Starting phenix.real_space_refine on Tue May 13 20:25:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjf_60143/05_2025/8zjf_60143.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjf_60143/05_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_60143/05_2025/8zjf_60143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjf_60143/05_2025/8zjf_60143.map" model { file = "/net/cci-nas-00/data/ceres_data/8zjf_60143/05_2025/8zjf_60143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjf_60143/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 6.35, per 1000 atoms: 0.58 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: 2.72 Conformation dependent library (CDL) restraints added in 1.4 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: 1.41 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: 4.30 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3741 1.34 - 1.46: 2390 1.46 - 1.58: 4908 1.58 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 11136 Sorted by residual: bond pdb=" CB CYS A 236 " pdb=" SG CYS A 236 " ideal model delta sigma weight residual 1.808 1.756 0.052 3.30e-02 9.18e+02 2.48e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.546 -0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" N PRO A 811 " pdb=" CA PRO A 811 " ideal model delta sigma weight residual 1.468 1.478 -0.011 7.90e-03 1.60e+04 1.80e+00 bond pdb=" N MET A 867 " pdb=" CA MET A 867 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.29e+00 bond pdb=" CB CYS A 239 " pdb=" SG CYS A 239 " ideal model delta sigma weight residual 1.808 1.771 0.037 3.30e-02 9.18e+02 1.26e+00 ... (remaining 11131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 14859 2.12 - 4.24: 203 4.24 - 6.35: 33 6.35 - 8.47: 3 8.47 - 10.59: 5 Bond angle restraints: 15103 Sorted by residual: angle pdb=" CA MET A 867 " pdb=" CB MET A 867 " pdb=" CG MET A 867 " ideal model delta sigma weight residual 114.10 122.82 -8.72 2.00e+00 2.50e-01 1.90e+01 angle pdb=" C THR A 936 " pdb=" N ALA A 937 " pdb=" CA ALA A 937 " ideal model delta sigma weight residual 121.54 128.44 -6.90 1.91e+00 2.74e-01 1.30e+01 angle pdb=" CB MET A 867 " pdb=" CG MET A 867 " pdb=" SD MET A 867 " ideal model delta sigma weight residual 112.70 123.29 -10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CB MET A 883 " pdb=" CG MET A 883 " pdb=" SD MET A 883 " ideal model delta sigma weight residual 112.70 123.08 -10.38 3.00e+00 1.11e-01 1.20e+01 angle pdb=" CB MET A 768 " pdb=" CG MET A 768 " pdb=" SD MET A 768 " ideal model delta sigma weight residual 112.70 121.84 -9.14 3.00e+00 1.11e-01 9.29e+00 ... (remaining 15098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 6132 21.43 - 42.86: 531 42.86 - 64.29: 119 64.29 - 85.72: 26 85.72 - 107.14: 8 Dihedral angle restraints: 6816 sinusoidal: 2759 harmonic: 4057 Sorted by residual: dihedral pdb=" CB CYS A 775 " pdb=" SG CYS A 775 " pdb=" SG CYS A 779 " pdb=" CB CYS A 779 " ideal model delta sinusoidal sigma weight residual 93.00 176.62 -83.62 1 1.00e+01 1.00e-02 8.53e+01 dihedral pdb=" CB CYS B 488 " pdb=" SG CYS B 488 " pdb=" SG CYS B 500 " pdb=" CB CYS B 500 " ideal model delta sinusoidal sigma weight residual -86.00 -9.12 -76.88 1 1.00e+01 1.00e-02 7.42e+01 dihedral pdb=" CB CYS B 527 " pdb=" SG CYS B 527 " pdb=" SG CYS B 543 " pdb=" CB CYS B 543 " ideal model delta sinusoidal sigma weight residual -86.00 -154.74 68.74 1 1.00e+01 1.00e-02 6.12e+01 ... (remaining 6813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1373 0.053 - 0.106: 282 0.106 - 0.159: 37 0.159 - 0.212: 3 0.212 - 0.265: 1 Chirality restraints: 1696 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.65e+00 chirality pdb=" CG LEU B 523 " pdb=" CB LEU B 523 " pdb=" CD1 LEU B 523 " pdb=" CD2 LEU B 523 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1693 not shown) Planarity restraints: 2003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 136 " 0.052 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO B 137 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 137 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 137 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 911 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO A 912 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 912 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 912 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 