Starting phenix.real_space_refine on Mon Jun 9 20:38:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjf_60143/06_2025/8zjf_60143.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjf_60143/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zjf_60143/06_2025/8zjf_60143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjf_60143/06_2025/8zjf_60143.map" model { file = "/net/cci-nas-00/data/ceres_data/8zjf_60143/06_2025/8zjf_60143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjf_60143/06_2025/8zjf_60143.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.98, per 1000 atoms: 0.64 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: 2.83 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.68 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: 4.37 Time building geometry restraints manager: 3.38 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.920 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:14.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.850 ------------------------------------------------------------------------------- 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 : 9.93 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP A 925 HIS 0.012 0.001 HIS B 453 PHE 0.013 0.001 PHE A 688 TYR 0.012 0.001 TYR B 162 ARG 0.006 0.000 ARG A 753 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 1) link_NAG-ASN : angle 1.60836 ( 3) link_BETA1-4 : bond 0.00507 ( 2) link_BETA1-4 : angle 1.49327 ( 6) hydrogen bonds : bond 0.21872 ( 308) hydrogen bonds : angle 8.81183 ( 873) SS BOND : bond 0.00177 ( 19) SS BOND : angle 2.08507 ( 38) covalent geometry : bond 0.00292 (11136) covalent geometry : angle 0.65191 (15103) *********************** 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 : 1.232 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: 0.9868 time to fit residues: 167.4746 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 : 1.123 ------------------------------------------------------------------------------- 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 119 optimal weight: 0.0670 chunk 106 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 0.0570 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 82 optimal weight: 50.0000 chunk 128 optimal weight: 5.9990 overall best weight: 2.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN B 224 GLN B 272 GLN B 274 GLN B 453 HIS ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 569 HIS A 797 GLN ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4529 r_free = 0.4529 target = 0.237305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.155907 restraints weight = 10243.804| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.38 r_work: 0.3220 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 11158 Z= 0.292 Angle : 0.803 10.097 15150 Z= 0.407 Chirality : 0.052 0.292 1696 Planarity : 0.006 0.056 2002 Dihedral : 7.925 58.711 1622 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 5.33 % Allowed : 18.50 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.22), residues: 1411 helix: 0.21 (0.38), residues: 205 sheet: -0.59 (0.25), residues: 427 loop : -1.69 (0.20), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 277 HIS 0.009 0.002 HIS B 293 PHE 0.019 0.003 PHE A 406 TYR 0.019 0.003 TYR B 162 ARG 0.010 0.001 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00863 ( 1) link_NAG-ASN : angle 3.44538 ( 3) link_BETA1-4 : bond 0.00762 ( 2) link_BETA1-4 : angle 2.80528 ( 6) hydrogen bonds : bond 0.05164 ( 308) hydrogen bonds : angle 6.63354 ( 873) SS BOND : bond 0.00289 ( 19) SS BOND : angle 1.47628 ( 38) covalent geometry : bond 0.00695 (11136) covalent geometry : angle 0.79777 (15103) *********************** 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 148 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 84 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.7889 (t0) REVERT: B 361 LYS cc_start: 0.8257 (mtmt) cc_final: 0.7978 (mtpt) REVERT: B 387 ASN cc_start: 0.8164 (t0) cc_final: 0.7523 (m110) REVERT: B 409 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: A 72 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8624 (mp) REVERT: A 84 HIS cc_start: 0.8773 (m170) cc_final: 0.8562 (m170) REVERT: A 113 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7910 (ttm170) REVERT: A 136 