Starting phenix.real_space_refine on Fri Sep 11 12:37:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/27oa_81298/09_2026/27oa_81298.cif Found real_map, /net/cci-nas-00/data/ceres_data/27oa_81298/09_2026/27oa_81298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/27oa_81298/09_2026/27oa_81298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/27oa_81298/09_2026/27oa_81298.map" model { file = "/net/cci-nas-00/data/ceres_data/27oa_81298/09_2026/27oa_81298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/27oa_81298/09_2026/27oa_81298.cif" } resolution = 3.55 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= 0.002 sd= 0.057 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: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 5749 2.51 5 N 1507 2.21 5 O 1751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9042 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 7264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 7264 Classifications: {'peptide': 901} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 860} Chain: "C" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1568 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.89, per 1000 atoms: 0.21 Number of scatterers: 9042 At special positions: 0 Unit cell: (103.32, 98.4, 119.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1751 8.00 N 1507 7.00 C 5749 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 754 " - pdb=" SG CYS B 761 " distance=2.03 Simple disulfide: pdb=" SG CYS B 791 " - pdb=" SG CYS B 827 " distance=2.04 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 396 " distance=2.03 Simple disulfide: pdb=" SG CYS C 414 " - pdb=" SG CYS C 467 " distance=2.03 Simple disulfide: pdb=" SG CYS C 426 " - pdb=" SG CYS C 571 " distance=2.03 Simple disulfide: pdb=" SG CYS C 495 " - pdb=" SG CYS C 515 " 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 A 1 " - " NAG A 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A 1 " - " ASN B 100 " " NAG B1001 " - " ASN B 122 " " NAG B1002 " - " ASN B 324 " " NAG B1003 " - " ASN B 732 " " NAG B1004 " - " ASN B 811 " " NAG C 601 " - " ASN C 387 " " NAG D 1 " - " ASN B 225 " " NAG E 1 " - " ASN B 362 " " NAG F 1 " - " ASN B 618 " " NAG G 1 " - " ASN B 595 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 263.7 milliseconds 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 13 sheets defined 46.8% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 207 through 211 removed outlier: 3.769A pdb=" N SER B 211 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 305 through 324 removed outlier: 3.547A pdb=" N LEU B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Proline residue: B 314 - end of helix Processing helix chain 'B' and resid 355 through 359 Processing helix chain 'B' and resid 366 through 387 removed outlier: 4.005A pdb=" N TRP B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 397 removed outlier: 3.730A pdb=" N ASP B 397 " --> pdb=" O TRP B 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 394 through 397' Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 403 through 417 Processing helix chain 'B' and resid 424 through 439 Processing helix chain 'B' and resid 449 through 453 Processing helix chain 'B' and resid 455 through 460 Processing helix chain 'B' and resid 464 through 482 removed outlier: 3.790A pdb=" N TYR B 468 " --> pdb=" O ASP B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 498 Processing helix chain 'B' and resid 504 through 519 removed outlier: 3.927A pdb=" N LEU B 508 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP B 509 " --> pdb=" O TYR B 505 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS B 519 " --> pdb=" O ALA B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 537 removed outlier: 3.678A pdb=" N TRP B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 574 removed outlier: 3.790A pdb=" N ASN B 573 " --> pdb=" O SER B 570 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR B 574 " --> pdb=" O PRO B 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 570 through 574' Processing helix chain 'B' and resid 603 through 606 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 628 through 642 Processing helix chain 'B' and resid 647 through 664 removed outlier: 3.643A pdb=" N ALA B 652 " --> pdb=" O VAL B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 676 removed outlier: 3.693A pdb=" N ALA B 672 " --> pdb=" O PRO B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 removed outlier: 3.791A pdb=" N GLN B 681 " --> pdb=" O PHE B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 703 Processing helix chain 'B' and resid 707 through 731 removed outlier: 3.633A pdb=" N MET B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 756 Processing helix chain 'B' and resid 758 through 775 Processing helix chain 'B' and resid 785 through 797 removed outlier: 3.908A pdb=" N CYS B 791 " --> pdb=" O SER B 787 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN B 792 " --> pdb=" O THR B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 812 removed outlier: 4.021A pdb=" N TRP B 802 " --> pdb=" O GLY B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 826 Processing helix chain 'B' and resid 830 through 841 Processing helix chain 'B' and resid 851 through 860 Processing helix chain 'B' and resid 865 through 876 removed outlier: 3.587A pdb=" N ALA B 869 " --> pdb=" O GLY B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 881 removed outlier: 3.824A pdb=" N LEU B 880 " --> pdb=" O ASN B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 890 No H-bonds generated for 'chain 'B' and resid 888 through 890' Processing helix chain 'B' and resid 891 through 