133 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO B 134 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 134 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 134 " -0.028 5.00e-02 4.00e+02 ... (remaining 2000 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 227 2.68 - 3.24: 10174 3.24 - 3.79: 17112 3.79 - 4.35: 23761 4.35 - 4.90: 38453 Nonbonded interactions: 89727 Sorted by model distance: nonbonded pdb=" OD2 ASP B 198 " pdb="CA CA B 902 " model vdw 2.127 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: 0.540 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: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 27.180 Find NCS groups from input model: 0.100 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:13.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.230 ------------------------------------------------------------------------------- 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 : 1.160 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: 0.9476 time to fit residues: 160.9512 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 : 1.069 ------------------------------------------------------------------------------- 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 = 10243.802| |-----------------------------------------------------------------------------| 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: 4.12 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 2.80527 ( 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 : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.7888 (t0) REVERT: B 361 LYS cc_start: 0.8253 (mtmt) cc_final: 0.7974 (mtpt) REVERT: B 387 ASN cc_start: 0.8165 (t0) cc_final: 0.7519 (m110) REVERT: B 409 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: A 72 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8623 (mp) REVERT: A 76 GLU cc_start: 0.6736 (tp30) cc_final: 0.6535 (tp30) REVERT: A 84 HIS cc_start: 0.8768 (m170) cc_final: 0.8556 (m170) REVERT: A 113 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7907 (ttm170) REVERT: A 136 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: A 228 MET cc_start: 0.8817 (ttp) cc_final: 0.8076 (tpt) REVERT: A 238 GLU cc_start: 0.7426 (pt0) cc_final: 0.7199 (mt-10) REVERT: A 513 TYR cc_start: 0.9327 (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: 0.7767 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: A 720 LEU cc_start: 0.2664 (OUTLIER) cc_final: 0.2020 (pp) REVERT: A 790 GLN cc_start: 0.8872 (tt0) cc_final: 0.8513 (tt0) outliers start: 64 outliers final: 26 residues processed: 140 average time/residue: 0.9988 time to fit residues: 153.3026 Evaluate side-chains 109 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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: 0.0670 chunk 119 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 135 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.4559 r_free = 0.4559 target = 0.240851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.158289 restraints weight = 10440.821| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.18 r_work: 0.3310 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11158 Z= 0.111 Angle : 0.598 9.333 15150 Z= 0.299 Chirality : 0.044 0.160 1696 Planarity : 0.004 0.050 2002 Dihedral : 6.552 55.682 1618 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.00 % Allowed : 20.75 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.34 (0.22), residues: 1411 helix: 0.51 (0.38), residues: 201 sheet: -0.46 (0.26), residues: 415 loop : -1.52 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 52 HIS 0.005 0.001 HIS A 486 PHE 0.023 0.001 PHE A 812 TYR 0.015 0.001 TYR A 789 ARG 0.006 0.000 ARG A 439 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 1) link_NAG-ASN : angle 2.19929 ( 3) link_BETA1-4 : bond 0.00557 ( 2) link_BETA1-4 : angle 2.39431 ( 6) hydrogen bonds : bond 0.03546 ( 308) hydrogen bonds : angle 6.00111 ( 873) SS BOND : bond 0.00304 ( 19) SS BOND : angle 1.02745 ( 38) covalent geometry : bond 0.00250 (11136) covalent geometry : angle 0.59398 (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 124 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 76 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7812 (t0) REVERT: B 387 ASN cc_start: 0.8109 (t0) cc_final: 0.7499 (m110) REVERT: B 444 GLN cc_start: 0.7024 (tp40) cc_final: 0.6660 (tp40) REVERT: A 76 GLU cc_start: 0.6702 (tp30) cc_final: 0.6450 (tp30) REVERT: A 228 MET cc_start: 0.8843 (ttp) cc_final: 0.8162 (tpt) REVERT: A 468 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8651 (mt) REVERT: A 498 GLU cc_start: 0.6233 (mm-30) cc_final: 0.5453 (tp30) REVERT: A 513 TYR cc_start: 0.9262 (OUTLIER) cc_final: 0.8799 (m-80) REVERT: A 584 MET cc_start: 0.8919 (mmm) cc_final: 0.8675 (mmm) REVERT: A 622 TRP cc_start: 0.6516 (m100) cc_final: 0.6280 (m100) REVERT: A 708 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: A 720 LEU cc_start: 0.2714 (OUTLIER) cc_final: 0.2067 (pp) REVERT: A 763 GLU cc_start: 0.6840 (tp30) cc_final: 0.6561 (tp30) REVERT: A 791 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7377 (mp) outliers start: 48 outliers final: 22 residues processed: 119 average time/residue: 0.9695 time to fit residues: 127.2957 Evaluate side-chains 99 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 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 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 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: 0.0970 chunk 54 optimal weight: 0.6980 chunk 126 optimal weight: 0.4980 chunk 4 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.6582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.238095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.154758 restraints weight = 10253.999| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.33 r_work: 0.3217 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 11158 Z= 0.181 Angle : 0.674 12.892 15150 Z= 0.335 Chirality : 0.047 0.228 1696 Planarity : 0.005 0.050 2002 Dihedral : 6.461 57.616 1617 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.92 % Allowed : 19.92 % Favored : 75.17 % 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: -1.33 (0.22), residues: 1411 helix: 0.55 (0.38), residues: 201 sheet: -0.45 (0.25), residues: 426 loop : -1.55 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 277 HIS 0.007 0.001 HIS B 293 PHE 0.017 0.002 PHE A 812 TYR 0.013 0.002 TYR B 162 ARG 0.007 0.000 ARG A 439 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 1) link_NAG-ASN : angle 2.75370 ( 3) link_BETA1-4 : bond 0.00759 ( 2) link_BETA1-4 : angle 2.51793 ( 6) hydrogen bonds : bond 0.03824 ( 308) hydrogen bonds : angle 5.89690 ( 873) SS BOND : bond 0.00500 ( 19) SS BOND : angle 2.43167 ( 38) covalent geometry : bond 0.00438 (11136) covalent geometry : angle 0.66112 (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 132 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 73 time to evaluate : 1.155 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: 0.8563 (OUTLIER) cc_final: 0.7818 (t0) REVERT: B 387 ASN cc_start: 0.8089 (t0) cc_final: 0.7548 (m110) REVERT: B 444 GLN cc_start: 0.7313 (tp40) cc_final: 0.6564 (tp40) REVERT: B 523 LEU cc_start: 0.4286 (OUTLIER) cc_final: 0.3810 (mp) REVERT: A 72 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8725 (mp) REVERT: A 76 GLU cc_start: 0.6780 (tp30) cc_final: 0.6550 (tp30) REVERT: A 99 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8602 (ppp-140) REVERT: A 113 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7978 (ttm170) REVERT: A 228 MET cc_start: 0.8813 (ttp) cc_final: 0.8099 (tpt) REVERT: A 468 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8774 (mp) REVERT: A 498 GLU cc_start: 0.6032 (mm-30) cc_final: 0.5272 (tp30) REVERT: A 584 MET cc_start: 0.8978 (mmm) cc_final: 0.8717 (mmm) REVERT: A 622 TRP cc_start: 0.6643 (m100) cc_final: 0.6401 (m100) REVERT: A 720 LEU cc_start: 0.2708 (OUTLIER) cc_final: 0.2154 (pp) REVERT: A 790 GLN cc_start: 0.8851 (tt0) cc_final: 0.8448 (tt0) REVERT: A 791 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7551 (mp) REVERT: A 816 GLN cc_start: 0.6518 (OUTLIER) cc_final: 0.6312 (pm20) outliers start: 59 outliers final: 28 residues processed: 128 average time/residue: 1.1282 time to fit residues: 157.7209 Evaluate side-chains 109 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 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 816 GLN 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: 1.9990 chunk 41 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 45 optimal weight: 50.0000 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: 1.9990 chunk 134 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 