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: A 228 MET cc_start: 0.8820 (ttp) cc_final: 0.8080 (tpt) REVERT: A 238 GLU cc_start: 0.7420 (pt0) cc_final: 0.7191 (mt-10) REVERT: A 513 TYR cc_start: 0.9328 (OUTLIER) cc_final: 0.8929 (m-80) REVERT: A 594 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7786 (p0) REVERT: A 708 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7468 (tt0) REVERT: A 720 LEU cc_start: 0.2673 (OUTLIER) cc_final: 0.2030 (pp) REVERT: A 790 GLN cc_start: 0.8876 (tt0) cc_final: 0.8522 (tt0) outliers start: 64 outliers final: 26 residues processed: 140 average time/residue: 1.0846 time to fit residues: 166.4145 Evaluate side-chains 110 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 290 ASP 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 48 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 136 GLN 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 486 HIS Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 713 THR 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 798 THR Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 56 optimal weight: 0.0470 chunk 119 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 HIS B 274 GLN B 453 HIS ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4557 r_free = 0.4557 target = 0.240562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.158181 restraints weight = 10440.098| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.24 r_work: 0.3246 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11158 Z= 0.116 Angle : 0.605 9.385 15150 Z= 0.303 Chirality : 0.044 0.168 1696 Planarity : 0.005 0.049 2002 Dihedral : 6.593 55.620 1618 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.25 % Allowed : 20.42 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.22), residues: 1411 helix: 0.50 (0.38), residues: 201 sheet: -0.47 (0.26), residues: 415 loop : -1.53 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 52 HIS 0.004 0.001 HIS B 453 PHE 0.023 0.001 PHE A 812 TYR 0.015 0.001 TYR A 789 ARG 0.005 0.000 ARG A 439 Details of bonding type rmsd link_NAG-ASN : bond 0.00001 ( 1) link_NAG-ASN : angle 2.28302 ( 3) link_BETA1-4 : bond 0.00571 ( 2) link_BETA1-4 : angle 2.43972 ( 6) hydrogen bonds : bond 0.03660 ( 308) hydrogen bonds : angle 6.02315 ( 873) SS BOND : bond 0.00216 ( 19) SS BOND : angle 1.07817 ( 38) covalent geometry : bond 0.00261 (11136) covalent geometry : angle 0.60109 (15103) *********************** 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 127 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 76 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.7819 (t0) REVERT: B 387 ASN cc_start: 0.8094 (t0) cc_final: 0.7483 (m110) REVERT: B 444 GLN cc_start: 0.7002 (tp40) cc_final: 0.6622 (tp40) REVERT: A 72 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8618 (mp) REVERT: A 228 MET cc_start: 0.8849 (ttp) cc_final: 0.8167 (tpt) REVERT: A 468 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8664 (mt) REVERT: A 498 GLU cc_start: 0.6242 (mm-30) cc_final: 0.5465 (tp30) REVERT: A 513 TYR cc_start: 0.9269 (OUTLIER) cc_final: 0.8881 (m-80) REVERT: A 584 MET cc_start: 0.8920 (mmm) cc_final: 0.8677 (mmm) REVERT: A 622 TRP cc_start: 0.6513 (m100) cc_final: 0.6274 (m100) REVERT: A 708 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: A 720 LEU cc_start: 0.2616 (OUTLIER) cc_final: 0.1961 (pp) REVERT: A 763 GLU cc_start: 0.6863 (tp30) cc_final: 0.6575 (tp30) REVERT: A 791 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7395 (mp) outliers start: 51 outliers final: 25 residues processed: 122 average time/residue: 1.0646 time to fit residues: 142.8099 Evaluate side-chains 105 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 73 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 GLN 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 72 LEU Chi-restraints excluded: chain A residue 87 ILE 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 437 SER 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 684 VAL Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 61 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 75 optimal weight: 40.0000 chunk 50 optimal weight: 0.2980 chunk 54 optimal weight: 0.7980 chunk 126 optimal weight: 0.0170 chunk 4 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 