Starting phenix.real_space_refine on Thu Jul 31 15:17:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t2v_40989/07_2025/8t2v_40989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t2v_40989/07_2025/8t2v_40989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t2v_40989/07_2025/8t2v_40989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t2v_40989/07_2025/8t2v_40989.map" model { file = "/net/cci-nas-00/data/ceres_data/8t2v_40989/07_2025/8t2v_40989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t2v_40989/07_2025/8t2v_40989.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 7 9.91 5 Mg 1 5.21 5 S 101 5.16 5 C 8225 2.51 5 N 2209 2.21 5 O 2591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13134 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7247 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 946, 7239 Classifications: {'peptide': 946} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 882} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 946, 7239 Classifications: {'peptide': 946} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 882} Chain breaks: 2 bond proxies already assigned to first conformer: 7403 Chain: "B" Number of atoms: 5502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5502 Classifications: {'peptide': 718} Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 682} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} 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: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Unusual residues: {' CA': 5, 'NAG': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 79 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 2, 'NAG': 1} Classifications: {'undetermined': 6, 'water': 6} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.48, per 1000 atoms: 0.87 Number of scatterers: 13134 At special positions: 0 Unit cell: (103.68, 166.32, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 7 19.99 S 101 16.00 Mg 1 11.99 O 2591 8.00 N 2209 7.00 C 8225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.04 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.11 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.07 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 484 " distance=2.06 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 545 " distance=2.05 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 608 " distance=2.06 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 687 " distance=2.05 Simple disulfide: pdb=" SG CYS A 826 " - pdb=" SG CYS A 890 " distance=2.06 Simple disulfide: pdb=" SG CYS A 880 " - pdb=" SG CYS A 885 " distance=2.04 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 23 " distance=2.02 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 435 " distance=2.06 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 38 " distance=2.07 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 49 " distance=2.07 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.02 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.12 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.07 Simple disulfide: pdb=" SG CYS B 406 " - pdb=" SG CYS B 433 " distance=2.04 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 457 " distance=2.06 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 460 " distance=2.06 Simple disulfide: pdb=" SG CYS B 460 " - pdb=" SG CYS B 471 " distance=2.06 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 471 " distance=2.05 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 503 " distance=2.06 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 501 " distance=2.05 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 506 " distance=2.04 Simple disulfide: pdb=" SG CYS B 508 " - pdb=" SG CYS B 521 " distance=2.07 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 544 " distance=2.05 Simple disulfide: pdb=" SG CYS B 528 " - pdb=" SG CYS B 542 " distance=2.05 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 547 " distance=2.04 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 558 " distance=2.05 Simple disulfide: pdb=" SG CYS B 560 " - pdb=" SG CYS B 583 " distance=2.06 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 581 " distance=2.05 Simple disulfide: pdb=" SG CYS B 575 " - pdb=" SG CYS B 586 " distance=2.02 Simple disulfide: pdb=" SG CYS B 588 " - pdb=" SG CYS B 598 " distance=2.08 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 604 " distance=2.05 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 655 " distance=2.08 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 635 " distance=2.06 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 631 " distance=2.06 Simple disulfide: pdb=" SG CYS B 663 " - pdb=" SG CYS B 687 " distance=2.07 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 BETA1-3 " BMA F 3 " - " BMA F 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " BETA1-6 " BMA F 3 " - " BMA F 5 " " BMA H 3 " - " BMA H 4 " NAG-ASN " NAG A1105 " - " ASN A 249 " " NAG A1106 " - " ASN A 680 " " NAG A1107 " - " ASN A 570 " " NAG A1108 " - " ASN A 15 " " NAG B 801 " - " ASN B 654 " " NAG C 1 " - " ASN A 931 " " NAG D 1 " - " ASN B 559 " " NAG E 1 " - " ASN B 320 " " NAG F 1 " - " ASN B 371 " " NAG G 1 " - " ASN B 99 " " NAG H 1 " - " ASN