Starting phenix.real_space_refine on Fri Jul 3 10:08:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t2v_40989/07_2026/8t2v_40989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t2v_40989/07_2026/8t2v_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8t2v_40989/07_2026/8t2v_40989.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t2v_40989/07_2026/8t2v_40989.cif" model { file = "/net/cci-nas-00/data/ceres_data/8t2v_40989/07_2026/8t2v_40989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t2v_40989/07_2026/8t2v_40989.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t2v_40989/07_2026/8t2v_40989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t2v_40989/07_2026/8t2v_40989.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 3.47, per 1000 atoms: 0.26 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: 1.22 Conformation dependent library (CDL) restraints added in 631.0 milliseconds 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: 0.54 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: 1.90 Time building geometry restraints manager: 1.59 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 - 18.08: 6854 18.08 - 36.16: 838 36.16 - 54.24: 216 54.24 - 72.32: 48 72.32 - 90.40: 18 Dihedral angle restraints: 7974 sinusoidal: 3212 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 7971 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.530 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 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 : 17.049 90.402 4812 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (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 ARG 0.020 0.002 ARG A 320 TYR 0.064 0.010 TYR A 288 PHE 0.081 0.010 PHE B 308 TRP 0.045 0.008 TRP A 100 HIS 0.018 0.003 HIS A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.01573 / 1.14 (13399) covalent geometry : angle 1.92879 / 1.33 (18224) SS BOND : bond 0.03287 / 1.97 ( 38) SS BOND : angle 2.44728 / 1.60 ( 76) hydrogen bonds : bond 0.15041 / 9.78 ( 468) hydrogen bonds : angle 7.72635 / 5.41 ( 1226) link_BETA1-3 : bond 0.00230 / 0.12 ( 1) link_BETA1-3 : angle 3.26883 / 1.72 ( 3) link_BETA1-4 : bond 0.01973 / 1.04 ( 10) link_BETA1-4 : angle 8.93797 / 3.40 ( 30) link_BETA1-6 : bond 0.01139 / 0.60 ( 2) link_BETA1-6 : angle 5.82030 / 2.89 ( 6) link_NAG-ASN : bond 0.01681 / 0.98 ( 11) link_NAG-ASN : angle 4.36011 / 2.97 ( 33) *********************** 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 : 0.515 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: 37 residues processed: 124 average time/residue: 0.0954 time to fit residues: 17.7082 Evaluate side-chains 87 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 44 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 GLN B 274 HIS B 313 ASN B 438 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.074177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.048565 restraints weight = 70986.015| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 5.33 r_work: 0.2795 rms_B_bonded: 5.02 restraints_weight: 2.0000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 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 = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 13461 Z= 0.163 Angle : 0.792 18.120 18372 Z= 0.380 Chirality : 0.048 0.371 2106 Planarity : 0.006 0.141 2354 Dihedral : 8.088 88.715 1895 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.86 % Favored : 93.78 % Rotamer: Outliers : 2.54 % Allowed : 18.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.20), residues: 1657 helix: 0.50 (0.41), residues: 170 sheet: -0.23 (0.22), residues: 550 loop : -1.48 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 216 TYR 0.019 0.002 TYR B 318 PHE 0.011 0.001 PHE B 248 TRP 0.017 0.002 TRP A 262 HIS 0.005 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (13399) covalent geometry : angle 0.76424 / 0.37 (18224) SS BOND : bond 0.00311 / 0.21 ( 38) SS BOND : angle 1.09368 / 0.74 ( 76) hydrogen bonds : bond 0.04007 / 2.73 ( 468) hydrogen bonds : angle 6.28419 / 4.41 ( 1226) link_BETA1-3 : bond 0.00294 / 0.15 ( 1) link_BETA1-3 : angle 2.75702 / 1.05 ( 3) link_BETA1-4 : bond 0.00778 / 0.45 ( 10) link_BETA1-4 : angle 2.72074 / 1.68 ( 30) link_BETA1-6 : bond 0.00699 / 0.37 ( 2) link_BETA1-6 : angle 2.07904 / 0.97 ( 6) link_NAG-ASN : bond 0.00735 / 0.47 ( 11) link_NAG-ASN : angle 3.97311 / 2.50 ( 33) *********************** 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 80 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 44 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 ARG cc_start: 0.2488 (OUTLIER) cc_final: -0.0549 (tpt170) REVERT: A 402 ARG cc_start: 0.2756 (OUTLIER) cc_final: 0.0219 (mtm-85) REVERT: A 549 