GLN ** B 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 ASN A 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.237950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.128713 restraints weight = 10236.121| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.56 r_work: 0.3137 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 11158 Z= 0.180 Angle : 0.672 12.119 15150 Z= 0.334 Chirality : 0.047 0.226 1696 Planarity : 0.005 0.050 2002 Dihedral : 6.449 57.604 1617 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.75 % Allowed : 20.25 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.22), residues: 1411 helix: 0.56 (0.38), residues: 201 sheet: -0.44 (0.25), residues: 426 loop : -1.55 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 277 HIS 0.007 0.001 HIS A 486 PHE 0.017 0.002 PHE A 812 TYR 0.013 0.002 TYR A 789 ARG 0.004 0.000 ARG A 439 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 1) link_NAG-ASN : angle 2.77791 ( 3) link_BETA1-4 : bond 0.00686 ( 2) link_BETA1-4 : angle 2.51072 ( 6) hydrogen bonds : bond 0.03830 ( 308) hydrogen bonds : angle 5.89154 ( 873) SS BOND : bond 0.00333 ( 19) SS BOND : angle 2.24946 ( 38) covalent geometry : bond 0.00433 (11136) covalent geometry : angle 0.66039 (15103) *********************** 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 134 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 77 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.7864 (t0) REVERT: B 387 ASN cc_start: 0.8127 (t0) cc_final: 0.7577 (m110) REVERT: B 444 GLN cc_start: 0.7298 (tp40) cc_final: 0.6539 (tp40) REVERT: B 523 LEU cc_start: 0.4066 (OUTLIER) cc_final: 0.3639 (mp) REVERT: A 72 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8716 (mp) REVERT: A 99 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8453 (ppp-140) REVERT: A 113 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7976 (ttm170) REVERT: A 228 MET cc_start: 0.8747 (ttp) cc_final: 0.8036 (tpt) REVERT: A 331 MET cc_start: 0.4615 (mpp) cc_final: 0.4405 (mpp) REVERT: A 468 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8787 (mp) REVERT: A 498 GLU cc_start: 0.6014 (mm-30) cc_final: 0.5260 (tp30) REVERT: A 584 MET cc_start: 0.8998 (mmm) cc_final: 0.8744 (mmm) REVERT: A 622 TRP cc_start: 0.6660 (m100) cc_final: 0.6415 (m100) REVERT: A 720 LEU cc_start: 0.2726 (OUTLIER) cc_final: 0.2211 (pp) REVERT: A 790 GLN cc_start: 0.8841 (tt0) cc_final: 0.8437 (tt0) REVERT: A 791 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7675 (mp) outliers start: 57 outliers final: 29 residues processed: 130 average time/residue: 1.2521 time to fit residues: 177.0277 Evaluate side-chains 112 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 75 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 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 523 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 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 494 LYS 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 662 ASP Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 713 THR 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 137 optimal weight: 30.0000 chunk 124 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 45 optimal weight: 40.0000 chunk 58 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 134 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 486 HIS A 556 GLN A 790 GLN A 792 GLN A 842 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.233451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.146125 restraints weight = 9969.063| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 6.68 r_work: 0.2848 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 11158 Z= 0.308 Angle : 0.783 10.694 15150 Z= 0.390 Chirality : 0.051 0.207 1696 Planarity : 0.006 0.074 2002 Dihedral : 6.646 59.269 1614 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 5.75 % Allowed : 19.