 (0.22), residues: 1411 helix: 0.44 (0.38), residues: 200 sheet: -0.50 (0.25), residues: 426 loop : -1.66 (0.20), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 677 TYR 0.019 0.002 TYR B 162 PHE 0.019 0.002 PHE A 406 TRP 0.018 0.002 TRP B 277 HIS 0.009 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00529 (11136) covalent geometry : angle 0.71238 (15103) SS BOND : bond 0.00989 ( 19) SS BOND : angle 1.26790 ( 38) hydrogen bonds : bond 0.04678 ( 308) hydrogen bonds : angle 6.19648 ( 873) link_BETA1-4 : bond 0.00997 ( 2) link_BETA1-4 : angle 2.69420 ( 6) link_NAG-ASN : bond 0.00629 ( 1) link_NAG-ASN : angle 3.12153 ( 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: 56 poor density : 78 time to evaluate : 0.425 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: 0.8492 (OUTLIER) cc_final: 0.7716 (t0) REVERT: B 387 ASN cc_start: 0.8070 (t0) cc_final: 0.7520 (m110) REVERT: B 444 GLN cc_start: 0.7333 (tp40) cc_final: 0.6929 (tp40) REVERT: A 76 GLU cc_start: 0.6777 (tp30) cc_final: 0.6520 (tp30) REVERT: A 113 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7935 (ttm170) REVERT: A 228 MET cc_start: 0.8836 (ttp) cc_final: 0.8114 (tpt) REVERT: A 238 GLU cc_start: 0.7327 (pt0) cc_final: 0.7108 (mt-10) REVERT: A 285 MET cc_start: 0.6801 (OUTLIER) cc_final: 0.6466 (mmm) REVERT: A 468 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8791 (mp) REVERT: A 498 GLU cc_start: 0.6158 (mm-30) cc_final: 0.5856 (mm-30) REVERT: A 513 TYR cc_start: 0.9391 (OUTLIER) cc_final: 0.8987 (m-80) REVERT: A 622 TRP cc_start: 0.6645 (m100) cc_final: 0.6369 (m100) REVERT: A 720 LEU cc_start: 0.2706 (OUTLIER) cc_final: 0.2159 (pp) REVERT: A 790 GLN cc_start: 0.8869 (tt0) cc_final: 0.8466 (tt0) outliers start: 56 outliers final: 29 residues processed: 128 average time/residue: 0.5398 time to fit residues: 75.7018 Evaluate side-chains 109 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 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 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 667 THR 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 845 VAL Chi-restraints excluded: chain A residue 846 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 3 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 131 optimal weight: 50.0000 chunk 59 optimal weight: 0.6980 chunk 102 optimal weight: 0.0020 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 40.0000 chunk 138 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 79 optimal weight: 50.0000 overall best weight: 2.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 GLN ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 486 HIS A 790 GLN A 792 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.233817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.147392 restraints weight = 10003.311| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 6.64 r_work: 0.2859 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 11158 Z= 0.276 Angle : 0.771 12.744 15150 Z= 0.382 Chirality : 0.051 0.244 1696 Planarity : 0.006 0.069 2002 Dihedral : 6.747 59.176 1618 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 5.17 % Allowed : 19.92 % 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 aren not related in a simple way. whole: -1.47 (0.22), residues: 1411 helix: 0.39 (0.38), residues: 202 sheet: -0.46 (0.25), residues: 423 loop : -1.68 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 482 TYR 0.020 0.003 TYR B 162 PHE 0.019 0.003 PHE A 19 TRP 0.021 0.003 TRP B 277 HIS 0.011 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00679 (11136) covalent geometry : angle 0.75818 (15103) SS BOND : bond 0.00525 ( 19) SS BOND : angle 2.51876 ( 38) hydrogen bonds : bond 0.04492 ( 308) hydrogen bonds : angle 6.03270 ( 873) link_BETA1-4 : bond 0.00415 ( 2) link_BETA1-4 : angle 2.66940 ( 6) link_NAG-ASN : bond 0.00860 ( 1) link_NAG-ASN : angle 3.86534 ( 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 139 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 77 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.7751 (t0) REVERT: B 387 ASN cc_start: 0.8209 (t0) cc_final: 0.7737 (m110) REVERT: B 444 GLN cc_start: 0.7697 (tp40) cc_final: 0.6951 (tp40) REVERT: A 72 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8805 (mp) REVERT: A 99 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8814 (ppp-140) REVERT: A 113 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.8077 (ttm170) REVERT: A 121 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8208 (mt-10) REVERT: A 228 MET cc_start: 0.8709 (ttp) cc_final: 0.7937 (tpt) REVERT: A 285 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.6396 (mmm) REVERT: A 498 GLU cc_start: 0.6192 (mm-30) cc_final: 0.5071 (tp30) REVERT: A 622 TRP cc_start: 0.6826 (m100) cc_final: 0.6558 (m100) REVERT: A 720 LEU cc_start: 0.3321 (OUTLIER) cc_final: 0.3007 (pp) REVERT: A 798 THR cc_start: 0.7774 (OUTLIER) cc_final: 0.7326 (p) outliers start: 62 outliers final: 27 residues processed: 134 average time/residue: 0.5155 time to fit residues: 75.5944 Evaluate side-chains 105 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 71 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 290 ASP 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 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 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 588 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 91 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 7 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 126 optimal weight: 0.0470 chunk 66 optimal weight: 8.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN B 316 ASN ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 486 HIS A 790 GLN A 792 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.239472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.154848 restraints weight = 10360.296| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.26 r_work: 0.3231 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 11158 Z= 0.110 Angle : 0.588 9.776 15150 Z= 0.294 Chirality : 0.043 0.168 1696 Planarity : 0.004 0.050 2002 Dihedral : 5.896 59.773 1615 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.42 % Allowed : 20.67 % 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 aren not related in a simple way. whole: -1.22 (0.22), residues: 1411 helix: 0.54 (0.38), residues: 204 sheet: -0.33 (0.26), residues: 424 loop : -1.47 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 753 TYR 0.013 0.001 TYR A 789 PHE 0.015 0.001 PHE A 812 TRP 0.009 0.001 TRP B 277 HIS 0.003 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00257 (11136) covalent geometry : angle 0.58172 (15103) SS BOND : bond 0.00303 ( 19) SS BOND : angle 1.58751 ( 38) hydrogen bonds : bond 0.03140 ( 308) hydrogen bonds : angle 5.57189 ( 873) link_BETA1-4 : bond 0.00509 ( 2) link_BETA1-4 : angle 1.81357 ( 6) link_NAG-ASN : bond 0.00006 ( 1) link_NAG-ASN : angle 2.09445 ( 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 128 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 75 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 387 ASN cc_start: 0.7969 (t0) cc_final: 0.7506 (m110) REVERT: B 444 GLN cc_start: 0.7427 (tp40) cc_final: 0.6781 (tp40) REVERT: B 523 LEU cc_start: 0.4262 (OUTLIER) cc_final: 0.3907 (mp) REVERT: A 72 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8733 (mt) REVERT: A 99 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8432 (ppp-140) REVERT: A 228 MET cc_start: 0.8838 (ttp) cc_final: 0.8055 (tpt) REVERT: A 285 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.6474 (mmm) REVERT: A 468 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8616 (mt) REVERT: A 498 GLU cc_start: 0.5980 (mm-30) cc_final: 0.5256 (tp30) REVERT: A 513 TYR cc_start: 0.9298 (OUTLIER) cc_final: 0.8904 (m-80) REVERT: A 622 TRP cc_start: 0.6621 (m100) cc_final: 0.6416 (m100) REVERT: A 708 GLU cc_start: 0.8158 (tt0) cc_final: 0.7537 (tt0) REVERT: A 720 LEU cc_start: 0.3134 (OUTLIER) cc_final: 0.2803 (pp) outliers start: 53 outliers final: 25 residues processed: 121 average time/residue: 0.5283 time to fit residues: 70.1813 Evaluate side-chains 100 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 225 SER Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 523 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 134 ARG Chi-restraints excluded: chain A residue 207 LEU 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 468 LEU Chi-restraints excluded: chain A residue 513 TYR 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 785 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 18 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 38 optimal weight: 0.1980 chunk 