B 452 " Time building additional restraints: 3.83 Conformation dependent library (CDL) restraints added in 2.6 seconds 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 30 sheets defined 16.1% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.904A pdb=" N TYR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 259 through 264 removed outlier: 3.605A pdb=" N THR A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.594A pdb=" N GLN A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 991 removed outlier: 3.832A pdb=" N VAL A 969 " --> pdb=" O PRO A 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 20 removed outlier: 4.353A pdb=" N SER B 20 " --> pdb=" O CYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 removed outlier: 3.823A pdb=" N ASP B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.582A pdb=" N VAL B 80 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 124 through 130 removed outlier: 3.581A pdb=" N TRP B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 169 through 175 removed outlier: 3.522A pdb=" N GLU B 174 " --> pdb=" O GLU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 207 removed outlier: 4.411A pdb=" N PHE B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 281 through 286 removed outlier: 4.532A pdb=" N THR B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B 286 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 302 removed outlier: 3.669A pdb=" N LYS B 302 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 323 removed outlier: 4.502A pdb=" N ASN B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 352 Processing helix chain 'B' and resid 435 through 441 removed outlier: 3.537A pdb=" N ALA B 441 " --> pdb=" O GLN B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 449 Processing helix chain 'B' and resid 493 through 498 Processing helix chain 'B' and resid 535 through 539 Processing helix chain 'B' and resid 573 through 578 Processing helix chain 'B' and resid 606 through 610 Processing helix chain 'B' and resid 611 through 621 removed outlier: 3.722A pdb=" N CYS B 617 " --> pdb=" O GLU B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 718 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.580A pdb=" N ASP A 434 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A 424 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 27 removed outlier: 4.734A pdb=" N VAL A 53 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 100 Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 364 removed outlier: 5.850A pdb=" N ASP A 373 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AB2, first strand: chain 'A' and resid 521 through 523 removed outlier: 5.513A pdb=" N VAL A 454 " --> pdb=" O HIS A 587 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 465 through 466 Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB5, first strand: chain 'A' and resid 612 through 619 removed outlier: 4.104A pdb=" N ARG A 661 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 674 through 678 removed outlier: 6.664A pdb=" N ALA A 647 " --> pdb=" O LEU A 689 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 748 through 755 removed outlier: 7.141A pdb=" N PHE A 908 " --> pdb=" O ILE A 815 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ILE A 815 " --> pdb=" O PHE A 908 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 758 through 760 removed outlier: 6.524A pdb=" N LEU A 759 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 922 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N GLN A 925 " --> pdb=" O PRO A 804 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN A 795 " --> pdb=" O GLU A 894 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU A 894 " --> pdb=" O ASN A 795 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 758 through 760 removed outlier: 6.524A pdb=" N LEU A 759 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 922 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 878 " --> pdb=" O GLN A 925 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N HIS A 927 " --> pdb=" O VAL A 878 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AC2, first strand: chain 'B' and resid 63 through 65 removed outlier: 5.160A pdb=" N VAL B 63 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA B 89 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AC4, first strand: chain 'B' and resid 190 through 197 removed outlier: 4.904A pdb=" N HIS B 192 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA B 155 " --> pdb=" O HIS B 192 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU B 196 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE B 151 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 310 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 355 Processing sheet with id=AC6, first strand: chain 'B' and resid 454 through 456 Processing sheet with id=AC7, first strand: chain 'B' and resid 500 through 502 Processing sheet with id=AC8, first strand: chain 'B' and resid 516 through 517 Processing sheet with id=AC9, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AD1, first strand: chain 'B' and resid 553 through 554 Processing sheet with id=AD2, first strand: chain 'B' and resid 580 through 582 Processing sheet