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.22), residues: 1411 helix: 0.42 (0.38), residues: 202 sheet: -0.49 (0.26), residues: 422 loop : -1.66 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 277 HIS 0.011 0.002 HIS B 293 PHE 0.022 0.003 PHE A 19 TYR 0.021 0.003 TYR B 162 ARG 0.009 0.001 ARG A 439 Details of bonding type rmsd link_NAG-ASN : bond 0.01085 ( 1) link_NAG-ASN : angle 3.74861 ( 3) link_BETA1-4 : bond 0.00330 ( 2) link_BETA1-4 : angle 2.72574 ( 6) hydrogen bonds : bond 0.04601 ( 308) hydrogen bonds : angle 6.03087 ( 873) SS BOND : bond 0.00360 ( 19) SS BOND : angle 1.91012 ( 38) covalent geometry : bond 0.00752 (11136) covalent geometry : angle 0.77482 (15103) *********************** 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 140 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 71 time to evaluate : 1.134 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: 0.8554 (OUTLIER) cc_final: 0.7745 (t0) REVERT: B 387 ASN cc_start: 0.8247 (t0) cc_final: 0.7765 (m110) REVERT: B 396 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7566 (mm-30) REVERT: B 444 GLN cc_start: 0.7677 (tp40) cc_final: 0.6954 (tp40) REVERT: B 523 LEU cc_start: 0.4257 (OUTLIER) cc_final: 0.3891 (mp) REVERT: A 99 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8807 (ppp-140) REVERT: A 113 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.8076 (ttm170) REVERT: A 121 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8188 (mt-10) REVERT: A 145 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7696 (mp0) REVERT: A 228 MET cc_start: 0.8752 (ttp) cc_final: 0.7904 (tpt) REVERT: A 285 MET cc_start: 0.6721 (OUTLIER) cc_final: 0.6484 (mmm) REVERT: A 493 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8730 (mp10) REVERT: A 498 GLU cc_start: 0.6314 (mm-30) cc_final: 0.6047 (mm-30) REVERT: A 584 MET cc_start: 0.8987 (mmm) cc_final: 0.8706 (mmm) REVERT: A 622 TRP cc_start: 0.6844 (m100) cc_final: 0.6563 (m100) REVERT: A 662 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7100 (p0) REVERT: A 720 LEU cc_start: 0.3569 (OUTLIER) cc_final: 0.3222 (pp) REVERT: A 727 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.6181 (m-80) REVERT: A 842 GLN cc_start: 0.3331 (OUTLIER) cc_final: 0.2735 (pp30) outliers start: 69 outliers final: 30 residues processed: 136 average time/residue: 1.2766 time to fit residues: 190.0458 Evaluate side-chains 107 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 67 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL 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 413 GLU 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 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 113 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 493 GLN 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 623 ASP Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 842 GLN Chi-restraints excluded: chain A residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 111 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 30.0000 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 108 optimal weight: 0.4980 chunk 103 optimal weight: 0.6980 chunk 134 optimal weight: 40.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 GLN B 316 ASN ** B 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 486 HIS A 556 GLN A 790 GLN A 792 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.235736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.151660 restraints weight = 9978.941| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 6.50 r_work: 0.2903 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11158 Z= 0.133 Angle : 0.616 10.269 15150 Z= 0.307 Chirality : 0.044 0.161 1696 Planarity : 0.004 0.048 2002 Dihedral : 6.069 59.999 1614 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.75 % Allowed : 20.42 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.22), residues: 1411 helix: 0.54 (0.38), residues: 204 sheet: -0.46 (0.26), residues: 421 loop : -1.52 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 277 HIS 0.006 0.001 HIS A 486 PHE 0.015 0.002 PHE A 812 TYR 0.015 0.002 TYR A 789 ARG 0.006 0.000 ARG A 439 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 1) link_NAG-ASN : angle 2.44469 ( 3) link_BETA1-4 : bond 0.00443 ( 2) link_BETA1-4 : angle 1.96610 ( 6) hydrogen bonds : bond 0.03342 ( 308) hydrogen bonds : angle 5.65549 ( 873) SS BOND : bond 0.00364 ( 19) SS BOND : angle 1.40429 ( 38) covalent geometry : bond 0.00311 (11136) covalent geometry : angle 0.61110 (15103) *********************** 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 128 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 71 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7518 (mm) REVERT: B 290 