106 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 51 optimal weight: 0.0000 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN B 316 ASN ** B 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 ASN A 231 ASN A 486 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.240617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.163730 restraints weight = 10422.524| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.37 r_work: 0.3288 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11158 Z= 0.096 Angle : 0.574 13.307 15150 Z= 0.283 Chirality : 0.043 0.175 1696 Planarity : 0.004 0.056 2002 Dihedral : 5.621 59.289 1614 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.92 % Allowed : 21.58 % 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 aren not related in a simple way. whole: -1.04 (0.22), residues: 1411 helix: 0.70 (0.38), residues: 204 sheet: -0.25 (0.26), residues: 423 loop : -1.34 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 439 TYR 0.015 0.001 TYR A 789 PHE 0.015 0.001 PHE A 812 TRP 0.008 0.001 TRP A 52 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00216 (11136) covalent geometry : angle 0.57076 (15103) SS BOND : bond 0.00210 ( 19) SS BOND : angle 1.14435 ( 38) hydrogen bonds : bond 0.02876 ( 308) hydrogen bonds : angle 5.28012 ( 873) link_BETA1-4 : bond 0.00600 ( 2) link_BETA1-4 : angle 1.71823 ( 6) link_NAG-ASN : bond 0.00037 ( 1) link_NAG-ASN : angle 1.58108 ( 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 114 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 67 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: B 220 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7472 (mm) REVERT: B 290 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.7771 (t0) REVERT: B 387 ASN cc_start: 0.8002 (t0) cc_final: 0.7606 (m110) REVERT: B 444 GLN cc_start: 0.7549 (tp40) cc_final: 0.6861 (tp40) REVERT: B 523 LEU cc_start: 0.4190 (OUTLIER) cc_final: 0.3873 (mp) REVERT: A 72 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8717 (mt) REVERT: A 99 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8462 (ppp-140) REVERT: A 228 MET cc_start: 0.8856 (ttp) cc_final: 0.8121 (tpt) REVERT: A 498 GLU cc_start: 0.5950 (mm-30) cc_final: 0.5309 (tp30) REVERT: A 513 TYR cc_start: 0.9315 (OUTLIER) cc_final: 0.8874 (m-80) REVERT: A 708 GLU cc_start: 0.8028 (tt0) cc_final: 0.7427 (tt0) REVERT: A 753 ARG cc_start: 0.7308 (ttm-80) cc_final: 0.6837 (mtt-85) outliers start: 47 outliers final: 23 residues processed: 108 average time/residue: 0.5561 time to fit residues: 65.8408 Evaluate side-chains 95 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 205 VAL Chi-restraints excluded: chain B residue 220 LEU 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 523 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 253 GLU 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 555 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 6 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 125 optimal weight: 0.0770 chunk 48 optimal weight: 0.1980 chunk 74 optimal weight: 0.9990 overall best weight: 1.0544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN B 453 HIS A 231 ASN A 619 ASN A 741 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.239120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.157481 restraints weight = 10369.421| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.27 r_work: 0.3195 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11158 Z= 0.130 Angle : 0.597 10.671 15150 Z= 0.293 Chirality : 0.044 0.163 1696 Planarity : 0.004 0.048 2002 Dihedral : 5.738 58.783 1613 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 4.25 % Allowed : 21.25 % 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 aren not related in a simple way. whole: -1.04 (0.22), residues: 1411 helix: 0.72 (0.38), residues: 204 sheet: -0.27 (0.26), residues: 425 loop : -1.33 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 753 TYR 0.014 0.002 TYR A 789 PHE 0.014 0.002 PHE A 812 TRP 0.011 0.001 TRP B 277 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00309 (11136) covalent geometry : angle 0.59346 (15103) SS BOND : bond 0.00187 ( 19) SS BOND : angle 1.08606 ( 38) hydrogen bonds : bond 0.03106 ( 308) hydrogen bonds : angle 5.35139 ( 873) link_BETA1-4 : bond 0.00512 ( 2) link_BETA1-4 : angle 1.79409 ( 