GLN B 427 GLN ** B 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 556 GLN A 790 GLN A 792 GLN A 842 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.234024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.147870 restraints weight = 9958.147| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 6.51 r_work: 0.2862 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 11158 Z= 0.262 Angle : 0.751 10.438 15150 Z= 0.372 Chirality : 0.050 0.202 1696 Planarity : 0.006 0.068 2002 Dihedral : 6.552 59.488 1614 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 5.50 % Allowed : 20.08 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.46 (0.22), residues: 1411 helix: 0.44 (0.38), residues: 202 sheet: -0.50 (0.26), residues: 422 loop : -1.65 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 277 HIS 0.009 0.001 HIS B 293 PHE 0.019 0.003 PHE A 577 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 0.00968 ( 1) link_NAG-ASN : angle 3.62886 ( 3) link_BETA1-4 : bond 0.00627 ( 2) link_BETA1-4 : angle 2.47551 ( 6) hydrogen bonds : bond 0.04356 ( 308) hydrogen bonds : angle 5.95908 ( 873) SS BOND : bond 0.00328 ( 19) SS BOND : angle 1.84516 ( 38) covalent geometry : bond 0.00641 (11136) covalent geometry : angle 0.74293 (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 139 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 73 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 290 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.7734 (t70) REVERT: B 387 ASN cc_start: 0.8248 (t0) cc_final: 0.7769 (m110) REVERT: B 396 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7568 (mm-30) REVERT: B 444 GLN cc_start: 0.7690 (tp40) cc_final: 0.6977 (tp40) REVERT: B 523 LEU cc_start: 0.4087 (OUTLIER) cc_final: 0.3769 (mp) REVERT: A 99 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8797 (ppp-140) REVERT: A 113 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8086 (ttm170) REVERT: A 121 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8202 (mt-10) REVERT: A 145 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7703 (mp0) REVERT: A 228 MET cc_start: 0.8665 (ttp) cc_final: 0.7843 (tpt) REVERT: A 285 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.6355 (mpt) REVERT: A 493 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8667 (mp10) REVERT: A 498 GLU cc_start: 0.6274 (mm-30) cc_final: 0.6002 (mm-30) REVERT: A 584 MET cc_start: 0.8990 (mmm) cc_final: 0.8749 (mmm) REVERT: A 622 TRP cc_start: 0.6809 (m100) cc_final: 0.6545 (m100) REVERT: A 662 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7128 (p0) REVERT: A 720 LEU cc_start: 0.3308 (OUTLIER) cc_final: 0.2989 (pp) REVERT: A 727 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.6145 (m-80) REVERT: A 798 THR cc_start: 0.7813 (OUTLIER) cc_final: 0.7349 (p) REVERT: A 816 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.6498 (pm20) REVERT: A 842 GLN cc_start: 0.3341 (OUTLIER) cc_final: 0.2715 (pp30) outliers start: 66 outliers final: 30 residues processed: 135 average time/residue: 1.0150 time to fit residues: 150.1637 Evaluate side-chains 111 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 69 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 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 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 588 SER 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 770 THR Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 816 GLN 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 902 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 111 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 30.0000 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 73 optimal weight: 0.4980 chunk 34 optimal weight: 5.9990 chunk 108 optimal weight: 0.4980 chunk 103 optimal weight: 0.6980 chunk 134 optimal weight: 30.