899 removed outlier: 3.713A pdb=" N ILE B 895 " --> pdb=" O PHE B 891 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B 896 " --> pdb=" O SER B 892 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 897 " --> pdb=" O ASN B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 918 Processing helix chain 'B' and resid 923 through 925 No H-bonds generated for 'chain 'B' and resid 923 through 925' Processing helix chain 'B' and resid 926 through 959 Processing helix chain 'C' and resid 374 through 379 Processing helix chain 'C' and resid 399 through 407 removed outlier: 4.244A pdb=" N LEU C 403 " --> pdb=" O ASN C 399 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU C 406 " --> pdb=" O LYS C 402 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 424 Processing helix chain 'C' and resid 438 through 446 removed outlier: 5.024A pdb=" N SER C 443 " --> pdb=" O SER C 440 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 444 " --> pdb=" O MET C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 457 removed outlier: 4.756A pdb=" N SER C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 522 removed outlier: 3.699A pdb=" N ARG C 522 " --> pdb=" O GLY C 518 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 129 through 132 removed outlier: 3.714A pdb=" N GLY B 99 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 97 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE B 96 " --> pdb=" O PRO B 85 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU B 98 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU B 83 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN B 100 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 81 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR B 102 " --> pdb=" O TYR B 79 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR B 79 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG B 104 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 129 through 132 removed outlier: 3.714A pdb=" N GLY B 99 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 97 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE B 96 " --> pdb=" O PRO B 85 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU B 98 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU B 83 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN B 100 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 81 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR B 102 " --> pdb=" O TYR B 79 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR B 79 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG B 104 " --> pdb=" O HIS B 77 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LYS B 221 " --> pdb=" O GLU B 75 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N HIS B 77 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET B 266 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 113 through 117 removed outlier: 3.581A pdb=" N ILE B 116 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 184 Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 189 Processing sheet with id=AA6, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AA7, first strand: chain 'B' and resid 279 through 284 removed outlier: 6.574A pdb=" N GLN B 290 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N GLN B 334 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG B 292 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N GLY B 336 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N TRP B 294 " --> pdb=" O GLY B 336 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 390 through 392 removed outlier: 6.555A pdb=" N THR B 391 " --> pdb=" O THR B 503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 599 through 601 removed outlier: 7.806A pdb=" N ASN B 626 " --> pdb=" O PRO B 542 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE B 544 " --> pdb=" O ASN B 626 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 587 through 588 Processing sheet with id=AB2, first strand: chain 'C' and resid 389 through 393 removed outlier: 3.871A pdb=" N SER C 389 " --> pdb=" O TRP C 434 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP C 434 " --> pdb=" O SER C 389 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 396 through 398 removed outlier: 4.018A pdb=" N CYS C 571 " --> pdb=" O CYS C 396 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N THR C 562 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 490 through 494 removed outlier: 5.744A pdb=" N GLY C 541 " --> pdb=" O SER C 493 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 536 " --> pdb=" O PHE C 533 " (cutoff:3.500A) 415 hydrogen bonds defined for protein. 1158 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: 1.75 Time building geometry restraints manager: 1.10 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: 2901 1.34 - 1.46: 2059 1.46 - 1.58: 4249 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 9265 Sorted by residual: bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.86e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.67e+00 bond pdb=" C1 NAG B1004 " pdb=" O5 NAG B1004 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" C1 NAG B1003 " pdb=" O5 NAG B1003 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.06e+00 ... (remaining 9260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 12260 1.65 - 3.31: 320 3.31 - 4.96: 35 4.96 - 6.62: 4 6.62 - 8.27: 3 Bond angle restraints: 12622 Sorted by residual: angle pdb=" C GLN B 204 " pdb=" N ALA B 205 " pdb=" CA ALA B 205 " ideal model delta sigma weight residual 121.54 128.18 -6.64 1.91e+00 2.74e-01 1.21e+01 angle pdb=" N PHE B 173 " pdb=" CA PHE B 173 " pdb=" C PHE B 173 " ideal model delta sigma weight