Starting phenix.real_space_refine on Thu Aug 6 08:46:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pnp_17782/08_2026/8pnp_17782.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pnp_17782/08_2026/8pnp_17782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pnp_17782/08_2026/8pnp_17782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pnp_17782/08_2026/8pnp_17782.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pnp_17782/08_2026/8pnp_17782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pnp_17782/08_2026/8pnp_17782.map" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 88 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 103 5.16 5 C 8978 2.51 5 N 2494 2.21 5 O 2854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14460 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 5748 Classifications: {'peptide': 708} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 675} Chain breaks: 1 Chain: "B" Number of atoms: 5850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5850 Classifications: {'peptide': 735} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 702} Chain breaks: 1 Chain: "C" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2024 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain: "V" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 616 Classifications: {'RNA': 29} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 12} Link IDs: {'rna2p': 7, 'rna3p': 21} Chain breaks: 1 Chain: "G" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 179 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 6, 'TRANS': 16} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "V" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.83, per 1000 atoms: 0.20 Number of scatterers: 14460 At special positions: 0 Unit cell: (94.08, 102.48, 144.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 103 16.00 P 31 15.00 O 2854 8.00 N 2494 7.00 C 8978 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 438.2 milliseconds 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3244 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 16 sheets defined 53.4% alpha, 12.6% beta 5 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 10 through 24 removed outlier: 3.712A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 139 removed outlier: 3.538A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 185 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.923A pdb=" N PHE A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 removed outlier: 3.676A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.503A pdb=" N SER A 409 " --> pdb=" O CYS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.765A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 529 through 538 Proline residue: A 534 - end of helix removed outlier: 3.860A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 582 through 601 removed outlier: 4.129A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 4.002A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 697 through 715 removed outlier: 3.547A pdb=" N LEU A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.690A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 removed outlier: 3.537A pdb=" N GLN B 115 " --> pdb=" O MET B 111 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.538A pdb=" N GLN B 124 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.532A pdb=" N GLU B 159 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 160 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 175 removed outlier: 3.639A pdb=" N ASP B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.751A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 294 removed outlier: 3.582A pdb=" N ASN B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER B 293 " --> pdb=" O MET B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.511A pdb=" N GLN B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.447A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 369 through 376 removed outlier: 4.159A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN B 375 " --> pdb=" O MET B 372 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 4.069A pdb=" N TYR B 380 " --> pdb=" O ASP B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 removed outlier: 3.519A pdb=" N THR B 417 " --> pdb=" O ASN B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 473 Processing helix chain 'B' and resid 505 through 512 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 672 through 678 removed outlier: 6.388A pdb=" N SER B 678 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 700 removed outlier: 4.150A pdb=" N LEU B 683 " --> pdb=" O GLN B 679 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 