MET cc_start: 0.7968 (mmm) cc_final: 0.7673 (mmm) REVERT: B 534 GLU cc_start: 0.4260 (OUTLIER) cc_final: 0.2487 (mp0) outliers start: 36 outliers final: 21 residues processed: 78 average time/residue: 0.0818 time to fit residues: 9.9916 Evaluate side-chains 68 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 44 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 628 ASP Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 916 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 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 148 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 126 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 GLN B 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.072904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.046907 restraints weight = 94026.232| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 5.95 r_work: 0.2737 rms_B_bonded: 5.51 restraints_weight: 2.0000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 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 = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 13461 Z= 0.221 Angle : 0.761 12.054 18372 Z= 0.368 Chirality : 0.047 0.374 2106 Planarity : 0.006 0.134 2354 Dihedral : 6.623 59.228 1836 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.19 % Favored : 92.51 % Rotamer: Outliers : 2.89 % Allowed : 19.24 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.21), residues: 1657 helix: 0.71 (0.41), residues: 171 sheet: -0.17 (0.22), residues: 549 loop : -1.35 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 530 TYR 0.022 0.001 TYR A 915 PHE 0.017 0.002 PHE A 289 TRP 0.017 0.002 TRP A 839 HIS 0.004 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 (13399) covalent geometry : angle 0.73581 / 0.36 (18224) SS BOND : bond 0.00348 / 0.20 ( 38) SS BOND : angle 1.05481 / 0.74 ( 76) hydrogen bonds : bond 0.03918 / 2.65 ( 468) hydrogen bonds : angle 6.07409 / 4.26 ( 1226) link_BETA1-3 : bond 0.00708 / 0.37 ( 1) link_BETA1-3 : angle 2.33361 / 0.95 ( 3) link_BETA1-4 : bond 0.00782 / 0.44 ( 10) link_BETA1-4 : angle 2.63117 / 1.61 ( 30) link_BETA1-6 : bond 0.00723 / 0.38 ( 2) link_BETA1-6 : angle 1.93726 / 0.89 ( 6) link_NAG-ASN : bond 0.00540 / 0.30 ( 11) link_NAG-ASN : angle 3.63688 / 2.22 ( 33) *********************** 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 86 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 45 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9351 (OUTLIER) cc_final: 0.7389 (t80) REVERT: A 402 ARG cc_start: 0.3330 (OUTLIER) cc_final: -0.1130 (mtm-85) REVERT: A 489 MET cc_start: 0.9175 (pmm) cc_final: 0.8956 (pmm) REVERT: A 549 MET cc_start: 0.7941 (mmm) cc_final: 0.7691 (mmm) REVERT: A 915 TYR cc_start: 0.9249 (m-80) cc_final: 0.8964 (m-80) REVERT: A 924 LEU cc_start: 0.9424 (tp) cc_final: 0.8982 (pp) REVERT: B 142 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8701 (tpt) REVERT: B 534 GLU cc_start: 0.4757 (OUTLIER) cc_final: 0.1098 (mp0) REVERT: B 568 MET cc_start: 0.9375 (tpp) cc_final: 0.9121 (tpt) outliers start: 41 outliers final: 29 residues processed: 82 average time/residue: 0.0799 time to fit residues: 10.6507 Evaluate side-chains 78 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 45 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 401 SER 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 839 TRP Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 916 GLN 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 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 378 GLU Chi-restraints excluded: chain B residue 385 SER 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 42 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 119 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 GLN B 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.073488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.047435 restraints weight = 81661.984| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 5.48 r_work: 0.2799 rms_B_bonded: 5.13 restraints_weight: 2.0000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 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 = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 13461 Z= 0.188 Angle : 0.732 18.023 18372 Z= 0.351 Chirality : 0.046 0.367 2106 Planarity : 0.005 0.131 2354 Dihedral : 6.373 56.462 1829 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.76 % Favored : 93.