with id=AD3, first strand: chain 'B' and resid 638 through 640 removed outlier: 3.523A pdb=" N ILE B 678 " --> pdb=" O TYR B 670 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1226 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: 5.26 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2227 1.30 - 1.44: 3331 1.44 - 1.57: 7712 1.57 - 1.71: 1 1.71 - 1.85: 128 Bond restraints: 13399 Sorted by residual: bond pdb=" C GLY A 423 " pdb=" O GLY A 423 " ideal model delta sigma weight residual 1.233 1.186 0.047 7.00e-03 2.04e+04 4.49e+01 bond pdb=" C PRO A 433 " pdb=" O PRO A 433 " ideal model delta sigma weight residual 1.233 1.159 0.074 1.16e-02 7.43e+03 4.03e+01 bond pdb=" C SER A 420 " pdb=" O SER A 420 " ideal model delta sigma weight residual 1.235 1.165 0.070 1.14e-02 7.69e+03 3.81e+01 bond pdb=" CA SER B 211 " pdb=" CB SER B 211 " ideal model delta sigma weight residual 1.534 1.458 0.076 1.34e-02 5.57e+03 3.25e+01 bond pdb=" N GLY A 641 " pdb=" CA GLY A 641 " ideal model delta sigma weight residual 1.442 1.483 -0.041 7.70e-03 1.69e+04 2.85e+01 ... (remaining 13394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 13964 2.25 - 4.50: 3793 4.50 - 6.74: 439 6.74 - 8.99: 25 8.99 - 11.24: 3 Bond angle restraints: 18224 Sorted by residual: angle pdb=" C PRO A 403 " pdb=" CA PRO A 403 " pdb=" CB PRO A 403 " ideal model delta sigma weight residual 111.56 102.38 9.18 1.09e+00 8.42e-01 7.09e+01 angle pdb=" CA GLY A 387 " pdb=" C GLY A 387 " pdb=" O GLY A 387 " ideal model delta sigma weight residual 122.22 116.88 5.34 6.50e-01 2.37e+00 6.76e+01 angle pdb=" CA GLY B 555 " pdb=" C GLY B 555 " pdb=" O GLY B 555 " ideal model delta sigma weight residual 122.22 117.90 4.32 6.50e-01 2.37e+00 4.41e+01 angle pdb=" N PRO A 403 " pdb=" CA PRO A 403 " pdb=" CB PRO A 403 " ideal model delta sigma weight residual 103.30 108.50 -5.20 8.00e-01 1.56e+00 4.22e+01 angle pdb=" CA GLY B 518 " pdb=" C GLY B 518 " pdb=" O GLY B 518 " ideal model delta sigma weight residual 122.22 118.22 4.00 6.50e-01 2.37e+00 3.80e+01 ... (remaining 18219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.38: 7726 24.38 - 48.75: 632 48.75 - 73.12: 138 73.12 - 97.50: 61 97.50 - 121.87: 19 Dihedral angle restraints: 8576 sinusoidal: 3814 harmonic: 4762 Sorted by residual: dihedral pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " pdb=" SG CYS B 38 " pdb=" CB CYS B 38 " ideal model delta sinusoidal sigma weight residual -86.00 -176.18 90.18 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS B 549 " pdb=" SG CYS B 549 " pdb=" SG CYS B 558 " pdb=" CB CYS B 558 " ideal model delta sinusoidal sigma weight residual 93.00 -179.32 -87.68 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS B 601 " pdb=" SG CYS B 601 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -164.75 78.75 1 1.00e+01 1.00e-02 7.73e+01 ... (remaining 8573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 1863 0.147 - 0.293: 238 0.293 - 0.440: 3 0.440 - 0.587: 1 0.587 - 0.733: 1 Chirality restraints: 2106 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.23e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.88e+01 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.74e+01 ... (remaining 2103 not shown) Planarity restraints: 2365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.145 2.00e-02 2.50e+03 1.25e-01 1.96e+02 pdb=" C7 NAG C 1 " -0.097 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.127 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.178 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 308 " -0.077 2.00e-02 2.50e+03 4.86e-02 4.13e+01 pdb=" CG PHE B 308 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE B 308 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE B 308 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 PHE B 308 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 308 " -0.027 2.00e-02 2.50e+03 pdb=" CZ PHE B 308 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1106 " 0.064 2.00e-02 2.50e+03 5.44e-02 3.70e+01 pdb=" C7 NAG A1106 " -0.032 2.00e-02 2.50e+03 pdb=" C8 NAG A1106 " 0.053 2.00e-02 2.50e+03 pdb=" N2 NAG A1106 " -0.082 2.00e-02 2.50e+03 pdb=" O7 NAG A1106 " -0.003 2.00e-02 2.50e+03 ... (remaining 2362 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 75 2.38 - 3.01: 7251 3.01 - 3.64: 19663 3.64 - 4.27: 28595 4.27 - 4.90: 46954 Nonbonded interactions: 102538 Sorted by model distance: nonbonded pdb=" OE1 GLU B 220 " pdb="CA CA B 805 " model vdw 1.751 2.510 nonbonded pdb=" OE1 GLU A 243 " pdb="CA CA A1102 " model vdw 1.789 2.510 nonbonded pdb=" OE2 GLU A 252 " pdb="CA CA A1102 " model vdw 1.794 2.510 nonbonded pdb=" OE2 GLU A 642 " pdb="CA CA A1109 " model vdw 1.822 2.510 nonbonded pdb="MG MG B 804 " pdb=" O HOH B 902 " model vdw 1.906 2.170 ... (remaining 102533 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 'C' selection = chain 'E' } ncs_group { reference = chain 'D' 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 38.950 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 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 : 0.016 0.092 13461 Z= 1.140 Angle : 1.973 45.462 18372 Z= 1.332 Chirality : 0.095 0.733 2106 Planarity : 0.009 0.152 2354 Dihedral : 20.167 121.873 5414 