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.7829 (t0) REVERT: B 321 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8241 (ptm-80) REVERT: B 387 ASN cc_start: 0.8197 (t0) cc_final: 0.7726 (m110) REVERT: B 444 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.6947 (tp40) REVERT: B 523 LEU cc_start: 0.4134 (OUTLIER) cc_final: 0.3808 (mp) REVERT: A 20 ASN cc_start: 0.7291 (m-40) cc_final: 0.6550 (m110) REVERT: A 99 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8572 (ppp-140) REVERT: A 113 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8098 (ttm170) REVERT: A 121 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8153 (mt-10) REVERT: A 145 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7634 (mp0) REVERT: A 228 MET cc_start: 0.8737 (ttp) cc_final: 0.7901 (tpt) REVERT: A 260 GLN cc_start: 0.6945 (OUTLIER) cc_final: 0.6690 (mp10) REVERT: A 331 MET cc_start: 0.4224 (mpp) cc_final: 0.4006 (mpp) REVERT: A 498 GLU cc_start: 0.6075 (mm-30) cc_final: 0.5451 (tp30) REVERT: A 513 TYR cc_start: 0.9356 (OUTLIER) cc_final: 0.8962 (m-80) REVERT: A 584 MET cc_start: 0.9038 (mmm) cc_final: 0.8670 (mmm) REVERT: A 622 TRP cc_start: 0.6922 (m100) cc_final: 0.6674 (m100) REVERT: A 720 LEU cc_start: 0.3420 (OUTLIER) cc_final: 0.3059 (pp) REVERT: A 791 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7813 (mp) REVERT: A 798 THR cc_start: 0.7843 (OUTLIER) cc_final: 0.7622 (p) outliers start: 57 outliers final: 22 residues processed: 121 average time/residue: 1.1053 time to fit residues: 146.5611 Evaluate side-chains 103 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 69 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 321 ARG Chi-restraints excluded: chain B residue 444 GLN 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 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 720 LEU 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 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 112 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 80 optimal weight: 50.0000 chunk 96 optimal weight: 2.9990 chunk 82 optimal weight: 50.0000 chunk 135 optimal weight: 50.0000 chunk 20 optimal weight: 0.2980 chunk 8 optimal weight: 0.1980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4486 r_free = 0.4486 target = 0.235795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.150112 restraints weight = 10156.216| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 6.67 r_work: 0.2914 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11158 Z= 0.149 Angle : 0.629 10.830 15150 Z= 0.309 Chirality : 0.045 0.166 1696 Planarity : 0.005 0.057 2002 Dihedral : 5.968 59.414 1613 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.17 % Allowed : 21.67 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.22), residues: 1411 helix: 0.59 (0.38), residues: 205 sheet: -0.42 (0.26), residues: 417 loop : -1.46 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 277 HIS 0.005 0.001 HIS B 293 PHE 0.014 0.002 PHE A 406 TYR 0.016 0.002 TYR A 789 ARG 0.007 0.000 ARG A 439 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 1) link_NAG-ASN : angle 2.37169 ( 3) link_BETA1-4 : bond 0.00530 ( 2) link_BETA1-4 : angle 1.95870 ( 6) hydrogen bonds : bond 0.03373 ( 308) hydrogen bonds : angle 5.52202 ( 873) SS BOND : bond 0.00195 ( 19) SS BOND : angle 1.22479 ( 38) covalent geometry : bond 0.00358 (11136) covalent geometry : angle 0.62502 (15103) *********************** 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 121 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 71 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7555 (mm) REVERT: B 290 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.7912 (t0) REVERT: B 321 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8331 (ptm-80) REVERT: B 387 ASN cc_start: 0.8206 (t0) cc_final: 0.7735 (m110) REVERT: B 444 GLN cc_start: 0.7676 (tp40) cc_final: 0.6975 (tp40) REVERT: B 523 LEU cc_start: 0.4276 (OUTLIER) cc_final: 0.4005 (mp) REVERT: A 20 ASN cc_start: 0.7416 (m-40) cc_final: 0.6584 (m110) REVERT: A 99 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8609 (ppp-140) REVERT: A 113 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8093 (ttm170) REVERT: A 121 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8082 (mt-10) REVERT: A 145 