699 " --> pdb=" O LEU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 705 removed outlier: 3.818A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.535A pdb=" N ALA B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 756 removed outlier: 3.696A pdb=" N ARG B 755 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN B 756 " --> pdb=" O GLU B 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.958A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 24 through 32 removed outlier: 4.142A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 4.102A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.522A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 236 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.321A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.682A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE B 447 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 293 removed outlier: 7.334A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL A 557 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU A 549 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A 542 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 321 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLY A 546 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N GLU A 319 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N MET A 548 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N TRP A 317 " --> pdb=" O MET A 548 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293 removed outlier: 5.338A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 378 removed outlier: 5.908A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.725A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 244 removed outlier: 3.986A pdb=" N THR B 226 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB4, first strand: chain 'B' and resid 642 through 645 Processing sheet with id=AB5, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.514A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 129 through 135 removed outlier: 4.721A pdb=" N MET C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 145 708 hydrogen bonds defined for protein. 1938 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4412 1.33 - 1.46: 2337 1.46 - 1.58: 7783 1.58 - 1.70: 64 1.70 - 1.82: 177 Bond restraints: 14773 Sorted by residual: bond pdb=" N TYR G 1 " pdb=" CA TYR G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" CB GLU C 158 " pdb=" CG GLU C 158 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.29e-01 bond pdb=" C8 G V 43 " pdb=" N7 G V 43 " ideal model delta sigma weight residual 1.305 1.300 0.005 6.00e-03 2.78e+04 7.16e-01 ... (remaining 14768 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 19747 1.76 - 3.52: 283 3.52 - 5.28: 37 5.28 - 7.04: 3 7.04 - 8.79: 1 Bond angle restraints: 20071 Sorted by residual: angle pdb=" O4' A V 7 " pdb=" C1' A V 7 " pdb=" N9 A V 7 " ideal model delta sigma weight residual 108.20 111.31 -3.11 8.00e-01 1.56e+00 1.51e+01 angle pdb=" C2' A V 4 " pdb=" C1' A V 4 " pdb=" N9 A V 4 " ideal model delta sigma weight residual 112.00 115.46 -3.46 1.10e+00 8.26e-01 9.91e+00 angle pdb=" O5' G V 5 " pdb=" C5' G V 5 " pdb=" C4' G V 5 " ideal model delta sigma weight residual 109.40 111.81 -2.41 8.00e-01 1.56e+00 9.11e+00 angle pdb=" O5' C V 44 " pdb=" C5' C V 44 " pdb=" C4' C V 44 " ideal model delta sigma weight residual 109.40 111.81 -2.41 8.00e-01 1.56e+00 9.07e+00 angle pdb=" O5' U V 46 " pdb=" C5' U V 46 " pdb=" C4' U V 46 " ideal model delta sigma weight residual 109.40 111.79 -2.39 8.00e-01 1.56e+00 8.96e+00 ... (remaining 20066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 7700 17.77 - 35.54: 945 35.54 - 53.32: 300 53.32 - 71.09: 113 71.09 - 88.86: 30 Dihedral angle restraints: 9088 sinusoidal: 4079 harmonic: 5009 Sorted by residual: dihedral pdb=" CA ASP C 161 " pdb=" CB ASP C 161 " pdb=" CG ASP C 161 " pdb=" OD1 ASP C 161 " ideal model delta sinusoidal sigma weight residual -30.00 -88.13 58.13 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA VAL A 517 " pdb=" C VAL A 517 " pdb=" N VAL A 518 " pdb=" CA VAL A 518 " ideal model delta harmonic sigma weight residual 180.00 163.53 16.47 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB GLU B 78 " pdb=" CG GLU B 78 " pdb=" CD GLU B 78 " pdb=" OE1 GLU B 78 " ideal model delta sinusoidal sigma weight residual 0.00 -88.86 88.86 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 9085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1716 0.041 - 0.081: 356 0.081 - 0.122: 130 0.122 - 0.163: 11 0.163 - 0.204: 1 Chirality restraints: 2214 Sorted by residual: chirality pdb=" CB VAL B 719 " pdb=" CA VAL B 719 " pdb=" CG1 VAL B 719 " pdb=" CG2 VAL B 719 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C1' A V 4 " pdb=" O4' A V 4 " pdb=" C2' A V 4 " pdb=" N9 A V 4 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CA VAL B 368 " pdb=" N VAL B 368 " pdb=" C VAL B 368 " pdb=" CB VAL B 368 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 2211 not shown) Planarity restraints: 2479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.028 2.00e-02 2.50e+03 1.27e-02 4.41e+00 pdb=" N9 A V 4 " 0.029 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 4 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 495 " 0.173 9.50e-02 1.11e+02 7.77e-02 4.27e+00 pdb=" NE ARG A 495 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 495 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 495 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 495 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 587 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C GLN A 587 " -0.030 2.00e-02 2.50e+03 pdb=" O GLN A 587 " 0.011 2.00e-02 2.50e+03 pdb=" N SER A 588 " 0.010 2.00e-02 2.50e+03 ... (remaining 2476 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 154 2.60 - 3.17: 12369 3.17 - 3.75: 23475 3.75 - 4.32: 33810 4.32 - 4.90: 54368 Nonbonded interactions: 124176 Sorted by model distance: nonbonded pdb=" OD2 ASP B 522 " pdb=" OH TYR B 559 " model vdw 2.019 3.040 nonbonded pdb=" OP1 A V 6 " pdb=" O HOH V 101 " model vdw 2.085 3.040 nonbonded pdb=" OE1 GLU A 524 " pdb=" O HOH A 801 " model vdw 2.097 3.040 nonbonded pdb=" OE1 GLU A 610 " pdb=" ND2 ASN A 614 " model vdw 2.137 3.120 nonbonded pdb=" O MET C 11 " pdb=" NH1 ARG C 17 " model vdw 2.160 3.120 ... (remaining 124171 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.770 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 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 0.035 14773 Z= 0.131 Angle : 0.512 8.794 20071 Z= 0.284 Chirality : 0.038 0.204 2214 Planarity : 0.004 0.078 2479 Dihedral : 18.516 88.860 5844 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.24 % Favored : 97.70 % Rotamer: Outliers : 1.24 % Allowed : 22.64 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.21), residues: 1697 helix: 1.64 (0.19), residues: 807 sheet: -0.13 (0.38), residues: 190 loop : -0.42 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 495 TYR 0.016 0.001 TYR A 305 PHE 0.010 0.001 PHE B 551 TRP 0.007 0.001 TRP A 88 HIS 0.002 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (14773) covalent geometry : angle 0.51233 / 0.28 (20071) hydrogen bonds : bond 0.13634 / 8.96 ( 717) hydrogen bonds : angle 6.04576 / 4.26 ( 1964) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 116 ARG cc_start: 0.6162 (ppt90) cc_final: 0.5523 (ppt90) REVERT: A 222 ASN cc_start: 0.8401 (p0) cc_final: 0.8171 (p0) REVERT: B 135 ARG cc_start: 0.8199 (ptp-110) cc_final: 0.7947 (ptt90) REVERT: B 653 LYS cc_start: 0.8365 (mtmm) cc_final: 0.7958 (mmtm) REVERT: C 146 ASP cc_start: 0.7066 (p0) cc_final: 0.6617 (p0) outliers start: 19 outliers final: 15 residues processed: 203 average time/residue: 0.5992 time to fit residues: 132.4177 Evaluate side-chains 200 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 21 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0010 chunk 149 optimal weight: 0.7980 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS A 388 ASN A 466 ASN A 513 ASN A 556 GLN A 670 GLN B 485 ASN C 82 ASN C 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.133577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.097173 restraints weight = 17421.977| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.59 r_work: 0.2978 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9166 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14773 Z= 0.165 Angle : 0.563 8.317 20071 Z= 0.297 Chirality : 0.042 0.147 2214 Planarity : 0.004 0.046 2479 Dihedral : 10.836 74.087 2343 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.30 % Favored : 97.64 % Rotamer: Outliers : 3.08 % Allowed : 20.09 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1697 helix: 1.57 (0.18), residues: 822 sheet: 0.16 (0.39), residues: 178 loop : -0.56 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 495 TYR 0.014 0.002 TYR B 555 PHE 0.013 0.001 PHE A 611 TRP 0.020 0.002 TRP A 188 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (14773) covalent geometry : angle 0.56282 / 0.30 (20071) hydrogen bonds : bond 0.05205 / 3.47 ( 717) hydrogen bonds : angle 4.82573 / 3.42 ( 1964) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 0.455 Fit side-chains REVERT: A 222 ASN cc_start: 0.8451 (p0) cc_final: 0.8175 (p0) REVERT: B 75 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8224 (mm-30) REVERT: B 331 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: C 64 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8063 (mmt) outliers start: 47 outliers final: 16 residues processed: 226 average time/residue: 0.5859 time to fit residues: 143.6150 Evaluate side-chains 202 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 14 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 25 optimal weight: 0.0060 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS A 74 HIS A 388 ASN A 556 GLN B 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.135196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099528 restraints weight = 17693.739| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.57 r_work: 0.2989 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14773 Z= 0.127 Angle : 0.509 7.448 20071 Z= 0.269 Chirality : 0.039 0.149 2214 Planarity : 0.004 0.052 2479 Dihedral : 10.593 73.786 2328 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.58 % Rotamer: Outliers : 2.42 % Allowed : 20.94 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.20), residues: 1697 helix: 1.70 (0.19), residues: 815 sheet: 0.23 (0.39), residues: 178 loop : -0.55 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 727 TYR 0.017 0.001 TYR A 305 PHE 0.010 0.001 PHE C 119 TRP 0.009 0.001 TRP B 438 HIS 0.003 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (14773) covalent geometry : angle 0.50866 / 0.27 (20071) hydrogen bonds : bond 0.04547 / 3.03 ( 717) hydrogen bonds : angle 4.62752 / 3.29 ( 1964) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 HIS cc_start: 0.6998 (OUTLIER) cc_final: 0.6670 (t-90) REVERT: A 222 ASN cc_start: 0.8408 (p0) cc_final: 0.8128 (p0) REVERT: B 75 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8238 (mm-30) REVERT: B 331 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: B 348 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8078 (mmm) REVERT: C 64 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.7739 (mmt) REVERT: G 21 SER cc_start: 0.9028 (p) cc_final: 0.8817 (t) outliers start: 37 outliers final: 14 residues processed: 217 average time/residue: 0.7759 time to fit residues: 182.1742 Evaluate side-chains 202 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 102 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS A 388 ASN A 556 GLN B 485 ASN C 13 GLN C 82 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.134615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.098578 restraints weight = 17578.233| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.62 r_work: 0.2973 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9156 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14773 Z= 0.141 Angle : 0.516 8.080 20071 Z= 0.271 Chirality : 0.040 0.158 2214 Planarity : 0.004 0.054 2479 Dihedral : 10.565 73.704 2325 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.59 % Favored : 97.35 % Rotamer: Outliers : 2.81 % Allowed : 20.94 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.20), residues: 1697 helix: 1.68 (0.19), residues: 815 sheet: 0.15 (0.38), residues: 186 loop : -0.56 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 269 TYR 0.018 0.001 TYR A 305 PHE 0.010 0.001 PHE A 520 TRP 0.010 0.001 TRP A 368 HIS 0.005 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (14773) covalent geometry : angle 0.51570 / 0.27 (20071) hydrogen bonds : bond 0.04612 / 3.07 ( 717) hydrogen bonds : angle 4.57310 / 3.26 ( 1964) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 HIS cc_start: 0.7385 (OUTLIER) cc_final: 0.6657 (t-90) REVERT: A 222 ASN cc_start: 0.8390 (p0) cc_final: 0.8101 (p0) REVERT: A 256 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7935 (ttm170) REVERT: B 75 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8206 (mm-30) REVERT: B 331 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: B 353 LYS cc_start: 0.9022 (mtpt) cc_final: 0.8789 (mtmm) REVERT: C 64 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.7769 (mmt) REVERT: C 90 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8112 (mmt) REVERT: G 21 SER cc_start: 0.9028 (OUTLIER) cc_final: 0.8821 (t) outliers start: 43 outliers final: 21 residues processed: 216 average time/residue: 0.6503 time to fit residues: 152.3276 Evaluate side-chains 209 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 21 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN A 556 GLN B 485 ASN C 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.132199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.096272 restraints weight = 17583.112| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.55 r_work: 0.2914 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9184 