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.97 % Allowed : 9.06 % Favored : 89.98 % Rotamer: Outliers : 5.50 % Allowed : 17.48 % Favored : 77.03 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.20), residues: 1657 helix: -0.68 (0.37), residues: 162 sheet: -0.46 (0.23), residues: 478 loop : -1.94 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.008 TRP A 100 HIS 0.018 0.003 HIS A 112 PHE 0.081 0.010 PHE B 308 TYR 0.064 0.010 TYR A 288 ARG 0.020 0.002 ARG A 320 Details of bonding type rmsd link_NAG-ASN : bond 0.01681 ( 11) link_NAG-ASN : angle 4.36011 ( 33) link_BETA1-4 : bond 0.01973 ( 10) link_BETA1-4 : angle 8.93797 ( 30) hydrogen bonds : bond 0.15041 ( 468) hydrogen bonds : angle 7.72635 ( 1226) link_BETA1-6 : bond 0.01139 ( 2) link_BETA1-6 : angle 5.82030 ( 6) SS BOND : bond 0.03287 ( 38) SS BOND : angle 2.44728 ( 76) link_BETA1-3 : bond 0.00230 ( 1) link_BETA1-3 : angle 3.26883 ( 3) covalent geometry : bond 0.01573 (13399) covalent geometry : angle 1.92879 (18224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 51 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.9255 (OUTLIER) cc_final: 0.9002 (m-30) REVERT: A 400 ARG cc_start: 0.1721 (OUTLIER) cc_final: 0.0346 (tpt170) REVERT: A 402 ARG cc_start: 0.3222 (OUTLIER) cc_final: 0.2560 (mtm-85) REVERT: A 549 MET cc_start: 0.8201 (mmm) cc_final: 0.7715 (mmm) REVERT: A 779 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8344 (tppt) REVERT: A 924 LEU cc_start: 0.9707 (OUTLIER) cc_final: 0.9478 (tp) REVERT: B 534 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.5473 (mp0) outliers start: 78 outliers final: 38 residues processed: 124 average time/residue: 0.2624 time to fit residues: 48.0816 Evaluate side-chains 89 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 45 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 692 PRO Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 642 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS B 313 ASN B 438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.074380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.047999 restraints weight = 116001.501| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 6.60 r_work: 0.2758 rms_B_bonded: 5.92 restraints_weight: 2.0000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 13461 Z= 0.159 Angle : 0.815 18.519 18372 Z= 0.385 Chirality : 0.050 0.394 2106 Planarity : 0.006 0.140 2354 Dihedral : 15.169 111.282 2499 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.74 % Favored : 93.90 % Rotamer: Outliers : 2.47 % Allowed : 18.11 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.20), residues: 1657 helix: 0.51 (0.41), residues: 170 sheet: -0.19 (0.22), residues: 544 loop : -1.47 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 262 HIS 0.005 0.001 HIS A 587 PHE 0.011 0.001 PHE B 248 TYR 0.020 0.002 TYR B 318 ARG 0.007 0.001 ARG B 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00767 ( 11) link_NAG-ASN : angle 4.32200 ( 33) link_BETA1-4 : bond 0.00802 ( 10) link_BETA1-4 : angle 3.40315 ( 30) hydrogen bonds : bond 0.03905 ( 468) hydrogen bonds : angle 6.25407 ( 1226) link_BETA1-6 : bond 0.01172 ( 2) link_BETA1-6 : angle 2.91608 ( 6) SS BOND : bond 0.00304 ( 38) SS BOND : angle 1.08958 ( 76) link_BETA1-3 : bond 0.00173 ( 1) link_BETA1-3 : angle 4.01688 ( 3) covalent geometry : bond 0.00366 (13399) covalent geometry : angle 0.77908 (18224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 44 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.2769 (OUTLIER) cc_final: -0.0691 (mtm-85) REVERT: A 549 MET cc_start: 0.7939 (mmm) cc_final: 0.7638 (mmm) REVERT: B 357 LEU cc_start: 0.9000 (mt) cc_final: 0.8744 (mt) REVERT: B 534 GLU cc_start: 0.4479 (OUTLIER) cc_final: 0.2450 (mp0) outliers start: 35 outliers final: 19 residues processed: 76 average time/residue: 0.2321 time to fit residues: 28.0566 Evaluate side-chains 65 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 534 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 21 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 ASN B 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.072239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.046865 restraints weight = 64745.756| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 5.03 r_work: 0.2757 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 13461 Z= 0.269 Angle : 0.813 11.395 18372 Z= 0.391 Chirality : 0.049 0.404 2106 Planarity : 0.006 0.135 2354 Dihedral : 13.092 102.389 2433 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.97 % Favored : 91.79 % Rotamer: Outliers : 3.10 % Allowed : 19.10 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1657 helix: 0.67 (0.41), residues: 171 sheet: -0.26 (0.22), residues: 558 loop : -1.43 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 839 HIS 0.006 0.001 HIS B 280 PHE 0.020 0.002 PHE A 289 TYR 0.015 0.002 TYR A 448 ARG 0.015 0.001 ARG B 530 Details of bonding type rmsd link_NAG-ASN : bond 0.00554 ( 11) link_NAG-ASN : angle 4.00149 ( 33) link_BETA1-4 : bond 0.00745 ( 10) link_BETA1-4 : angle 3.35113 ( 30) hydrogen bonds : bond 0.04121 ( 468) hydrogen bonds : angle 6.17256 ( 1226) link_BETA1-6 : bond 0.00928 ( 2) link_BETA1-6 : angle 2.68919 ( 6) SS BOND : bond 0.00436 ( 38) SS BOND : angle 1.09272 ( 76) link_BETA1-3 : bond 0.00782 ( 1) link_BETA1-3 : angle 3.52274 ( 3) covalent geometry : bond 0.00605 (13399) covalent geometry : angle 0.78083 (18224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 44 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9411 (OUTLIER) cc_final: 0.7070 (t80) REVERT: A 400 ARG cc_start: 0.3177 (OUTLIER) cc_final: -0.1758 (mmm-85) REVERT: A 402 ARG cc_start: 0.3258 (OUTLIER) cc_final: -0.1720 (mtm-85) REVERT: A 489 MET cc_start: 0.9188 (pmm) cc_final: 0.8974 (pmm) REVERT: A 549 MET cc_start: 0.7902 (mmm) cc_final: 0.7654 (mmm) REVERT: A 924 LEU cc_start: 0.9447 (tp) cc_final: 0.9030 (pp) REVERT: B 142 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8750 (tpt) REVERT: B 534 GLU cc_start: 0.5043 (OUTLIER) cc_final: 0.0861 (mp0) REVERT: B 568 MET cc_start: 0.9404 (tpp) cc_final: 0.9197 (tpt) REVERT: B 590 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7518 (tm-30) outliers start: 44 outliers final: 31 residues processed: 84 average time/residue: 0.2274 time to fit residues: 30.2836 Evaluate side-chains 81 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 44 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 655 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 126 optimal weight: 0.5980 chunk 91 optimal weight: 0.0870 chunk 102 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.073664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.047826 restraints weight = 79701.915| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 5.50 r_work: 0.2781 rms_B_bonded: 5.20 restraints_weight: 2.0000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 13461 Z= 0.140 Angle : 0.730 18.281 18372 Z= 0.343 Chirality : 0.047 0.382 2106 Planarity : 0.005 0.131 2354 Dihedral : 11.775 95.454 2432 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.22 % Favored : 93.60 % Rotamer: Outliers : 2.40 % Allowed : 20.72 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.21), residues: 1657 helix: 0.79 (0.40), residues: 172 sheet: -0.09 (0.22), residues: 555 loop : -1.18 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 839 HIS 0.003 0.001 HIS A 587 PHE 0.024 0.001 PHE A 930 TYR 0.012 0.001 TYR A 288 ARG 0.004 0.000 ARG A 683 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 11) link_NAG-ASN : angle 3.77972 ( 33) link_BETA1-4 : bond 0.00740 ( 10) link_BETA1-4 : angle 3.32382 ( 30) hydrogen bonds : bond 0.03282 ( 468) hydrogen bonds : angle 5.78212 ( 1226) link_BETA1-6 : bond 0.01000 ( 2) link_BETA1-6 : angle 2.21392 ( 6) SS BOND : bond 0.00224 ( 38) SS BOND : angle 0.92975 ( 76) link_BETA1-3 : bond 0.00856 ( 1) link_BETA1-3 : angle 3.73469 ( 3) covalent geometry : bond 0.00324 (13399) covalent geometry : angle 0.69679 (18224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 45 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9333 (OUTLIER) cc_final: 0.7483 (t80) REVERT: A 402 ARG cc_start: 0.2581 (OUTLIER) cc_final: -0.1124 (mtm-85) REVERT: A 489 MET cc_start: 0.9185 (pmm) cc_final: 0.8869 (pmm) REVERT: A 549 MET cc_start: 0.7947 (mmm) cc_final: 0.7677 (mmm) REVERT: A 880 CYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7153 (p) REVERT: A 917 ARG cc_start: 0.9241 (ptp90) cc_final: 0.8952 (ptt90) REVERT: A 924 LEU cc_start: 0.9480 (tp) cc_final: 0.9074 (pp) REVERT: B 180 MET cc_start: 0.9350 (pmm) cc_final: 0.9036 (pmm) REVERT: B 335 MET cc_start: 0.9030 (mmm) cc_final: 0.8645 (tpt) REVERT: B 357 LEU cc_start: 0.8977 (mt) cc_final: 0.8714 (mt) outliers start: 34 outliers final: 23 residues processed: 76 average time/residue: 0.2413 time to fit residues: 28.9131 Evaluate side-chains 71 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 45 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 957 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 655 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 48 optimal weight: 8.9990 chunk 126 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 153 optimal weight: 0.5980 chunk 120 optimal weight: 0.0570 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.074111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.048073 restraints weight = 93018.076| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 6.03 r_work: 0.2783 rms_B_bonded: 5.66 restraints_weight: 2.0000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 13461 Z= 0.122 Angle : 0.709 14.209 18372 Z= 0.331 Chirality : 0.047 0.379 2106 Planarity : 0.005 0.126 2354 Dihedral : 10.748 90.112 2426 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.40 % Favored : 93.36 % Rotamer: Outliers : 2.96 % Allowed : 20.30 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.21), residues: 1657 helix: 0.62 (0.39), residues: 179 sheet: 0.12 (0.22), residues: 567 loop : -1.09 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 929 HIS 0.003 0.001 HIS B 509 PHE 0.011 0.001 PHE B 248 TYR 0.013 0.001 TYR B 318 ARG 0.003 0.000 ARG A 683 Details of bonding type rmsd link_NAG-ASN : bond 0.00584 ( 11) link_NAG-ASN : angle 3.63266 ( 33) link_BETA1-4 : bond 0.00720 ( 10) link_BETA1-4 : angle 3.29429 ( 30) hydrogen bonds : bond 0.03047 ( 468) hydrogen bonds : angle 5.58896 ( 1226) link_BETA1-6 : bond 0.01062 ( 2) link_BETA1-6 : angle 1.82795 ( 6) SS BOND : bond 0.00196 ( 38) SS BOND : angle 0.80726 ( 76) link_BETA1-3 : bond 0.00611 ( 1) link_BETA1-3 : angle 3.29763 ( 3) covalent geometry : bond 0.00286 (13399) covalent geometry : angle 0.67759 (18224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 49 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9269 (OUTLIER) cc_final: 0.7780 (t80) REVERT: A 402 ARG cc_start: 0.2536 (OUTLIER) cc_final: -0.1284 (mtm-85) REVERT: A 489 MET cc_start: 0.9172 (pmm) cc_final: 0.8788 (pmm) REVERT: A 549 MET cc_start: 0.8014 (mmm) cc_final: 0.7749 (mmm) REVERT: A 880 CYS cc_start: 0.7391 (OUTLIER) cc_final: 0.7155 (p) REVERT: A 917 ARG cc_start: 0.9186 (ptp90) cc_final: 0.8876 (ptt90) REVERT: A 924 LEU cc_start: 0.9484 (tp) cc_final: 0.9071 (pp) outliers start: 42 outliers final: 24 residues processed: 87 average time/residue: 0.2269 time to fit residues: 31.2858 Evaluate side-chains 74 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 47 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 655 CYS Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 1 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 131 optimal weight: 0.3980 chunk 143 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN ** B 509 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 = 0.3786 r_free = 0.3786 target = 0.074349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.048605 restraints weight = 73038.826| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 5.41 r_work: 0.2815 rms_B_bonded: 5.12 restraints_weight: 2.0000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 13461 Z= 0.119 Angle : 0.708 13.831 18372 Z= 0.332 Chirality : 0.046 0.374 2106 Planarity : 0.005 0.124 2354 Dihedral : 10.178 89.165 2425 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.40 % Favored : 93.48 % Rotamer: Outliers : 2.54 % Allowed : 20.72 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.21), residues: 1657 helix: 0.64 (0.39), residues: 179 sheet: 0.20 (0.22), residues: 566 loop : -1.07 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 929 HIS 0.011 0.001 HIS A 787 PHE 0.011 0.001 PHE B 248 TYR 0.013 0.001 TYR B 166 ARG 0.003 0.000 ARG A 683 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 11) link_NAG-ASN : angle 3.52379 ( 33) link_BETA1-4 : bond 0.00727 ( 10) link_BETA1-4 : angle 3.26957 ( 30) hydrogen bonds : bond 0.03025 ( 468) hydrogen bonds : angle 5.49510 ( 1226) link_BETA1-6 : bond 0.01078 ( 2) link_BETA1-6 : angle 1.72271 ( 6) SS BOND : bond 0.00273 ( 38) SS BOND : angle 1.11800 ( 76) link_BETA1-3 : bond 0.00754 ( 1) link_BETA1-3 : angle 3.04035 ( 3) covalent geometry : bond 0.00277 (13399) covalent geometry : angle 0.67646 (18224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 45 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9224 (OUTLIER) cc_final: 0.7801 (t80) REVERT: A 402 ARG cc_start: 0.2462 (OUTLIER) cc_final: -0.1310 (mtm-85) REVERT: A 549 MET cc_start: 0.7993 (mmm) cc_final: 0.7736 (mmm) REVERT: A 917 ARG cc_start: 0.9228 (ptp90) cc_final: 0.8952 (ptt90) REVERT: A 924 LEU cc_start: 0.9490 (tp) cc_final: 0.9114 (pp) REVERT: A 955 LEU cc_start: 0.9722 (mm) cc_final: 0.9449 (tp) REVERT: B 409 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.9033 (tp30) outliers start: 36 outliers final: 26 residues processed: 76 average time/residue: 0.2377 time to fit residues: 28.8347 Evaluate side-chains 73 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 44 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 43 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 126 optimal weight: 0.3980 chunk 102 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 84 optimal weight: 30.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.073176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.047750 restraints weight = 64235.800| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 4.97 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 13461 Z= 0.176 Angle : 0.726 12.584 18372 Z= 0.342 Chirality : 0.046 0.375 2106 Planarity : 0.005 0.123 2354 Dihedral : 9.690 88.896 2424 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.52 % Favored : 93.30 % Rotamer: Outliers : 2.89 % Allowed : 20.86 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.21), residues: 1657 helix: 0.63 (0.39), residues: 180 sheet: 0.14 (0.22), residues: 568 loop : -1.09 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 929 HIS 0.003 0.001 HIS B 280 PHE 0.013 0.001 PHE A 289 TYR 0.012 0.001 TYR A 288 ARG 0.010 0.000 ARG B 530 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 11) link_NAG-ASN : angle 3.51839 ( 33) link_BETA1-4 : bond 0.00661 ( 10) link_BETA1-4 : angle 3.21219 ( 30) hydrogen bonds : bond 0.03202 ( 468) hydrogen bonds : angle 5.56378 ( 1226) link_BETA1-6 : bond 0.00977 ( 2) link_BETA1-6 : angle 1.69187 ( 6) SS BOND : bond 0.00262 ( 38) SS BOND : angle 1.05486 ( 76) link_BETA1-3 : bond 0.00526 ( 1) link_BETA1-3 : angle 2.91483 ( 3) covalent geometry : bond 0.00400 (13399) covalent geometry : angle 0.69620 (18224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 44 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9256 (OUTLIER) cc_final: 0.7290 (t80) REVERT: A 402 ARG cc_start: 0.2347 (OUTLIER) cc_final: -0.1516 (mtm-85) REVERT: A 489 