residual 108.34 112.65 -4.31 1.31e+00 5.83e-01 1.08e+01 angle pdb=" C VAL B 566 " pdb=" N THR B 567 " pdb=" CA THR B 567 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C LEU B 400 " pdb=" N ASN B 401 " pdb=" CA ASN B 401 " ideal model delta sigma weight residual 121.54 127.27 -5.73 1.91e+00 2.74e-01 9.00e+00 angle pdb=" CA TRP B 832 " pdb=" CB TRP B 832 " pdb=" CG TRP B 832 " ideal model delta sigma weight residual 113.60 118.92 -5.32 1.90e+00 2.77e-01 7.84e+00 ... (remaining 12617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 4840 17.33 - 34.65: 642 34.65 - 51.98: 170 51.98 - 69.30: 45 69.30 - 86.63: 10 Dihedral angle restraints: 5707 sinusoidal: 2448 harmonic: 3259 Sorted by residual: dihedral pdb=" CA TRP B 399 " pdb=" C TRP B 399 " pdb=" N LEU B 400 " pdb=" CA LEU B 400 " ideal model delta harmonic sigma weight residual 180.00 154.68 25.32 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ASN B 811 " pdb=" C ASN B 811 " pdb=" N ALA B 812 " pdb=" CA ALA B 812 " ideal model delta harmonic sigma weight residual -180.00 -158.12 -21.88 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CB CYS C 495 " pdb=" SG CYS C 495 " pdb=" SG CYS C 515 " pdb=" CB CYS C 515 " ideal model delta sinusoidal sigma weight residual 93.00 127.66 -34.66 1 1.00e+01 1.00e-02 1.70e+01 ... (remaining 5704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1380 0.097 - 0.194: 55 0.194 - 0.291: 1 0.291 - 0.389: 1 0.389 - 0.486: 1 Chirality restraints: 1438 Sorted by residual: chirality pdb=" C1 NAG B1004 " pdb=" ND2 ASN B 811 " pdb=" C2 NAG B1004 " pdb=" O5 NAG B1004 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.90e+00 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C4 NAG A 1 " pdb=" C3 NAG A 1 " pdb=" C5 NAG A 1 " pdb=" O4 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.31 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1435 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 811 " -0.001 2.00e-02 2.50e+03 2.43e-02 7.35e+00 pdb=" CG ASN B 811 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN B 811 " -0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN B 811 " 0.031 2.00e-02 2.50e+03 pdb=" C1 NAG B1004 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 944 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C VAL B 944 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL B 944 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN B 945 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 313 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO B 314 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 314 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 314 " 0.030 5.00e-02 4.00e+02 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 721 2.74 - 3.28: 8954 3.28 - 3.82: 14956 3.82 - 4.36: 17656 4.36 - 4.90: 31479 Nonbonded interactions: 73766 Sorted by model distance: nonbonded pdb=" O PHE B 726 " pdb=" OG1 THR B 730 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP B 703 " pdb=" NH1 ARG B 901 " model vdw 2.218 3.120 nonbonded pdb=" O LEU B 309 " pdb=" OH TYR C 539 " model vdw 2.275 3.040 nonbonded pdb=" O SER C 428 " pdb=" OG1 THR C 569 " model vdw 2.278 3.040 nonbonded pdb=" NZ LYS B 331 " pdb=" OD2 ASP B 333 " model vdw 2.294 3.120 ... (remaining 73761 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 group one per residue 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: 4.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.600 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 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 : 0.004 0.063 9286 Z= 0.174 Angle : 0.661 18.348 12679 Z= 0.332 Chirality : 0.046 0.486 1438 Planarity : 0.004 0.057 1607 Dihedral : 16.856 86.631 3581 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.84 % Favored : 93.80 % Rotamer: Outliers : 0.21 % Allowed : 24.97 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.25), residues: 1096 helix: 0.21 (0.25), residues: 448 sheet: -0.51 (0.40), residues: 181 loop : -1.61 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 476 TYR 0.014 0.001 TYR B 592 PHE 0.022 0.001 PHE B 481 TRP 0.007 0.001 TRP B 385 HIS 0.004 0.001 HIS B 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 ( 9265) covalent geometry : angle 0.60427 / 0.32 (12622) SS BOND : bond 0.00333 / 0.16 ( 6) SS BOND : angle 1.45502 / 1.42 ( 12) hydrogen bonds : bond 0.18467 / 12.26 ( 400) hydrogen bonds : angle 6.84695 / 4.70 ( 1158) link_BETA1-4 : bond 0.01674 / 0.88 ( 5) link_BETA1-4 : angle 4.99642 / 3.19 ( 15) link_NAG-ASN : bond 0.00769 / 0.47 ( 10) link_NAG-ASN : angle 4.18028 / 2.75 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 202 time to evaluate : 0.352 Fit side-chains REVERT: B 254 ASN cc_start: 0.8092 (m-40) cc_final: 0.7858 (t0) REVERT: B 565 ASN cc_start: 0.7589 (m-40) cc_final: 0.7262 (t0) REVERT: B 854 SER cc_start: 0.8858 (t) cc_final: 0.8620 (m) REVERT: B 921 ILE cc_start: 0.7502 (pt) cc_final: 0.7279 (mp) REVERT: C 399 ASN cc_start: 0.4709 (p0) cc_final: 0.4454 (p0) REVERT: C 416 LYS cc_start: 0.8038 (mtmt) cc_final: 0.7695 (mtmt) REVERT: C 481 MET cc_start: 0.7026 (pmm) cc_final: 0.6727 (mmm) outliers start: 2 outliers final: 0 residues processed: 202 average time/residue: 0.0967 time to fit residues: 27.1852 Evaluate side-chains 118 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 HIS B 159 ASN ** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN B 629 GLN ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 940 ASN C 380 ASN C 460 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.114880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.092389 restraints weight = 13514.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.095141 restraints weight = 7723.