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14773 Z= 0.219 Angle : 0.586 9.285 20071 Z= 0.307 Chirality : 0.043 0.165 2214 Planarity : 0.005 0.053 2479 Dihedral : 10.700 73.563 2325 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.08 % Allowed : 21.14 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.20), residues: 1697 helix: 1.47 (0.18), residues: 822 sheet: -0.07 (0.37), residues: 194 loop : -0.68 (0.21), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 560 TYR 0.023 0.002 TYR A 305 PHE 0.015 0.002 PHE B 551 TRP 0.012 0.002 TRP A 368 HIS 0.005 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 (14773) covalent geometry : angle 0.58628 / 0.31 (20071) hydrogen bonds : bond 0.05500 / 3.66 ( 717) hydrogen bonds : angle 4.68872 / 3.35 ( 1964) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 74 HIS cc_start: 0.7368 (OUTLIER) cc_final: 0.6964 (t-90) REVERT: A 136 ASN cc_start: 0.5837 (OUTLIER) cc_final: 0.4426 (m110) REVERT: A 222 ASN cc_start: 0.8431 (p0) cc_final: 0.8153 (p0) REVERT: A 256 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.8004 (ttm170) REVERT: B 75 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8220 (mm-30) REVERT: B 135 ARG cc_start: 0.8519 (ptp-110) cc_final: 0.8093 (ptm-80) REVERT: B 331 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: B 353 LYS cc_start: 0.9148 (mtpt) cc_final: 0.8922 (mtmm) REVERT: B 744 MET cc_start: 0.7121 (mmm) cc_final: 0.6901 (mmt) REVERT: C 64 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8012 (mmt) REVERT: C 90 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8081 (mmt) REVERT: C 146 ASP cc_start: 0.8699 (p0) cc_final: 0.8138 (p0) outliers start: 47 outliers final: 23 residues processed: 217 average time/residue: 0.7264 time to fit residues: 170.6653 Evaluate side-chains 211 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain G residue 21 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 49 optimal weight: 0.9990 chunk 90 optimal weight: 0.0670 chunk 41 optimal weight: 0.0170 chunk 16 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN C 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.135059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.099179 restraints weight = 17723.719| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.59 r_work: 0.2971 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9150 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14773 Z= 0.116 Angle : 0.511 9.875 20071 Z= 0.268 Chirality : 0.039 0.162 2214 Planarity : 0.004 0.056 2479 Dihedral : 10.597 73.699 2325 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.36 % Allowed : 22.05 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.20), residues: 1697 helix: 1.64 (0.18), residues: 815 sheet: 0.26 (0.37), residues: 183 loop : -0.62 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 495 TYR 0.023 0.001 TYR A 305 PHE 0.011 0.001 PHE C 119 TRP 0.012 0.001 TRP A 368 HIS 0.002 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (14773) covalent geometry : angle 0.51147 / 0.27 (20071) hydrogen bonds : bond 0.04306 / 2.87 ( 717) hydrogen bonds : angle 4.52512 / 3.23 ( 1964) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 74 HIS cc_start: 0.7359 (OUTLIER) cc_final: 0.6962 (t-90) REVERT: A 222 ASN cc_start: 0.8392 (p0) cc_final: 0.8095 (p0) REVERT: A 256 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7910 (ttm170) REVERT: B 75 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8222 (mm-30) REVERT: B 331 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: B 353 LYS cc_start: 0.8994 (mtpt) cc_final: 0.8775 (mtmm) REVERT: B 642 ASN cc_start: 0.8656 (t0) cc_final: 0.8393 (t0) REVERT: C 64 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.7654 (mmt) REVERT: C 90 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8053 (mmt) REVERT: C 146 ASP cc_start: 0.8618 (p0) cc_final: 0.8022 (p0) outliers start: 36 outliers final: 18 residues processed: 210 average time/residue: 0.7438 time to fit residues: 169.2363 Evaluate side-chains 209 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 139 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 73 optimal weight: 0.0980 chunk 110 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN B 413 ASN C 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.134574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.099060 restraints weight = 17471.528| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.54 r_work: 0.2986 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14773 Z= 0.130 Angle : 0.522 10.025 20071 Z= 0.272 Chirality : 0.039 0.168 2214 Planarity : 0.004 0.054 2479 Dihedral : 10.576 73.654 2325 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.42 % Allowed : 21.99 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.20), residues: 1697 helix: 1.65 (0.18), residues: 815 sheet: 0.07 (0.37), residues: 192 loop : -0.58 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 495 TYR 0.021 0.001 TYR A 305 PHE 0.010 0.001 PHE A 520 TRP 0.011 0.001 TRP A 368 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (14773) covalent geometry : angle 0.52168 / 0.27 (20071) hydrogen bonds : bond 0.04416 / 2.94 ( 717) hydrogen bonds : angle 4.52191 / 3.23 ( 1964) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 74 HIS cc_start: 0.7367 (OUTLIER) cc_final: 0.6933 (t-90) REVERT: A 136 ASN cc_start: 0.5900 (OUTLIER) cc_final: 0.4465 (m110) REVERT: A 222 ASN cc_start: 0.8414 (p0) cc_final: 0.8116 (p0) REVERT: A 256 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7908 (ttm170) REVERT: A 495 ARG cc_start: 0.8485 (ptp-110) cc_final: 0.8279 (ptm160) REVERT: B 75 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8180 (mm-30) REVERT: B 331 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: B 353 LYS cc_start: 0.9052 (mtpt) cc_final: 0.8831 (mtmm) REVERT: C 64 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.7699 (mmt) REVERT: C 65 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8176 (pt0) REVERT: C 90 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8062 (mmt) REVERT: C 146 ASP cc_start: 0.8593 (p0) cc_final: 0.8010 (p0) outliers start: 37 outliers final: 22 residues processed: 214 average time/residue: 0.6389 time to fit residues: 148.0805 Evaluate side-chains 216 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 143 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 23 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 ASN A 388 ASN B 413 ASN B 642 ASN C 13 GLN C 82 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.134004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.097635 restraints weight = 17430.858| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.62 r_work: 0.2980 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9155 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14773 Z= 0.126 Angle : 0.527 11.501 20071 Z= 0.273 Chirality : 0.039 0.177 2214 Planarity : 0.004 0.054 2479 Dihedral : 10.555 73.622 2325 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.62 % Allowed : 21.86 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1697 helix: 1.65 (0.18), residues: 821 sheet: 0.08 (0.37), residues: 192 loop : -0.65 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 495 TYR 0.022 0.001 TYR A 305 PHE 0.010 0.001 PHE A 520 TRP 0.011 0.001 TRP A 368 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (14773) covalent geometry : angle 0.52711 / 0.27 (20071) hydrogen bonds : bond 0.04315 / 2.87 ( 717) hydrogen bonds : angle 4.48710 / 3.21 ( 1964) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 74 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.6909 (t-90) REVERT: A 222 ASN cc_start: 0.8411 (p0) cc_final: 0.8108 (p0) REVERT: A 256 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7898 (ttm170) REVERT: B 75 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8213 (mm-30) REVERT: B 156 THR cc_start: 0.8958 (p) cc_final: 0.8740 (p) REVERT: B 331 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: B 353 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8807 (mtmm) REVERT: C 65 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8185 (pt0) REVERT: C 90 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8063 (mmt) REVERT: C 146 ASP cc_start: 0.8605 (p0) cc_final: 0.7996 (p0) outliers start: 40 outliers final: 23 residues processed: 213 average time/residue: 0.6725 time to fit residues: 155.7247 Evaluate side-chains 216 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 26 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 ASN A 388 ASN A 614 ASN B 413 ASN C 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.134287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.098007 restraints weight = 17582.462| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.59 r_work: 0.2971 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9145 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14773 Z= 0.121 Angle : 0.532 12.047 20071 Z= 0.274 Chirality : 0.039 0.164 2214 Planarity : 0.004 0.054 2479 Dihedral : 10.532 73.624 2325 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.23 % Allowed : 21.99 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.20), residues: 1697 helix: 1.70 (0.18), residues: 815 sheet: 0.12 (0.37), residues: 192 loop : -0.55 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 287 TYR 0.029 0.001 TYR A 305 PHE 0.010 0.001 PHE A 520 TRP 0.011 0.001 TRP A 