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.21), residues: 1657 helix: 0.81 (0.40), residues: 172 sheet: -0.15 (0.22), residues: 557 loop : -1.30 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 530 TYR 0.021 0.001 TYR A 915 PHE 0.020 0.002 PHE A 930 TRP 0.015 0.002 TRP A 839 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (13399) covalent geometry : angle 0.70807 / 0.35 (18224) SS BOND : bond 0.00272 / 0.16 ( 38) SS BOND : angle 0.96284 / 0.69 ( 76) hydrogen bonds : bond 0.03548 / 2.39 ( 468) hydrogen bonds : angle 5.89027 / 4.14 ( 1226) link_BETA1-3 : bond 0.00706 / 0.37 ( 1) link_BETA1-3 : angle 2.30309 / 0.93 ( 3) link_BETA1-4 : bond 0.00753 / 0.41 ( 10) link_BETA1-4 : angle 2.49245 / 1.54 ( 30) link_BETA1-6 : bond 0.00741 / 0.39 ( 2) link_BETA1-6 : angle 1.83693 / 0.84 ( 6) link_NAG-ASN : bond 0.00529 / 0.29 ( 11) link_NAG-ASN : angle 3.54347 / 2.17 ( 33) *********************** 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 84 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 42 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9322 (OUTLIER) cc_final: 0.7321 (t80) REVERT: A 402 ARG cc_start: 0.3149 (OUTLIER) cc_final: -0.0920 (mtm-85) REVERT: A 489 MET cc_start: 0.9215 (pmm) cc_final: 0.8907 (pmm) REVERT: A 549 MET cc_start: 0.7988 (mmm) cc_final: 0.7758 (mmm) REVERT: A 880 CYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7145 (p) REVERT: A 915 TYR cc_start: 0.9225 (m-80) cc_final: 0.8966 (m-80) REVERT: A 924 LEU cc_start: 0.9488 (tp) cc_final: 0.9080 (pp) REVERT: B 180 MET cc_start: 0.9288 (pmm) cc_final: 0.9077 (pmm) REVERT: B 590 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7535 (tm-30) outliers start: 42 outliers final: 26 residues processed: 80 average time/residue: 0.0826 time to fit residues: 10.5604 Evaluate side-chains 72 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 42 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 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 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 916 GLN 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 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 359 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 462 CYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 158 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 120 optimal weight: 0.4980 chunk 116 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 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 = 0.3796 r_free = 0.3796 target = 0.074111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.048372 restraints weight = 72848.716| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 5.40 r_work: 0.2831 rms_B_bonded: 5.07 restraints_weight: 2.0000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 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 = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 13461 Z= 0.141 Angle : 0.699 15.031 18372 Z= 0.333 Chirality : 0.045 0.361 2106 Planarity : 0.005 0.126 2354 Dihedral : 5.962 57.113 1824 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.58 % Favored : 93.18 % Rotamer: Outliers : 2.61 % Allowed : 20.79 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.21), residues: 1657 helix: 0.71 (0.40), residues: 180 sheet: -0.01 (0.22), residues: 572 loop : -1.18 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 917 TYR 0.017 0.001 TYR A 915 PHE 0.012 0.001 PHE B 248 TRP 0.013 0.001 TRP A 839 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (13399) covalent geometry : angle 0.67624 / 0.33 (18224) SS BOND : bond 0.00218 / 0.13 ( 38) SS BOND : angle 0.84867 / 0.60 ( 76) hydrogen bonds : bond 0.03207 / 2.16 ( 468) hydrogen bonds : angle 5.66684 / 3.98 ( 1226) link_BETA1-3 : bond 0.00809 / 0.43 ( 1) link_BETA1-3 : angle 2.28265 / 0.93 ( 3) link_BETA1-4 : bond 0.00778 / 0.42 ( 10) link_BETA1-4 : angle 2.41010 / 1.49 ( 30) link_BETA1-6 : bond 0.00779 / 0.41 ( 2) link_BETA1-6 : angle 1.74888 / 0.80 ( 6) link_NAG-ASN : bond 0.00541 / 0.31 ( 11) link_NAG-ASN : angle 3.34065 / 2.04 ( 33) *********************** 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 80 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 43 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9284 (OUTLIER) cc_final: 0.7596 (t80) REVERT: A 402 ARG cc_start: 0.2625 (OUTLIER) cc_final: -0.1123 (mtm-85) REVERT: A 489 MET cc_start: 0.9197 (pmm) cc_final: 0.8851 (pmm) REVERT: A 549 MET cc_start: 0.7935 (mmm) cc_final: 0.7727 (mmm) REVERT: A 924 LEU cc_start: 0.9486 (tp) cc_final: 0.9083 (pp) REVERT: B 180 MET cc_start: 0.9279 (pmm) cc_final: 0.9025 (pmm) outliers start: 37 outliers final: 24 residues processed: 76 average time/residue: 0.0828 time to fit residues: 10.1788 Evaluate side-chains 69 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 43 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 401 SER 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 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 