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.097019 restraints weight = 5218.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.098239 restraints weight = 3921.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.099164 restraints weight = 3216.418| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9286 Z= 0.272 Angle : 0.767 17.618 12679 Z= 0.386 Chirality : 0.050 0.461 1438 Planarity : 0.006 0.073 1607 Dihedral : 6.663 59.805 1512 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.76 % Favored : 91.79 % Rotamer: Outliers : 5.86 % Allowed : 21.07 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.25), residues: 1096 helix: 0.19 (0.25), residues: 455 sheet: -0.98 (0.38), residues: 187 loop : -1.84 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 390 TYR 0.019 0.002 TYR B 468 PHE 0.026 0.002 PHE B 105 TRP 0.025 0.002 TRP B 832 HIS 0.008 0.002 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.27 ( 9265) covalent geometry : angle 0.72286 / 0.38 (12622) SS BOND : bond 0.00401 / 0.18 ( 6) SS BOND : angle 1.19702 / 0.65 ( 12) hydrogen bonds : bond 0.07292 / 4.65 ( 400) hydrogen bonds : angle 5.57182 / 3.85 ( 1158) link_BETA1-4 : bond 0.01778 / 0.93 ( 5) link_BETA1-4 : angle 4.70642 / 3.03 ( 15) link_NAG-ASN : bond 0.00599 / 0.37 ( 10) link_NAG-ASN : angle 4.10564 / 2.68 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 123 time to evaluate : 0.351 Fit side-chains REVERT: B 74 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8650 (mt) REVERT: B 75 GLU cc_start: 0.8170 (pt0) cc_final: 0.7898 (pt0) REVERT: B 254 ASN cc_start: 0.8308 (m-40) cc_final: 0.7757 (t0) REVERT: B 555 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.7012 (pp30) REVERT: B 565 ASN cc_start: 0.7691 (m-40) cc_final: 0.7411 (t0) REVERT: B 684 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6501 (tt0) REVERT: B 854 SER cc_start: 0.8813 (t) cc_final: 0.8489 (m) REVERT: B 921 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7366 (mp) REVERT: C 555 MET cc_start: 0.7739 (tpp) cc_final: 0.7081 (mmp) outliers start: 57 outliers final: 31 residues processed: 169 average time/residue: 0.0773 time to fit residues: 19.6197 Evaluate side-chains 136 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 787 SER Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 889 PHE Chi-restraints excluded: chain B residue 895 ILE Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 499 ASP Chi-restraints excluded: chain C residue 560 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.1980 chunk 101 optimal weight: 0.0370 chunk 84 optimal weight: 0.8980 chunk 52 optimal weight: 0.0270 chunk 107 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 HIS B 253 ASN B 369 ASN B 557 HIS ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.121049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.099490 restraints weight = 13247.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.102139 restraints weight = 7702.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.103969 restraints weight = 5242.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.105066 restraints weight = 3965.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.105969 restraints weight = 3256.467| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9286 Z= 0.134 Angle : 0.636 16.776 12679 Z= 0.320 Chirality : 0.046 0.423 1438 Planarity : 0.005 0.052 1607 Dihedral : 6.278 57.399 1512 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.57 % Favored : 93.98 % Rotamer: Outliers : 4.01 % Allowed : 22.30 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.25), residues: 1096 helix: 0.37 (0.25), residues: 450 sheet: -0.83 (0.37), residues: 190 loop : -1.81 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 526 TYR 0.017 0.001 TYR C 491 PHE 0.023 0.001 PHE B 481 TRP 0.018 0.001 TRP B 832 HIS 0.003 0.001 HIS B 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 9265) covalent geometry : angle 0.59298 / 0.31 (12622) SS BOND : bond 0.00169 / 0.08 ( 6) SS BOND : angle 1.26321 / 0.66 ( 12) hydrogen bonds : bond 0.06012 / 3.86 ( 400) hydrogen bonds : angle 5.31739 / 3.68 ( 1158) link_BETA1-4 : bond 0.01666 / 0.88 ( 5) link_BETA1-4 : angle 4.57984 / 2.93 ( 15) link_NAG-ASN : bond 0.00932 / 0.51 ( 10) link_NAG-ASN : angle 3.41401 / 2.24 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.339 Fit side-chains REVERT: B 94 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8658 (pp) REVERT: B 254 ASN cc_start: 0.8165 (m-40) cc_final: 0.7712 (t0) REVERT: B 309 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7867 (tt) REVERT: B 565 ASN cc_start: 0.7630 (m-40) cc_final: 0.7405 (t0) REVERT: B 718 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6571 (mt0) REVERT: B 854 SER cc_start: 0.8802 (t) cc_final: 0.8509 (m) REVERT: C 390 ARG cc_start: 0.8786 (ttm110) cc_final: 0.8572 (ttm110) REVERT: C 457 ASN cc_start: 0.8564 (m-40) cc_final: 0.8130 (m-40) REVERT: C 555 MET cc_start: 0.7730 (tpp) cc_final: 0.7172 (mmp) outliers start: 39 outliers final: 23 residues processed: 163 average time/residue: 0.0819 time to fit residues: 19.9666 Evaluate side-chains 142 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 840 TYR Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 889 PHE Chi-restraints excluded: chain B residue 895 ILE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 499 ASP Chi-restraints excluded: chain C residue 560 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 104 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 HIS ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.119896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.098652 restraints weight = 13517.