368 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (14773) covalent geometry : angle 0.53211 / 0.27 (20071) hydrogen bonds : bond 0.04209 / 2.80 ( 717) hydrogen bonds : angle 4.47113 / 3.19 ( 1964) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 136 ASN cc_start: 0.5945 (OUTLIER) cc_final: 0.4479 (m110) REVERT: A 182 MET cc_start: 0.3311 (ppp) cc_final: 0.2990 (pmt) REVERT: A 222 ASN cc_start: 0.8417 (p0) cc_final: 0.8115 (p0) REVERT: A 256 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7860 (ttm170) REVERT: B 75 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8198 (mm-30) REVERT: B 331 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: B 353 LYS cc_start: 0.8981 (mtpt) cc_final: 0.8761 (mtmm) REVERT: C 146 ASP cc_start: 0.8568 (p0) cc_final: 0.7962 (p0) outliers start: 34 outliers final: 20 residues processed: 210 average time/residue: 0.6926 time to fit residues: 157.0857 Evaluate side-chains 209 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 75 optimal weight: 0.9980 chunk 100 optimal weight: 0.2980 chunk 74 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 118 optimal weight: 0.0370 chunk 113 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 97 optimal weight: 0.3980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN A 350 ASN A 388 ASN B 413 ASN C 13 GLN C 82 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.135001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.098762 restraints weight = 17507.163| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.86 r_work: 0.2975 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9153 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14773 Z= 0.110 Angle : 0.528 12.398 20071 Z= 0.272 Chirality : 0.039 0.175 2214 Planarity : 0.004 0.054 2479 Dihedral : 10.492 73.632 2325 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.83 % Allowed : 22.64 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.20), residues: 1697 helix: 1.67 (0.18), residues: 821 sheet: 0.16 (0.37), residues: 192 loop : -0.61 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 287 TYR 0.013 0.001 TYR B 555 PHE 0.011 0.001 PHE B 333 TRP 0.011 0.001 TRP A 368 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (14773) covalent geometry : angle 0.52763 / 0.27 (20071) hydrogen bonds : bond 0.03987 / 2.66 ( 717) hydrogen bonds : angle 4.44133 / 3.17 ( 1964) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 74 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.6865 (t-90) REVERT: A 136 ASN cc_start: 0.5926 (OUTLIER) cc_final: 0.4441 (m110) REVERT: A 182 MET cc_start: 0.3277 (ppp) cc_final: 0.2959 (ppp) REVERT: A 222 ASN cc_start: 0.8451 (p0) cc_final: 0.8138 (p0) REVERT: A 256 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7873 (ttm170) REVERT: B 75 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8261 (mm-30) REVERT: B 331 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: B 353 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8767 (mtmm) REVERT: C 146 ASP cc_start: 0.8594 (p0) cc_final: 0.7983 (p0) outliers start: 28 outliers final: 21 residues processed: 207 average time/residue: 0.6612 time to fit residues: 148.4476 Evaluate side-chains 211 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 148 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 27 optimal weight: 3.9990 chunk 97 optimal weight: 0.0870 chunk 117 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 ASN A 388 ASN B 413 ASN B 485 ASN ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 82 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.132849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.095518 restraints weight = 17472.564| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.74 r_work: 0.2947 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9176 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14773 Z= 0.167 Angle : 0.573 12.674 20071 Z= 0.295 Chirality : 0.041 0.180 2214 Planarity : 0.004 0.053 2479 Dihedral : 10.575 73.472 2325 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.03 % Allowed : 22.71 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.20), residues: 1697 helix: 1.56 (0.18), residues: 822 sheet: 0.09 (0.37), residues: 192 loop : -0.61 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 495 TYR 0.028 0.002 TYR A 305 PHE 0.014 0.001 PHE B 551 TRP 0.012 0.002 TRP A 188 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (14773) covalent geometry : angle 0.57340 / 0.30 (20071) hydrogen bonds : bond 0.04748 / 3.16 ( 717) hydrogen bonds : angle 4.53657 / 3.25 ( 1964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5466.69 seconds wall clock time: 93 minutes 53.20 seconds (5633.20 seconds total)