6) link_NAG-ASN : bond 0.00268 ( 1) link_NAG-ASN : angle 2.15246 ( 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 120 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 69 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: B 220 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7550 (mm) REVERT: B 290 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.7872 (t0) REVERT: B 321 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8201 (ptm-80) REVERT: B 387 ASN cc_start: 0.7965 (t0) cc_final: 0.7498 (m110) REVERT: B 444 GLN cc_start: 0.7600 (tp40) cc_final: 0.6910 (tp40) REVERT: B 523 LEU cc_start: 0.4309 (OUTLIER) cc_final: 0.4069 (mp) REVERT: A 72 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8745 (mt) REVERT: A 99 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8460 (ppp-140) REVERT: A 121 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8002 (mt-10) REVERT: A 228 MET cc_start: 0.8851 (ttp) cc_final: 0.8061 (tpt) REVERT: A 285 MET cc_start: 0.6793 (OUTLIER) cc_final: 0.6582 (mpt) REVERT: A 498 GLU cc_start: 0.5912 (mm-30) cc_final: 0.5256 (tp30) REVERT: A 513 TYR cc_start: 0.9345 (OUTLIER) cc_final: 0.8916 (m-80) REVERT: A 708 GLU cc_start: 0.7971 (tt0) cc_final: 0.7346 (tt0) REVERT: A 741 GLN cc_start: 0.6114 (OUTLIER) cc_final: 0.5851 (pp30) outliers start: 51 outliers final: 27 residues processed: 113 average time/residue: 0.5557 time to fit residues: 68.6692 Evaluate side-chains 103 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 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 523 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 253 GLU 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 443 LEU Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 741 GLN 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 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: 0.0470 chunk 31 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 76 optimal weight: 40.0000 chunk 78 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 overall best weight: 2.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN B 427 GLN B 453 HIS A 231 ASN A 802 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.234562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.150165 restraints weight = 9919.663| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 6.21 r_work: 0.2872 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 11158 Z= 0.242 Angle : 0.713 11.178 15150 Z= 0.349 Chirality : 0.048 0.161 1696 Planarity : 0.005 0.062 2002 Dihedral : 5.852 58.269 1607 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.92 % Allowed : 21.83 % Favored : 74.25 % 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 aren not related in a simple way. whole: -1.23 (0.22), residues: 1411 helix: 0.58 (0.38), residues: 204 sheet: -0.34 (0.26), residues: 423 loop : -1.49 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 753 TYR 0.019 0.003 TYR A 789 PHE 0.018 0.003 PHE A 514 TRP 0.020 0.002 TRP B 277 HIS 0.010 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00589 (11136) covalent geometry : angle 0.70882 (15103) SS BOND : bond 0.00190 ( 19) SS BOND : angle 1.28909 ( 38) hydrogen bonds : bond 0.03964 ( 308) hydrogen bonds : angle 5.64549 ( 873) link_BETA1-4 : bond 0.00340 ( 2) link_BETA1-4 : angle 2.24354 ( 6) link_NAG-ASN : bond 0.00831 ( 1) link_NAG-ASN : angle 2.89031 ( 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 115 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 68 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7632 (mm) REVERT: B 290 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.7720 (t0) REVERT: B 321 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8312 (ptm-80) REVERT: B 387 ASN cc_start: 0.8176 (t0) cc_final: 0.7731 (m110) REVERT: B 444 GLN cc_start: 0.7627 (tp40) cc_final: 0.6972 (tp40) REVERT: A 72 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8841 (mp) REVERT: A 99 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8793 (ppp-140) REVERT: A 121 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8252 (mt-10) REVERT: A 228 MET cc_start: 0.8727 (ttp) cc_final: 0.7892 (tpt) REVERT: A 260 GLN cc_start: 0.6945 (OUTLIER) cc_final: 0.6669 (mp10) REVERT: A 285 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.6461 (mpt) REVERT: A 498 GLU cc_start: 0.6122 (mm-30) cc_final: 0.5516 (tp30) REVERT: A 708 GLU cc_start: 0.8176 (tt0) cc_final: 0.7595 (tt0) REVERT: A 753 ARG cc_start: 0.7698 (mtt-85) cc_final: 0.7494 (mtt-85) outliers start: 47 outliers final: 25 residues processed: 109 average time/residue: 0.5027 time to fit residues: 60.1097 Evaluate side-chains 98 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 66 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 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 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 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 626 SER Chi-restraints excluded: chain A residue 684 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 902 VAL Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 92 optimal weight: 0.7980 chunk 128 optimal weight: 50.0000 chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 50.0000 chunk 41 optimal weight: 1.9990 chunk 77 optimal weight: 30.0000 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN B 316 ASN B 453 HIS A 231 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.236870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.154529 restraints weight = 9856.191| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 6.13 r_work: 0.2897 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11158 Z= 0.121 Angle : 0.606 10.759 15150 Z= 0.298 Chirality : 0.044 0.161 1696 Planarity : 0.005 0.052 2002 Dihedral : 5.504 57.950 1607 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.17 % Allowed : 22.25 % Favored : 74.58 % 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 aren not related in a simple way. whole: -1.16 (0.22), residues: 1411 helix: 0.56 (0.38), residues: 209 sheet: -0.31 (0.26), residues: 421 loop : -1.42 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 753 TYR 0.016 0.002 TYR A 789 PHE 0.015 0.001 PHE A 812 TRP 0.012 0.002 TRP B 277 HIS 0.004 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00286 (11136) covalent geometry : angle 0.60270 (15103) SS BOND : bond 0.00171 ( 19) SS BOND : angle 1.16496 ( 38) hydrogen bonds : bond 0.03090 ( 308) hydrogen bonds : angle 5.44164 ( 873) link_BETA1-4 : bond 0.00543 ( 2) link_BETA1-4 : angle 1.77958 ( 6) link_NAG-ASN : bond 0.00140 ( 1) link_NAG-ASN : angle 1.97307 ( 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 107 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 69 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.7944 (t0) REVERT: B 321 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8257 (ptm-80) REVERT: B 387 ASN cc_start: 0.8178 (t0) cc_final: 0.7713 (m110) REVERT: B 444 GLN cc_start: 0.7674 (tp40) cc_final: 0.6995 (tp40) REVERT: A 72 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8741 (mt) REVERT: A 99 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8544 (ppp-140) REVERT: A 121 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8198 (mt-10) REVERT: A 228 MET cc_start: 0.8663 (ttp) cc_final: 0.7839 (tpt) REVERT: A 260 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6563 (mp10) REVERT: A 498 GLU cc_start: 0.6013 (mm-30) cc_final: 0.5423 (tp30) REVERT: A 513 TYR cc_start: 0.9333 (OUTLIER) cc_final: 0.8926 (m-80) REVERT: A 708 GLU cc_start: 0.8200 (tt0) cc_final: 0.7624 (tt0) outliers start: 38 outliers final: 25 residues processed: 103 average time/residue: 0.5483 time to fit residues: 61.5811 Evaluate side-chains 100 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 69 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 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 253 GLU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL 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 626 SER Chi-restraints excluded: chain A residue 684 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 902 VAL Chi-restraints excluded: chain A residue 904 ILE 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 82 optimal weight: 20.0000 chunk 109 optimal weight: 0.0040 chunk 36 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 0.0770 chunk 137 optimal weight: 50.0000 chunk 52 optimal weight: 0.8980 chunk 116 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 49 optimal weight: 0.3980 overall best weight: 0.3350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 HIS B 274 GLN B 316 ASN B 453 HIS A 231 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.240189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.161343 