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.101272 restraints weight = 7840.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.103034 restraints weight = 5309.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.104216 restraints weight = 4026.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.105114 restraints weight = 3272.784| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9286 Z= 0.138 Angle : 0.622 17.093 12679 Z= 0.313 Chirality : 0.046 0.423 1438 Planarity : 0.005 0.070 1607 Dihedral : 6.026 55.884 1512 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.84 % Favored : 93.70 % Rotamer: Outliers : 5.34 % Allowed : 22.51 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.25), residues: 1096 helix: 0.52 (0.25), residues: 448 sheet: -0.81 (0.38), residues: 185 loop : -1.83 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 900 TYR 0.018 0.001 TYR C 491 PHE 0.024 0.001 PHE B 481 TRP 0.017 0.001 TRP B 832 HIS 0.003 0.001 HIS B 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 9265) covalent geometry : angle 0.57876 / 0.30 (12622) SS BOND : bond 0.00262 / 0.13 ( 6) SS BOND : angle 1.27011 / 0.66 ( 12) hydrogen bonds : bond 0.05801 / 3.69 ( 400) hydrogen bonds : angle 5.19687 / 3.61 ( 1158) link_BETA1-4 : bond 0.01710 / 0.90 ( 5) link_BETA1-4 : angle 4.57528 / 2.94 ( 15) link_NAG-ASN : bond 0.00745 / 0.42 ( 10) link_NAG-ASN : angle 3.38839 / 2.22 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 122 time to evaluate : 0.268 Fit side-chains REVERT: B 94 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8643 (pp) REVERT: B 254 ASN cc_start: 0.8239 (m-40) cc_final: 0.7706 (t0) REVERT: B 309 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7882 (tt) REVERT: B 544 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8306 (mm) REVERT: B 555 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.6920 (pp30) REVERT: B 565 ASN cc_start: 0.7688 (m-40) cc_final: 0.7442 (t0) REVERT: B 718 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6544 (mt0) REVERT: B 854 SER cc_start: 0.8830 (t) cc_final: 0.8526 (m) REVERT: C 390 ARG cc_start: 0.8757 (ttm110) cc_final: 0.8327 (ttm110) REVERT: C 433 ASP cc_start: 0.7727 (m-30) cc_final: 0.7419 (m-30) REVERT: C 555 MET cc_start: 0.7701 (tpp) cc_final: 0.7466 (tpp) outliers start: 52 outliers final: 32 residues processed: 167 average time/residue: 0.0754 time to fit residues: 19.0482 Evaluate side-chains 150 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 889 PHE Chi-restraints excluded: chain B residue 895 ILE Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 499 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 62 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 chunk 88 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.118572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.097696 restraints weight = 13359.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.100105 restraints weight = 8017.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.101836 restraints weight = 5583.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.102941 restraints weight = 4252.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.103808 restraints weight = 3488.163| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9286 Z= 0.166 Angle : 0.659 16.967 12679 Z= 0.328 Chirality : 0.048 0.559 1438 Planarity : 0.005 0.062 1607 Dihedral : 5.849 55.898 1512 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.20 % Favored : 94.34 % Rotamer: Outliers : 6.37 % Allowed : 21.69 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.25), residues: 1096 helix: 0.54 (0.25), residues: 446 sheet: -0.93 (0.37), residues: 186 loop : -1.83 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 900 TYR 0.019 0.001 TYR B 468 PHE 0.024 0.001 PHE B 481 TRP 0.018 0.001 TRP B 832 HIS 0.005 0.001 HIS B 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 9265) covalent geometry : angle 0.61168 / 0.32 (12622) SS BOND : bond 0.00493 / 0.24 ( 6) SS BOND : angle 1.55027 / 0.98 ( 12) hydrogen bonds : bond 0.06071 / 3.86 ( 400) hydrogen bonds : angle 5.13996 / 3.58 ( 1158) link_BETA1-4 : bond 0.01604 / 0.84 ( 5) link_BETA1-4 : angle 4.55744 / 2.93 ( 15) link_NAG-ASN : bond 0.00861 / 0.47 ( 10) link_NAG-ASN : angle 3.85500 / 2.48 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 115 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: B 94 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8683 (pp) REVERT: B 195 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8289 (tttm) REVERT: B 254 ASN cc_start: 0.8251 (m-40) cc_final: 0.7738 (t0) REVERT: B 309 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8077 (tt) REVERT: B 544 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8394 (mm) REVERT: B 555 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.6965 (pp30) REVERT: B 565 ASN cc_start: 0.7731 (m-40) cc_final: 0.7484 (t0) REVERT: B 718 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6770 (mt0) REVERT: B 788 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8557 (p) REVERT: B 854 SER cc_start: 0.8788 (t) cc_final: 0.8538 (m) REVERT: C 520 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8416 (mp) REVERT: C 555 MET cc_start: 0.7664 (tpp) cc_final: 0.7450 (tpp) outliers start: 62 outliers final: 38 residues processed: 169 average time/residue: 0.0814 time to fit residues: 20.7490 Evaluate side-chains 160 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 114 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 787 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 840 TYR Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 889 PHE Chi-restraints excluded: chain B residue 895 ILE Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 499 ASP Chi-restraints excluded: chain C residue 520 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 0.0010 chunk 88 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.098958 restraints weight = 13333.