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7669 (mp0) REVERT: A 149 ASP cc_start: 0.5958 (m-30) cc_final: 0.5653 (p0) REVERT: A 228 MET cc_start: 0.8715 (ttp) cc_final: 0.7877 (tpt) REVERT: A 260 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6641 (mp10) REVERT: A 493 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8728 (mp10) REVERT: A 498 GLU cc_start: 0.6039 (mm-30) cc_final: 0.5442 (tp30) REVERT: A 622 TRP cc_start: 0.6862 (m100) cc_final: 0.6627 (m100) REVERT: A 720 LEU cc_start: 0.3367 (OUTLIER) cc_final: 0.3012 (pp) outliers start: 50 outliers final: 25 residues processed: 114 average time/residue: 1.2215 time to fit residues: 152.2261 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 : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 494 LYS 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 626 SER Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 720 LEU 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 903 LEU 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 7 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 43 optimal weight: 50.0000 chunk 66 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 GLN B 316 ASN B 427 GLN B 453 HIS A 231 ASN A 802 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.232810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.147108 restraints weight = 9969.715| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 6.57 r_work: 0.2843 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 11158 Z= 0.308 Angle : 0.796 12.909 15150 Z= 0.389 Chirality : 0.051 0.204 1696 Planarity : 0.006 0.075 2002 Dihedral : 6.152 58.667 1607 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 4.33 % Allowed : 21.67 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.22), residues: 1411 helix: 0.31 (0.38), residues: 208 sheet: -0.45 (0.26), residues: 424 loop : -1.57 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 277 HIS 0.011 0.002 HIS B 293 PHE 0.031 0.003 PHE A 19 TYR 0.020 0.003 TYR A 789 ARG 0.006 0.001 ARG A 753 Details of bonding type rmsd link_NAG-ASN : bond 0.01152 ( 1) link_NAG-ASN : angle 3.22081 ( 3) link_BETA1-4 : bond 0.00529 ( 2) link_BETA1-4 : angle 2.35945 ( 6) hydrogen bonds : bond 0.04424 ( 308) hydrogen bonds : angle 5.87266 ( 873) SS BOND : bond 0.00261 ( 19) SS BOND : angle 1.76145 ( 38) covalent geometry : bond 0.00759 (11136) covalent geometry : angle 0.79004 (15103) *********************** 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 120 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 68 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7642 (mm) REVERT: B 290 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.7654 (t0) REVERT: B 321 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8266 (ptm-80) REVERT: B 387 ASN cc_start: 0.8274 (t0) cc_final: 0.7784 (m110) REVERT: B 396 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7617 (mm-30) REVERT: B 444 GLN cc_start: 0.7727 (tp40) cc_final: 0.7017 (tp40) REVERT: B 523 LEU cc_start: 0.4134 (OUTLIER) cc_final: 0.3930 (mp) REVERT: A 99 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8836 (ppp-140) REVERT: A 113 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8146 (ttm170) REVERT: A 121 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8231 (mt-10) REVERT: A 145 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7689 (mp0) REVERT: A 149 ASP cc_start: 0.5989 (m-30) cc_final: 0.5596 (p0) REVERT: A 228 MET cc_start: 0.8740 (ttp) cc_final: 0.7904 (tpt) REVERT: A 260 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6718 (mp10) REVERT: A 493 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8668 (mp10) REVERT: A 498 GLU cc_start: 0.6139 (mm-30) cc_final: 0.5471 (tp30) REVERT: A 622 TRP cc_start: 0.6901 (m100) cc_final: 0.6677 (m100) REVERT: A 720 LEU cc_start: 0.3783 (OUTLIER) cc_final: 0.3537 (pp) REVERT: A 727 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.6412 (m-80) REVERT: A 730 ASP cc_start: 0.7954 (t0) cc_final: 0.7532 (t0) outliers start: 52 outliers final: 25 residues processed: 117 average time/residue: 1.2339 time to fit residues: 158.6595 Evaluate side-chains 103 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 68 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 321 ARG 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 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 493 GLN 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 626 SER Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 754 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 132 optimal weight: 50.0000 chunk 44 optimal weight: 0.8980 chunk 139 optimal weight: 0.3980 chunk 112 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 133 optimal weight: 30.