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 260 GLN 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 = 0.4492 r_free = 0.4492 target = 0.236449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.154823 restraints weight = 9985.238| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 6.20 r_work: 0.2900 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11158 Z= 0.110 Angle : 0.589 10.203 15150 Z= 0.294 Chirality : 0.043 0.162 1696 Planarity : 0.004 0.048 2002 Dihedral : 5.922 59.816 1614 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.50 % Allowed : 20.83 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.56 (0.38), residues: 205 sheet: -0.43 (0.26), residues: 430 loop : -1.46 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 277 HIS 0.002 0.000 HIS B 293 PHE 0.017 0.001 PHE A 812 TYR 0.014 0.001 TYR A 789 ARG 0.005 0.000 ARG A 753 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 1) link_NAG-ASN : angle 2.08418 ( 3) link_BETA1-4 : bond 0.00472 ( 2) link_BETA1-4 : angle 1.78783 ( 6) hydrogen bonds : bond 0.03115 ( 308) hydrogen bonds : angle 5.55953 ( 873) SS BOND : bond 0.00245 ( 19) SS BOND : angle 1.25634 ( 38) covalent geometry : bond 0.00250 (11136) covalent geometry : angle 0.58513 (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 129 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 75 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7429 (mm) REVERT: B 290 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.7823 (t0) REVERT: B 321 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8300 (ptm-80) REVERT: B 387 ASN cc_start: 0.8205 (t0) cc_final: 0.7731 (m110) REVERT: B 444 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.6921 (tp40) REVERT: B 523 LEU cc_start: 0.4106 (OUTLIER) cc_final: 0.3794 (mp) REVERT: A 99 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8456 (ppp-140) REVERT: A 113 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8070 (ttm170) REVERT: A 121 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8218 (mt-10) REVERT: A 145 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7627 (mp0) REVERT: A 228 MET cc_start: 0.8695 (ttp) cc_final: 0.7868 (tpt) REVERT: A 285 MET cc_start: 0.6682 (OUTLIER) cc_final: 0.6452 (mpt) REVERT: A 498 GLU cc_start: 0.6023 (mm-30) cc_final: 0.5400 (tp30) REVERT: A 513 TYR cc_start: 0.9343 (OUTLIER) cc_final: 0.8959 (m-80) REVERT: A 622 TRP cc_start: 0.6904 (m100) cc_final: 0.6632 (m100) REVERT: A 720 LEU cc_start: 0.3218 (OUTLIER) cc_final: 0.2899 (pp) REVERT: A 798 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7542 (p) REVERT: A 816 GLN cc_start: 0.6674 (OUTLIER) cc_final: 0.6468 (pm20) outliers start: 54 outliers final: 24 residues processed: 122 average time/residue: 1.0647 time to fit residues: 142.3478 Evaluate side-chains 108 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 72 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 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 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 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 684 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU 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: 1.9990 chunk 104 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 80 optimal weight: 50.0000 chunk 96 optimal weight: 0.5980 chunk 82 optimal weight: 50.0000 chunk 135 optimal weight: 50.0000 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.235039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.148049 restraints weight = 10102.585| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 6.92 r_work: 0.2875 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11158 Z= 0.195 Angle : 0.671 12.026 15150 Z= 0.329 Chirality : 0.046 0.170 1696 Planarity : 0.005 0.060 2002 Dihedral : 6.121 59.381 1613 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.58 % Allowed : 21.25 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.27 (0.22), residues: 1411 helix: 0.57 (0.38), residues: 205 sheet: -0.41 (0.26), residues: 425 loop : -1.51 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 277 HIS 0.007 0.001 HIS B 293 PHE 0.016 0.002 PHE A 406 TYR 0.017 0.002 TYR A 789 ARG 0.004 0.000 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00646 ( 1) link_NAG-ASN : angle 2.67299 ( 3) link_BETA1-4 : bond 0.00453 ( 2) link_BETA1-4 : angle 2.09001 ( 6) hydrogen bonds : bond 0.03668 ( 308) hydrogen bonds : angle 5.64560 ( 873) SS BOND : bond 0.00228 ( 19) SS BOND : angle 1.53297 ( 38) covalent geometry : bond 0.00479 (11136) covalent geometry : angle 0.66573 (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 124 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 69 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7580 (mm) REVERT: B 290 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.7734 (t0) REVERT: B 321 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8274 (ptm-80) REVERT: B 387 ASN cc_start: 0.8239 (t0) cc_final: 0.7751 (m110) REVERT: B 444 GLN cc_start: 0.7717 (tp40) cc_final: 0.6962 (tp40) REVERT: B 523 LEU cc_start: 0.4335 (OUTLIER) cc_final: 0.4034 (mp) REVERT: A 99 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8698 (ppp-140) REVERT: A 113 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8096 (ttm170) REVERT: A 121 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8258 (mt-10) REVERT: A 145 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7645 (mp0) REVERT: A 228 MET cc_start: 0.8749 (ttp) cc_final: 0.7920 (tpt) REVERT: A 260 GLN cc_start: 0.6943 (OUTLIER) cc_final: 0.6630 (mp10) REVERT: A 285 MET cc_start: 0.6708 (OUTLIER) cc_final: 0.6474 (mpt) REVERT: A 498 GLU cc_start: 0.6078 (mm-30) cc_final: 0.5451 (tp30) REVERT: A 622 TRP cc_start: 0.6901 (m100) cc_final: 0.6670 (m100) REVERT: A 720 LEU cc_start: 0.3369 (OUTLIER) cc_final: 0.3076 (pp) REVERT: A 798 THR cc_start: 0.7864 (OUTLIER) cc_final: 0.7602 (p) REVERT: A 816 GLN cc_start: 0.6785 (OUTLIER) cc_final: 0.6536 (pm20) outliers start: 55 outliers final: 27 residues processed: 118 average time/residue: 1.0823 time to fit residues: 139.7076 Evaluate side-chains 104 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 66 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 225 SER 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 48 THR Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 594 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 770 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 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: 8.9990 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 43 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 ASN B 453 HIS A 231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.232297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.145653 restraints weight = 9964.995| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 6.69 r_work: 0.2829 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 11158 Z= 0.355 Angle : 0.823 11.461 15150 Z= 0.406 Chirality : 0.054 0.249 1696 Planarity : 0.006 0.084 2002 Dihedral : 6.329 58.166 1607 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 4.50 % Allowed : 21.58 % Favored : 73.92 % 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: -1.48 (0.22), residues: 1411 helix: 0.28 (0.38), residues: 208 sheet: -0.51 (0.26), residues: 419 loop : -1.64 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 277 HIS 0.012 0.002 HIS B 293 PHE 0.038 0.004 PHE A 19 TYR 0.021 0.004 TYR A 789 ARG 0.008 0.001 ARG A 547 Details of bonding type rmsd link_NAG-ASN : bond 0.01248 ( 1) link_NAG-ASN : angle 3.45914 ( 3) link_BETA1-4 : bond 0.00228 ( 2) link_BETA1-4 : angle 2.43101 ( 6) hydrogen bonds : bond 0.04737 ( 308) hydrogen bonds : angle 6.00502 ( 873) SS BOND : bond 0.00251 ( 19) SS BOND : angle 1.75430 ( 38) covalent geometry : bond 0.00877 (11136) covalent geometry : angle 0.81695 (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: 54 poor density : 66 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7867 (mm) REVERT: B 290 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.7762 (t70) REVERT: B 321 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8343 (ptm-80) REVERT: B 387 ASN cc_start: 0.8263 (t0) cc_final: 0.7776 (m110) REVERT: B 396 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7619 (mm-30) REVERT: B 444 GLN cc_start: 0.7657 (tp40) cc_final: 0.6966 (tp40) REVERT: A 99 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8817 (ppp-140) REVERT: A 113 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7964 (ttm170) REVERT: A 121 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8292 (mt-10) REVERT: A 145 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7693 (mp0) REVERT: A 149 ASP cc_start: 0.6260 (m-30) cc_final: 0.5938 (p0) REVERT: A 228 MET cc_start: 0.8696 (ttp) cc_final: 0.7833 (tpt) REVERT: A 493 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8701 (mp10) REVERT: A 498 GLU cc_start: 0.6086 (mm-30) cc_final: 0.5108 (tp30) REVERT: A 730 ASP cc_start: 0.7905 (t0) cc_final: 0.7604 (t0) outliers start: 54 outliers final: 30 residues processed: 115 average time/residue: 1.1101 time to fit residues: 141.0975 Evaluate side-chains 103 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 67 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 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 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 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 588 SER Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 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: 5.9990 chunk 44 optimal weight: 3.9990 chunk 139 optimal weight: 40.0000 chunk 112 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 0.2980 chunk 140 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 133 optimal weight: 40.