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.101573 restraints weight = 7820.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.103326 restraints weight = 5342.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.104598 restraints weight = 4036.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.105354 restraints weight = 3266.957| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9286 Z= 0.131 Angle : 0.625 16.933 12679 Z= 0.312 Chirality : 0.046 0.406 1438 Planarity : 0.004 0.057 1607 Dihedral : 5.526 55.316 1512 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.38 % Favored : 94.16 % Rotamer: Outliers : 5.55 % Allowed : 22.40 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.25), residues: 1096 helix: 0.62 (0.25), residues: 446 sheet: -0.91 (0.37), residues: 189 loop : -1.86 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 900 TYR 0.020 0.001 TYR B 468 PHE 0.023 0.001 PHE B 481 TRP 0.018 0.001 TRP B 832 HIS 0.003 0.001 HIS B 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 9265) covalent geometry : angle 0.57802 / 0.30 (12622) SS BOND : bond 0.00380 / 0.19 ( 6) SS BOND : angle 1.55705 / 0.93 ( 12) hydrogen bonds : bond 0.05642 / 3.59 ( 400) hydrogen bonds : angle 5.10675 / 3.56 ( 1158) link_BETA1-4 : bond 0.01705 / 0.90 ( 5) link_BETA1-4 : angle 4.53556 / 2.92 ( 15) link_NAG-ASN : bond 0.00670 / 0.39 ( 10) link_NAG-ASN : angle 3.63082 / 2.29 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 119 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: B 195 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8165 (tttm) REVERT: B 254 ASN cc_start: 0.8169 (m-40) cc_final: 0.7737 (t0) REVERT: B 309 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8109 (tt) REVERT: B 544 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8352 (mm) REVERT: B 718 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6729 (mt0) REVERT: B 788 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8589 (p) REVERT: B 854 SER cc_start: 0.8772 (t) cc_final: 0.8557 (m) REVERT: C 390 ARG cc_start: 0.8573 (ttm110) cc_final: 0.7486 (ttm110) REVERT: C 520 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8398 (mp) REVERT: C 555 MET cc_start: 0.7661 (tpp) cc_final: 0.7454 (tpp) outliers start: 54 outliers final: 39 residues processed: 164 average time/residue: 0.0819 time to fit residues: 20.0070 Evaluate side-chains 160 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 115 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 591 HIS Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 787 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 840 TYR Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 889 PHE Chi-restraints excluded: chain B residue 895 ILE Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 499 ASP Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 569 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 chunk 39 optimal weight: 0.0170 chunk 21 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 388 ASN ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.131657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.113054 restraints weight = 12556.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.115264 restraints weight = 8009.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.116796 restraints weight = 5767.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.117797 restraints weight = 4495.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118578 restraints weight = 3732.729| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9286 Z= 0.133 Angle : 0.633 16.950 12679 Z= 0.316 Chirality : 0.046 0.403 1438 Planarity : 0.004 0.055 1607 Dihedral : 5.409 55.491 1512 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.02 % Favored : 94.43 % Rotamer: Outliers : 5.14 % Allowed : 24.05 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.99 (0.25), residues: 1096 helix: 0.65 (0.25), residues: 446 sheet: -0.92 (0.37), residues: 190 loop : -1.84 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 476 TYR 0.020 0.001 TYR B 468 PHE 0.025 0.001 PHE C 456 TRP 0.017 0.001 TRP B 832 HIS 0.004 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 9265) covalent geometry : angle 0.58746 / 0.31 (12622) SS BOND : bond 0.00310 / 0.15 ( 6) SS BOND : angle 1.36675 / 0.70 ( 12) hydrogen bonds : bond 0.05569 / 3.52 ( 400) hydrogen bonds : angle 5.06657 / 3.53 ( 1158) link_BETA1-4 : bond 0.01704 / 0.90 ( 5) link_BETA1-4 : angle 4.54066 / 2.92 ( 15) link_NAG-ASN : bond 0.00717 / 0.41 ( 10) link_NAG-ASN : angle 3.62006 / 2.27 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: B 195 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8143 (tttm) REVERT: B 254 ASN cc_start: 0.8279 (m-40) cc_final: 0.7698 (t0) REVERT: B 309 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7979 (tt) REVERT: B 544 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8198 (mm) REVERT: B 555 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.6964 (pp30) REVERT: B 788 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8560 (p) REVERT: B 854 SER cc_start: 0.8677 (t) cc_final: 0.8446 (m) REVERT: C 390 ARG cc_start: 0.8441 (ttm110) cc_final: 0.7337 (ttm110) REVERT: C 555 MET cc_start: 0.7603 (tpp) cc_final: 0.7372 (tpp) outliers start: 50 outliers final: 38 residues processed: 160 average time/residue: 0.0804 time to fit residues: 19.2885 Evaluate side-chains 157 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 591 HIS Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 840 TYR Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 889 PHE Chi-restraints excluded: chain B residue 895 ILE Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 499 ASP Chi-restraints excluded: chain C residue 569 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 104 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.110806 restraints weight = 12574.