restraints weight = 10306.401| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 8.39 r_work: 0.3093 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5291 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 : 0.584 11.972 15150 Z= 0.284 Chirality : 0.043 0.174 1696 Planarity : 0.004 0.053 2002 Dihedral : 5.213 57.919 1607 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.92 % Allowed : 22.42 % Favored : 74.67 % 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 aren not related in a simple way. whole: -1.01 (0.22), residues: 1411 helix: 0.88 (0.39), residues: 203 sheet: -0.25 (0.26), residues: 418 loop : -1.35 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 753 TYR 0.015 0.001 TYR A 789 PHE 0.017 0.001 PHE A 812 TRP 0.010 0.001 TRP A 925 HIS 0.004 0.000 HIS B 430 Details of bonding type rmsd covalent geometry : bond 0.00206 (11136) covalent geometry : angle 0.58038 (15103) SS BOND : bond 0.00359 ( 19) SS BOND : angle 1.17833 ( 38) hydrogen bonds : bond 0.02699 ( 308) hydrogen bonds : angle 5.25359 ( 873) link_BETA1-4 : bond 0.00605 ( 2) link_BETA1-4 : angle 1.59895 ( 6) link_NAG-ASN : bond 0.00092 ( 1) link_NAG-ASN : angle 1.27378 ( 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 109 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7490 (mm) REVERT: B 321 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8200 (ptm-80) REVERT: B 387 ASN cc_start: 0.8160 (t0) cc_final: 0.7757 (m110) REVERT: B 444 GLN cc_start: 0.7697 (tp40) cc_final: 0.7045 (tp40) REVERT: A 99 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8531 (ppp-140) REVERT: A 121 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8170 (mt-10) REVERT: A 149 ASP cc_start: 0.5953 (m-30) cc_final: 0.5696 (p0) REVERT: A 228 MET cc_start: 0.8805 (ttp) cc_final: 0.7988 (tpt) REVERT: A 260 GLN cc_start: 0.6971 (OUTLIER) cc_final: 0.6741 (mp10) REVERT: A 474 LEU cc_start: 0.7782 (mp) cc_final: 0.7488 (mt) REVERT: A 498 GLU cc_start: 0.6042 (mm-30) cc_final: 0.5386 (tp30) REVERT: A 513 TYR cc_start: 0.9251 (OUTLIER) cc_final: 0.8912 (m-80) REVERT: A 708 GLU cc_start: 0.8156 (tt0) cc_final: 0.7580 (tt0) outliers start: 35 outliers final: 24 residues processed: 105 average time/residue: 0.5378 time to fit residues: 61.8874 Evaluate side-chains 100 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 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 106 ILE Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL 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 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 904 ILE 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: 0.3980 chunk 55 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 52 optimal weight: 0.0670 chunk 101 optimal weight: 0.2980 chunk 100 optimal weight: 0.5980 chunk 81 optimal weight: 50.0000 chunk 78 optimal weight: 0.0870 chunk 104 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 HIS B 274 GLN B 453 HIS A 231 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.240967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.163252 restraints weight = 10386.987| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 8.05 r_work: 0.3134 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5375 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 : 0.579 12.239 15150 Z= 0.281 Chirality : 0.043 0.176 1696 Planarity : 0.004 0.049 2002 Dihedral : 5.091 57.677 1607 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % 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 aren not related in a simple way. whole: -0.92 (0.22), residues: 1411 helix: 0.88 (0.38), residues: 203 sheet: -0.17 (0.26), residues: 420 loop : -1.27 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 753 TYR 0.015 0.001 TYR A 789 PHE 0.017 0.001 PHE A 812 TRP 0.009 0.001 TRP A 925 HIS 0.004 0.000 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00202 (11136) covalent geometry : angle 0.57608 (15103) SS BOND : bond 0.00186 ( 19) SS BOND : angle 1.14153 ( 38) hydrogen bonds : bond 0.02645 ( 308) hydrogen bonds : angle 5.07536 ( 873) link_BETA1-4 : bond 0.00590 ( 2) link_BETA1-4 : angle 1.50980 ( 6) link_NAG-ASN : bond 0.00048 ( 1) link_NAG-ASN : angle 1.15553 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4517.94 seconds wall clock time: 77 minutes 32.90 seconds (4652.90 seconds total)