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN B 274 GLN B 316 ASN B 453 HIS A 231 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.234259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.148532 restraints weight = 10026.617| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 6.75 r_work: 0.2869 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11158 Z= 0.176 Angle : 0.663 10.727 15150 Z= 0.327 Chirality : 0.046 0.161 1696 Planarity : 0.005 0.062 2002 Dihedral : 5.638 48.957 1604 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.42 % Allowed : 22.92 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.17 (0.37), residues: 216 sheet: -0.48 (0.26), residues: 423 loop : -1.57 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 277 HIS 0.007 0.001 HIS B 293 PHE 0.014 0.002 PHE A 406 TYR 0.017 0.002 TYR A 789 ARG 0.006 0.000 ARG A 753 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 1) link_NAG-ASN : angle 2.46122 ( 3) link_BETA1-4 : bond 0.00473 ( 2) link_BETA1-4 : angle 1.90400 ( 6) hydrogen bonds : bond 0.03621 ( 308) hydrogen bonds : angle 5.72443 ( 873) SS BOND : bond 0.00182 ( 19) SS BOND : angle 1.30600 ( 38) covalent geometry : bond 0.00429 (11136) covalent geometry : angle 0.65888 (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 112 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 71 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7489 (mm) REVERT: B 290 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.7697 (t70) REVERT: B 321 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8309 (ptm-80) REVERT: B 387 ASN cc_start: 0.8165 (t0) cc_final: 0.7709 (m110) REVERT: B 396 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7604 (mm-30) REVERT: B 444 GLN cc_start: 0.7710 (tp40) cc_final: 0.7010 (tp40) REVERT: A 99 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8680 (ppp-140) REVERT: A 113 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.8071 (ttm170) REVERT: A 121 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8177 (mt-10) REVERT: A 145 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7630 (mp0) REVERT: A 149 ASP cc_start: 0.6227 (m-30) cc_final: 0.5871 (p0) REVERT: A 228 MET cc_start: 0.8780 (ttp) cc_final: 0.7889 (tpt) REVERT: A 493 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8675 (mp10) REVERT: A 498 GLU cc_start: 0.5979 (mm-30) cc_final: 0.5356 (tp30) REVERT: A 730 ASP cc_start: 0.7889 (t0) cc_final: 0.7561 (t0) REVERT: A 753 ARG cc_start: 0.7911 (ttm-80) cc_final: 0.7350 (mtt-85) REVERT: A 798 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7725 (p) outliers start: 41 outliers final: 29 residues processed: 108 average time/residue: 1.2041 time to fit residues: 141.4471 Evaluate side-chains 108 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 72 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 506 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 378 LEU 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 588 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 80 optimal weight: 20.0000 chunk 133 optimal weight: 40.0000 chunk 70 optimal weight: 5.9990 chunk 128 optimal weight: 50.0000 chunk 111 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN B 274 GLN B 316 ASN 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 = 0.4471 r_free = 0.4471 target = 0.234259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.148966 restraints weight = 9957.660| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 6.57 r_work: 0.2880 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11158 Z= 0.179 Angle : 0.667 11.632 15150 Z= 0.326 Chirality : 0.046 0.172 1696 Planarity : 0.005 0.046 2002 Dihedral : 5.537 48.917 1604 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.58 % Allowed : 23.00 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.37 (0.22), residues: 1411 helix: 0.38 (0.37), residues: 210 sheet: -0.41 (0.26), residues: 421 loop : -1.58 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 277 HIS 0.006 0.001 HIS B 293 PHE 0.025 0.002 PHE A 19 TYR 0.017 0.002 TYR A 789 ARG 0.007 0.000 ARG A 753 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 1) link_NAG-ASN : angle 2.34812 ( 3) link_BETA1-4 : bond 0.00488 ( 2) link_BETA1-4 : angle 1.86541 ( 6) hydrogen bonds : bond 0.03563 ( 308) hydrogen bonds : angle 5.63563 ( 873) SS BOND : bond 0.00202 ( 19) SS BOND : angle 1.28532 ( 38) covalent geometry : bond 0.00434 (11136) covalent geometry : angle 0.66350 (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 117 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 74 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 VAL cc_start: 0.7874 (t) cc_final: 0.7655 (t) REVERT: B 220 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7665 (mm) REVERT: B 290 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.7713 (t0) REVERT: B 321 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8271 (ptm-80) REVERT: B 387 ASN cc_start: 0.8167 (t0) cc_final: 0.7712 (m110) REVERT: B 396 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7544 (mm-30) REVERT: B 444 GLN cc_start: 0.7758 (tp40) cc_final: 0.7075 (tp40) REVERT: A 99 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8693 (ppp-140) REVERT: A 113 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8090 (ttm170) REVERT: A 121 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8130 (mt-10) REVERT: A 145 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7646 (mp0) REVERT: A 149 ASP cc_start: 0.6225 (m-30) cc_final: 0.5868 (p0) REVERT: A 228 MET cc_start: 0.8753 (ttp) cc_final: 0.7828 (tpt) REVERT: A 493 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8672 (mp10) REVERT: A 498 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5466 (tp30) REVERT: A 720 LEU cc_start: 0.3858 (OUTLIER) cc_final: 0.3492 (pp) REVERT: A 730 ASP cc_start: 0.7932 (t0) cc_final: 0.7484 (t0) REVERT: A 741 GLN cc_start: 0.6145 (OUTLIER) cc_final: 0.5889 (pm20) REVERT: A 753 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7403 (mtt-85) REVERT: A 798 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7708 (p) outliers start: 43 outliers final: 29 residues processed: 111 average time/residue: 1.1286 time to fit residues: 136.3821 Evaluate side-chains 111 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 72 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 294 THR Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 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 494 LYS Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 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 741 GLN Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 95 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 45 optimal weight: 50.0000 chunk 92 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN B 274 GLN B 316 ASN B 453 HIS A 227 ASN A 231 ASN A 574 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.234821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.151164 restraints weight = 9930.690| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 6.40 r_work: 0.2898 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11158 Z= 0.126 Angle : 0.628 11.922 15150 Z= 0.306 Chirality : 0.044 0.167 1696 Planarity : 0.004 0.046 2002 Dihedral : 5.339 48.917 1604 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.08 % Allowed : 23.50 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.28 (0.22), residues: 1411 helix: 0.52 (0.37), residues: 210 sheet: -0.37 (0.26), residues: 425 loop : -1.54 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 277 HIS 0.004 0.001 HIS B 293 PHE 0.012 0.001 PHE A 577 TYR 0.017 0.002 TYR A 789 ARG 0.007 0.000 ARG A 753 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 1) link_NAG-ASN : angle 2.02493 ( 3) link_BETA1-4 : bond 0.00612 ( 2) link_BETA1-4 : angle 1.71021 ( 6) hydrogen bonds : bond 0.03161 ( 308) hydrogen bonds : angle 5.44662 ( 873) SS BOND : bond 0.00172 ( 19) SS BOND : angle 1.15589 ( 38) covalent geometry : bond 0.00299 (11136) covalent geometry : angle 0.62490 (15103) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8094.73 seconds wall clock time: 139 minutes 44.51 seconds (8384.51 seconds total)