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.112969 restraints weight = 8076.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.114457 restraints weight = 5849.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.115451 restraints weight = 4595.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.116227 restraints weight = 3829.835| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9286 Z= 0.155 Angle : 0.649 16.988 12679 Z= 0.324 Chirality : 0.047 0.402 1438 Planarity : 0.004 0.055 1607 Dihedral : 5.412 55.679 1512 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.29 % Favored : 94.25 % Rotamer: Outliers : 5.45 % Allowed : 23.64 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.25), residues: 1096 helix: 0.64 (0.25), residues: 444 sheet: -1.00 (0.37), residues: 193 loop : -1.82 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 476 TYR 0.037 0.001 TYR B 697 PHE 0.025 0.001 PHE C 456 TRP 0.018 0.001 TRP B 832 HIS 0.004 0.001 HIS B 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 9265) covalent geometry : angle 0.60546 / 0.31 (12622) SS BOND : bond 0.00467 / 0.23 ( 6) SS BOND : angle 1.39630 / 0.73 ( 12) hydrogen bonds : bond 0.05880 / 3.69 ( 400) hydrogen bonds : angle 5.06903 / 3.54 ( 1158) link_BETA1-4 : bond 0.01694 / 0.89 ( 5) link_BETA1-4 : angle 4.54672 / 2.93 ( 15) link_NAG-ASN : bond 0.00677 / 0.39 ( 10) link_NAG-ASN : angle 3.59269 / 2.26 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 117 time to evaluate : 0.343 Fit side-chains REVERT: B 195 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8167 (tttm) REVERT: B 254 ASN cc_start: 0.8277 (m-40) cc_final: 0.7695 (t0) REVERT: B 309 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8059 (tt) REVERT: B 544 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8292 (mm) REVERT: B 555 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.6971 (pp30) REVERT: B 788 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8588 (p) REVERT: B 854 SER cc_start: 0.8659 (t) cc_final: 0.8443 (m) REVERT: C 390 ARG cc_start: 0.8440 (ttm110) cc_final: 0.7303 (ttm110) REVERT: C 520 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8414 (mp) REVERT: C 555 MET cc_start: 0.7600 (tpp) cc_final: 0.7363 (tpp) outliers start: 53 outliers final: 42 residues processed: 160 average time/residue: 0.0779 time to fit residues: 18.9279 Evaluate side-chains 159 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 111 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 591 HIS Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 787 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 889 PHE Chi-restraints excluded: chain B residue 895 ILE Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 499 ASP Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 569 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 58 optimal weight: 0.3980 chunk 101 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.119785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.100282 restraints weight = 13163.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.102481 restraints weight = 8090.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.104012 restraints weight = 5682.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.105045 restraints weight = 4378.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.105775 restraints weight = 3587.816| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9286 Z= 0.142 Angle : 0.687 21.798 12679 Z= 0.333 Chirality : 0.046 0.393 1438 Planarity : 0.004 0.053 1607 Dihedral : 5.599 55.332 1512 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.11 % Favored : 94.43 % Rotamer: Outliers : 5.65 % Allowed : 23.54 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.98 (0.25), residues: 1096 helix: 0.67 (0.25), residues: 445 sheet: -0.99 (0.37), residues: 194 loop : -1.81 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 476 TYR 0.038 0.001 TYR B 697 PHE 0.022 0.001 PHE B 481 TRP 0.019 0.001 TRP B 832 HIS 0.003 0.001 HIS B 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 9265) covalent geometry : angle 0.61413 / 0.32 (12622) SS BOND : bond 0.00321 / 0.16 ( 6) SS BOND : angle 1.43320 / 0.71 ( 12) hydrogen bonds : bond 0.05680 / 3.57 ( 400) hydrogen bonds : angle 5.07071 / 3.54 ( 1158) link_BETA1-4 : bond 0.01697 / 0.89 ( 5) link_BETA1-4 : angle 4.52034 / 2.91 ( 15) link_NAG-ASN : bond 0.00532 / 0.34 ( 10) link_NAG-ASN : angle 5.47399 / 4.06 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 113 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: B 195 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8128 (tttm) REVERT: B 254 ASN cc_start: 0.8275 (m-40) cc_final: 0.7709 (t0) REVERT: B 309 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8041 (tt) REVERT: B 355 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7947 (mt-10) REVERT: B 544 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8249 (mm) REVERT: B 555 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.6995 (pp30) REVERT: B 700 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8752 (tt) REVERT: B 788 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8578 (p) REVERT: B 854 SER cc_start: 0.8650 (t) cc_final: 0.8448 (m) REVERT: C 390 ARG cc_start: 0.8410 (ttm110) cc_final: 0.7483 (ttm110) REVERT: C 520 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8400 (mp) REVERT: C 555 MET cc_start: 0.7611 (tpp) cc_final: 0.7379 (tpp) outliers start: 55 outliers final: 43 residues processed: 159 average time/residue: 0.0786 time to fit residues: 18.9348 Evaluate side-chains 163 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 113 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 591 HIS Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 787 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 840 TYR Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 889 PHE Chi-restraints excluded: chain B residue 895 ILE Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 499 ASP Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 569 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 0.0570 chunk 45 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 589 GLN ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.124056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.103414 restraints weight = 12921.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105952 restraints weight = 7833.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.107669 restraints weight = 5453.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.108887 restraints weight = 4167.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.109751 restraints weight = 3394.703| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9286 Z= 0.130 Angle : 0.651 16.841 12679 Z= 0.321 Chirality : 0.045 0.384 1438 Planarity : 0.004 0.051 1607 Dihedral : 5.391 55.376 1512 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.02 % Favored : 94.53 % Rotamer: Outliers : 5.04 % Allowed : 24.05 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.25), residues: 1096 helix: 0.72 (0.25), residues: 445 sheet: -0.90 (0.37), residues: 193 loop : -1.82 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 624 TYR 0.017 0.001 TYR C 491 PHE 0.020 0.001 PHE B 481 TRP 0.017 0.001 TRP B 832 HIS 0.003 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 ( 9265) covalent geometry : angle 0.59941 / 0.31 (12622) SS BOND : bond 0.00267 / 0.13 ( 6) SS BOND : angle 1.39572 / 0.68 ( 12) hydrogen bonds : bond 0.05456 / 3.42 ( 400) hydrogen bonds : angle 5.02101 / 3.50 ( 1158) link_BETA1-4 : bond 0.01692 / 0.89 ( 5) link_BETA1-4 : angle 4.50930 / 2.90 ( 15) link_NAG-ASN : bond 0.00497 / 0.33 ( 10) link_NAG-ASN : angle 4.11664 / 2.90 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 114 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: B 195 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8071 (tttm) REVERT: B 254 ASN cc_start: 0.8276 (m-40) cc_final: 0.7703 (t0) REVERT: B 309 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7996 (tt) REVERT: B 544 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8171 (mm) REVERT: B 555 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.6981 (pp30) REVERT: B 788 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8560 (p) REVERT: C 390 ARG cc_start: 0.8498 (ttm110) cc_final: 0.7089 (ttm110) REVERT: C 433 ASP cc_start: 0.8139 (m-30) cc_final: 0.7892 (m-30) REVERT: C 520 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8367 (mp) REVERT: C 555 MET cc_start: 0.7583 (tpp) cc_final: 0.7329 (tpp) outliers start: 49 outliers final: 37 residues processed: 155 average time/residue: 0.0775 time to fit residues: 18.2108 Evaluate side-chains 153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 110 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 591 HIS Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 787 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 889 PHE Chi-restraints excluded: chain B residue 895 ILE Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 499 ASP Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 573 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 98 optimal weight: 0.0770 chunk 75 optimal weight: 4.9990 chunk 74 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.122613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.102124 restraints weight = 12857.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.104623 restraints weight = 7813.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.106339 restraints weight = 5447.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.107381 restraints weight = 4179.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.108296 restraints weight = 3456.001| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9286 Z= 0.138 Angle : 0.651 16.891 12679 Z= 0.323 Chirality : 0.045 0.383 1438 Planarity : 0.004 0.052 1607 Dihedral : 5.341 55.491 1512 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.29 % Favored : 94.25 % Rotamer: Outliers : 4.62 % Allowed : 24.67 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.95 (0.25), residues: 1096 helix: 0.70 (0.25), residues: 445 sheet: -0.96 (0.37), residues: 194 loop : -1.81 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 476 TYR 0.033 0.001 TYR B 697 PHE 0.021 0.001 PHE B 481 TRP 0.016 0.001 TRP B 832 HIS 0.003 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 9265) covalent geometry : angle 0.60436 / 0.31 (12622) SS BOND : bond 0.00343 / 0.16 ( 6) SS BOND : angle 1.36122 / 0.66 ( 12) hydrogen bonds : bond 0.05524 / 3.47 ( 400) hydrogen bonds : angle 5.01467 / 3.49 ( 1158) link_BETA1-4 : bond 0.01706 / 0.90 ( 5) link_BETA1-4 : angle 4.52079 / 2.91 ( 15) link_NAG-ASN : bond 0.00505 / 0.33 ( 10) link_NAG-ASN : angle 3.79814 / 2.66 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1644.91 seconds wall clock time: 29 minutes 13.51 seconds (1753.51 seconds total)