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 GLN B 316 ASN A 231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.235608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.152803 restraints weight = 10071.502| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 6.35 r_work: 0.2885 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11158 Z= 0.122 Angle : 0.622 11.257 15150 Z= 0.303 Chirality : 0.044 0.160 1696 Planarity : 0.004 0.048 2002 Dihedral : 5.618 58.377 1607 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.08 % Allowed : 22.92 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.22), residues: 1411 helix: 0.61 (0.38), residues: 205 sheet: -0.40 (0.26), residues: 420 loop : -1.51 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 277 HIS 0.003 0.001 HIS B 293 PHE 0.012 0.001 PHE A 577 TYR 0.016 0.002 TYR A 789 ARG 0.008 0.000 ARG A 753 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 1) link_NAG-ASN : angle 2.04970 ( 3) link_BETA1-4 : bond 0.00547 ( 2) link_BETA1-4 : angle 1.78068 ( 6) hydrogen bonds : bond 0.03169 ( 308) hydrogen bonds : angle 5.50881 ( 873) SS BOND : bond 0.00198 ( 19) SS BOND : angle 1.25059 ( 38) covalent geometry : bond 0.00286 (11136) covalent geometry : angle 0.61839 (15103) *********************** 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 111 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 74 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7462 (mm) REVERT: B 290 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.7822 (t0) REVERT: B 321 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8313 (ptm-80) REVERT: B 387 ASN cc_start: 0.8220 (t0) cc_final: 0.7731 (m110) REVERT: B 444 GLN cc_start: 0.7693 (tp40) cc_final: 0.7003 (tp40) REVERT: A 20 ASN cc_start: 0.7583 (m-40) cc_final: 0.6700 (m110) REVERT: A 99 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8534 (ppp-140) REVERT: A 113 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.8043 (ttm170) REVERT: A 121 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8110 (mt-10) REVERT: A 145 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7679 (mp0) REVERT: A 228 MET cc_start: 0.8620 (ttp) cc_final: 0.7797 (tpt) REVERT: A 439 ARG cc_start: 0.8079 (mtp85) cc_final: 0.7717 (mtp180) REVERT: A 498 GLU cc_start: 0.6011 (mm-30) cc_final: 0.5404 (tp30) REVERT: A 513 TYR cc_start: 0.9354 (OUTLIER) cc_final: 0.8956 (m-80) REVERT: A 622 TRP cc_start: 0.6993 (m100) cc_final: 0.6793 (m100) REVERT: A 720 LEU cc_start: 0.3521 (OUTLIER) cc_final: 0.3230 (pp) REVERT: A 730 ASP cc_start: 0.7779 (t0) cc_final: 0.7370 (t0) REVERT: A 753 ARG cc_start: 0.7714 (ttm-80) cc_final: 0.7312 (mtt-85) outliers start: 37 outliers final: 24 residues processed: 108 average time/residue: 1.2291 time to fit residues: 144.3979 Evaluate side-chains 103 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 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 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 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 754 GLU 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 903 LEU 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 80 optimal weight: 50.0000 chunk 133 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 128 optimal weight: 50.0000 chunk 111 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 129 optimal weight: 9.9990 chunk 78 optimal weight: 0.