MET cc_start: 0.9085 (pmm) cc_final: 0.8866 (pmm) REVERT: A 549 MET cc_start: 0.7873 (mmm) cc_final: 0.7672 (mmm) REVERT: A 880 CYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6585 (p) REVERT: A 917 ARG cc_start: 0.9329 (ptp90) cc_final: 0.9125 (ptt90) REVERT: A 924 LEU cc_start: 0.9503 (tp) cc_final: 0.9097 (pp) REVERT: B 568 MET cc_start: 0.9381 (tpp) cc_final: 0.9098 (tpp) outliers start: 41 outliers final: 32 residues processed: 80 average time/residue: 0.2332 time to fit residues: 29.2119 Evaluate side-chains 79 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 44 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 957 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 655 CYS Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 149 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 83 optimal weight: 30.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** 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 = 0.3772 r_free = 0.3772 target = 0.073824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.047463 restraints weight = 101423.821| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 6.33 r_work: 0.2769 rms_B_bonded: 5.75 restraints_weight: 2.0000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 13461 Z= 0.134 Angle : 0.700 12.691 18372 Z= 0.328 Chirality : 0.046 0.364 2106 Planarity : 0.005 0.121 2354 Dihedral : 9.189 87.734 2424 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.34 % Favored : 93.48 % Rotamer: Outliers : 2.89 % Allowed : 20.58 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.21), residues: 1657 helix: 0.65 (0.39), residues: 180 sheet: 0.18 (0.22), residues: 568 loop : -1.08 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 929 HIS 0.002 0.001 HIS B 509 PHE 0.011 0.001 PHE B 248 TYR 0.012 0.001 TYR A 288 ARG 0.004 0.000 ARG A 683 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 11) link_NAG-ASN : angle 3.50204 ( 33) link_BETA1-4 : bond 0.00658 ( 10) link_BETA1-4 : angle 3.05137 ( 30) hydrogen bonds : bond 0.02978 ( 468) hydrogen bonds : angle 5.44824 ( 1226) link_BETA1-6 : bond 0.00999 ( 2) link_BETA1-6 : angle 1.69763 ( 6) SS BOND : bond 0.00209 ( 38) SS BOND : angle 0.90959 ( 76) link_BETA1-3 : bond 0.00693 ( 1) link_BETA1-3 : angle 2.72207 ( 3) covalent geometry : bond 0.00311 (13399) covalent geometry : angle 0.67145 (18224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 44 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9301 (OUTLIER) cc_final: 0.7768 (t80) REVERT: A 402 ARG cc_start: 0.2969 (OUTLIER) cc_final: -0.1494 (mtm-85) REVERT: A 489 MET cc_start: 0.9193 (pmm) cc_final: 0.8984 (pmm) REVERT: A 549 MET cc_start: 0.8031 (mmm) cc_final: 0.7781 (mmm) REVERT: A 693 MET cc_start: 0.8648 (ppp) cc_final: 0.8292 (ppp) REVERT: A 880 CYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6920 (p) REVERT: A 917 ARG cc_start: 0.9206 (ptp90) cc_final: 0.8908 (ptt90) REVERT: A 924 LEU cc_start: 0.9505 (tp) cc_final: 0.9160 (pp) REVERT: A 955 LEU cc_start: 0.9725 (mm) cc_final: 0.9471 (tp) REVERT: B 335 MET cc_start: 0.9043 (mmm) cc_final: 0.8494 (tpp) REVERT: B 409 GLU cc_start: 0.9263 (OUTLIER) cc_final: 0.9045 (tp30) outliers start: 41 outliers final: 35 residues processed: 82 average time/residue: 0.2376 time to fit residues: 30.4837 Evaluate side-chains 82 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 43 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 957 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 655 CYS Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 120 optimal weight: 0.0980 chunk 73 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 chunk 112 optimal weight: 0.9980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN B 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.074589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.049385 restraints weight = 69302.253| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 5.21 r_work: 0.2854 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 13461 Z= 0.110 Angle : 0.695 13.220 18372 Z= 0.325 Chirality : 0.046 0.354 2106 Planarity : 0.005 0.118 2354 Dihedral : 8.719 84.603 2424 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.04 % Favored : 93.78 % Rotamer: Outliers : 2.75 % Allowed : 20.93 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1657 helix: 0.56 (0.40), residues: 180 sheet: 0.31 (0.22), residues: 561 loop : -1.01 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 238 HIS 0.002 0.000 HIS B 509 PHE 0.010 0.001 PHE B 248 TYR 0.013 0.001 TYR A 288 ARG 0.002 0.000 ARG B 636 Details of bonding type rmsd link_NAG-ASN : bond 0.00606 ( 11) link_NAG-ASN : angle 3.47433 ( 33) link_BETA1-4 : bond 0.00718 ( 10) link_BETA1-4 : angle 2.87260 ( 30) hydrogen bonds : bond 0.02786 ( 468) hydrogen bonds : angle 5.28948 ( 1226) link_BETA1-6 : bond 0.00951 ( 2) link_BETA1-6 : angle 1.62550 ( 6) SS BOND : bond 0.00171 ( 38) SS BOND : angle 0.86131 ( 76) link_BETA1-3 : bond 0.00777 ( 1) link_BETA1-3 : angle 2.40304 ( 3) covalent geometry : bond 0.00258 (13399) covalent geometry : angle 0.66854 (18224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 43 time to evaluate : 1.546 Fit side-chains revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9136 (OUTLIER) cc_final: 0.8019 (t80) REVERT: A 402 ARG cc_start: 0.2217 (OUTLIER) cc_final: -0.1501 (mtm-85) REVERT: A 489 MET cc_start: 0.9192 (pmm) cc_final: 0.8979 (pmm) REVERT: A 549 MET cc_start: 0.8003 (mmm) cc_final: 0.7734 (mmm) REVERT: A 693 MET cc_start: 0.8571 (ppp) cc_final: 0.8123 (ppp) REVERT: A 880 CYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6787 (p) REVERT: A 917 ARG cc_start: 0.9274 (ptp90) cc_final: 0.9011 (ptt90) REVERT: A 924 LEU cc_start: 0.9490 (tp) cc_final: 0.9130 (pp) REVERT: A 955 LEU cc_start: 0.9715 (mm) cc_final: 0.9432 (tp) REVERT: B 409 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.9020 (tp30) outliers start: 39 outliers final: 30 residues processed: 78 average time/residue: 0.2512 time to fit residues: 30.3597 Evaluate side-chains 76 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 42 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 957 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 655 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 140 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 154 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 151 optimal weight: 0.0070 chunk 148 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.074483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.048998 restraints weight = 77749.049| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 5.54 r_work: 0.2837 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 13461 Z= 0.112 Angle : 0.699 14.294 18372 Z= 0.326 Chirality : 0.046 0.356 2106 Planarity : 0.005 0.116 2354 Dihedral : 8.548 82.926 2424 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.80 % Favored : 94.02 % Rotamer: Outliers : 2.40 % Allowed : 21.28 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1657 helix: 0.59 (0.39), residues: 180 sheet: 0.35 (0.22), residues: 561 loop : -1.00 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 238 HIS 0.002 0.001 HIS B 509 PHE 0.010 0.001 PHE B 248 TYR 0.015 0.001 TYR B 318 ARG 0.003 0.000 ARG B 530 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 11) link_NAG-ASN : angle 3.41853 ( 33) link_BETA1-4 : bond 0.00698 ( 10) link_BETA1-4 : angle 2.81416 ( 30) hydrogen bonds : bond 0.02829 ( 468) hydrogen bonds : angle 5.26099 ( 1226) link_BETA1-6 : bond 0.00970 ( 2) link_BETA1-6 : angle 1.59836 ( 6) SS BOND : bond 0.00165 ( 38) SS BOND : angle 0.84855 ( 76) link_BETA1-3 : bond 0.00648 ( 1) link_BETA1-3 : angle 2.31621 ( 3) covalent geometry : bond 0.00266 (13399) covalent geometry : angle 0.67316 (18224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 43 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9159 (OUTLIER) cc_final: 0.8102 (t80) REVERT: A 402 ARG cc_start: 0.2432 (OUTLIER) cc_final: -0.1967 (mpp80) REVERT: A 489 MET cc_start: 0.9164 (pmm) cc_final: 0.8956 (pmm) REVERT: A 549 MET cc_start: 0.7895 (mmm) cc_final: 0.7637 (mmm) REVERT: A 693 MET cc_start: 0.8581 (ppp) cc_final: 0.8126 (ppp) REVERT: A 880 CYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6901 (p) REVERT: A 902 MET cc_start: 0.8038 (tpp) cc_final: 0.7697 (tpt) REVERT: A 917 ARG cc_start: 0.9303 (ptp90) cc_final: 0.9033 (ptt90) REVERT: A 924 LEU cc_start: 0.9505 (tp) cc_final: 0.9146 (pp) REVERT: B 409 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.9076 (tp30) outliers start: 34 outliers final: 26 residues processed: 75 average time/residue: 0.2435 time to fit residues: 29.0742 Evaluate side-chains 73 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 43 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 655 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.0000 chunk 100 optimal weight: 3.9990 chunk 81 optimal weight: 0.0980 chunk 162 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 GLN ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.074741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.049768 restraints weight = 69127.110| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 5.01 r_work: 0.2860 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 0.082 13461 Z= 0.108 Angle : 0.690 13.930 18372 Z= 0.321 Chirality : 0.045 0.352 2106 Planarity : 0.005 0.115 2354 Dihedral : 8.360 80.804 2424 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.04 % Favored : 93.78 % Rotamer: Outliers : 2.54 % Allowed : 21.07 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1657 helix: 0.61 (0.39), residues: 180 sheet: 0.45 (0.22), residues: 557 loop : -1.02 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 238 HIS 0.002 0.001 HIS B 509 PHE 0.031 0.001 PHE A 930 TYR 0.015 0.001 TYR B 318 ARG 0.002 0.000 ARG B 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 11) link_NAG-ASN : angle 3.37610 ( 33) link_BETA1-4 : bond 0.00699 ( 10) link_BETA1-4 : angle 2.72063 ( 30) hydrogen bonds : bond 0.02744 ( 468) hydrogen bonds : angle 5.19490 ( 1226) link_BETA1-6 : bond 0.00955 ( 2) link_BETA1-6 : angle 1.53052 ( 6) SS BOND : bond 0.00169 ( 38) SS BOND : angle 0.81185 ( 76) link_BETA1-3 : bond 0.00630 ( 1) link_BETA1-3 : angle 2.14357 ( 3) covalent geometry : bond 0.00255 (13399) covalent geometry : angle 0.66523 (18224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11156.27 seconds wall clock time: 190 minutes 8.19 seconds (11408.19 seconds total)