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 GLN B 316 ASN B 427 GLN B 453 HIS A 231 ASN A 741 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.233279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.149582 restraints weight = 9979.613| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 6.50 r_work: 0.2852 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 11158 Z= 0.239 Angle : 0.734 11.637 15150 Z= 0.357 Chirality : 0.048 0.185 1696 Planarity : 0.005 0.061 2002 Dihedral : 5.940 58.023 1607 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.33 % Allowed : 23.08 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.22), residues: 1411 helix: 0.27 (0.37), residues: 216 sheet: -0.42 (0.26), residues: 421 loop : -1.59 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 277 HIS 0.008 0.001 HIS B 293 PHE 0.020 0.003 PHE A 19 TYR 0.020 0.003 TYR A 789 ARG 0.007 0.001 ARG A 753 Details of bonding type rmsd link_NAG-ASN : bond 0.00809 ( 1) link_NAG-ASN : angle 2.80931 ( 3) link_BETA1-4 : bond 0.00490 ( 2) link_BETA1-4 : angle 2.03448 ( 6) hydrogen bonds : bond 0.03936 ( 308) hydrogen bonds : angle 5.67223 ( 873) SS BOND : bond 0.00207 ( 19) SS BOND : angle 1.49743 ( 38) covalent geometry : bond 0.00585 (11136) covalent geometry : angle 0.72893 (15103) ********************** 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 110 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 70 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7746 (mm) REVERT: B 290 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.7724 (t0) REVERT: B 321 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8297 (ptm-80) REVERT: B 387 ASN cc_start: 0.8240 (t0) cc_final: 0.7759 (m110) REVERT: B 444 GLN cc_start: 0.7740 (tp40) cc_final: 0.7066 (tp40) REVERT: A 99 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8777 (ppp-140) REVERT: A 113 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8075 (ttm170) REVERT: A 121 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8233 (mt-10) REVERT: A 145 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7668 (mp0) REVERT: A 228 MET cc_start: 0.8706 (ttp) cc_final: 0.7851 (tpt) REVERT: A 498 GLU cc_start: 0.6038 (mm-30) cc_final: 0.5394 (tp30) REVERT: A 720 LEU cc_start: 0.3733 (OUTLIER) cc_final: 0.3447 (pp) REVERT: A 730 ASP cc_start: 0.7940 (t0) cc_final: 0.7507 (t0) REVERT: A 741 GLN cc_start: 0.6129 (OUTLIER) cc_final: 0.5874 (pm20) REVERT: A 753 ARG cc_start: 0.7736 (ttm-80) cc_final: 0.7334 (mtt-85) outliers start: 40 outliers final: 27 residues processed: 107 average time/residue: 1.2253 time to fit residues: 142.2823 Evaluate side-chains 103 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 69 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL 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 321 ARG 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 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 378 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 494 LYS 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 720 LEU Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 754 GLU 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 903 LEU 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 95 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 45 optimal weight: 40.0000 chunk 92 optimal weight: 0.0870 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 96 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 GLN B 316 ASN B 453 HIS ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.235789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.157390 restraints weight = 9944.060| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 5.85 r_work: 0.2902 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11158 Z= 0.108 Angle : 0.617 12.531 15150 Z= 0.301 Chirality : 0.044 0.167 1696 Planarity : 0.004 0.047 2002 Dihedral : 5.495 57.817 1607 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.08 % Allowed : 23.33 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.22), residues: 1411 helix: 0.77 (0.38), residues: 203 sheet: -0.35 (0.26), residues: 419 loop : -1.47 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 52 HIS 0.003 0.001 HIS A 486 PHE 0.012 0.001 PHE A 645 TYR 0.017 0.001 TYR A 789 ARG 0.007 0.000 ARG A 753 Details of bonding type rmsd link_NAG-ASN : bond 0.00052 ( 1) link_NAG-ASN : angle 1.75924 ( 3) link_BETA1-4 : bond 0.00585 ( 2) link_BETA1-4 : angle 1.74193 ( 6) hydrogen bonds : bond 0.03000 ( 308) hydrogen bonds : angle 5.38386 ( 873) SS BOND : bond 0.00204 ( 19) SS BOND : angle 1.13580 ( 38) covalent geometry : bond 0.00247 (11136) covalent geometry : angle 0.61417 (15103) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8704.00 seconds wall clock time: 149 minutes 24.06 seconds (8964.06 seconds total)