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 642 VAL Chi-restraints excluded: chain B residue 655 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 118 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 143 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 GLN B 438 GLN B 449 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.072820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.046587 restraints weight = 95652.539| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 5.93 r_work: 0.2763 rms_B_bonded: 5.48 restraints_weight: 2.0000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 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 = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 13461 Z= 0.246 Angle : 0.755 14.236 18372 Z= 0.364 Chirality : 0.046 0.370 2106 Planarity : 0.006 0.126 2354 Dihedral : 6.143 57.878 1824 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.31 % Favored : 92.51 % Rotamer: Outliers : 3.38 % Allowed : 20.51 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.21), residues: 1657 helix: 0.78 (0.40), residues: 173 sheet: -0.12 (0.22), residues: 574 loop : -1.27 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 530 TYR 0.013 0.001 TYR A 448 PHE 0.017 0.002 PHE A 289 TRP 0.015 0.002 TRP A 839 HIS 0.004 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.25 (13399) covalent geometry : angle 0.73407 / 0.36 (18224) SS BOND : bond 0.00343 / 0.21 ( 38) SS BOND : angle 1.07085 / 0.76 ( 76) hydrogen bonds : bond 0.03585 / 2.40 ( 468) hydrogen bonds : angle 5.85430 / 4.12 ( 1226) link_BETA1-3 : bond 0.00683 / 0.36 ( 1) link_BETA1-3 : angle 2.17042 / 0.86 ( 3) link_BETA1-4 : bond 0.00672 / 0.37 ( 10) link_BETA1-4 : angle 2.35781 / 1.50 ( 30) link_BETA1-6 : bond 0.00680 / 0.36 ( 2) link_BETA1-6 : angle 1.76726 / 0.80 ( 6) link_NAG-ASN : bond 0.00527 / 0.26 ( 11) link_NAG-ASN : angle 3.28447 / 1.99 ( 33) *********************** 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 93 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 45 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9392 (OUTLIER) cc_final: 0.7057 (t80) REVERT: A 402 ARG cc_start: 0.3316 (OUTLIER) cc_final: -0.1495 (mtm-85) REVERT: A 489 MET cc_start: 0.9184 (pmm) cc_final: 0.8807 (pmm) REVERT: A 915 TYR cc_start: 0.9199 (m-10) cc_final: 0.8978 (m-80) REVERT: A 924 LEU cc_start: 0.9514 (tp) cc_final: 0.9130 (pp) REVERT: B 590 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7555 (tm-30) outliers start: 48 outliers final: 34 residues processed: 90 average time/residue: 0.0910 time to fit residues: 12.9475 Evaluate side-chains 82 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 45 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 401 SER Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 474 VAL 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 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 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 256 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 303 ASN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 104 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 158 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 111 optimal weight: 0.0980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.073807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.048059 restraints weight = 72634.272| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 5.44 r_work: 0.2826 rms_B_bonded: 5.04 restraints_weight: 2.0000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 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 = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2184 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= 0.145 Angle : 0.713 13.217 18372 Z= 0.339 Chirality : 0.045 0.355 2106 Planarity : 0.005 0.123 2354 Dihedral : 5.954 58.804 1824 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.64 % Favored : 93.18 % Rotamer: Outliers : 2.82 % Allowed : 21.00 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.21), residues: 1657 helix: 0.83 (0.40), residues: 175 sheet: 0.01 (0.22), residues: 568 loop : -1.16 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 530 TYR 0.015 0.001 TYR A 915 PHE 0.012 0.001 PHE B 248 TRP 0.012 0.001 TRP A 839 HIS 0.005 0.001 HIS B 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (13399) covalent geometry : angle 0.69184 / 0.33 (18224) SS BOND : bond 0.00223 / 0.13 ( 38) SS BOND : angle 1.15624 / 0.93 ( 76) hydrogen bonds : bond 0.03201 / 2.13 ( 468) hydrogen bonds : angle 5.70286 / 4.01 ( 1226) link_BETA1-3 : bond 0.00858 / 0.45 ( 1) link_BETA1-3 : angle 2.19493 / 0.90 ( 3) link_BETA1-4 : bond 0.00741 / 0.40 ( 10) link_BETA1-4 : angle 2.29548 / 1.45 ( 30) link_BETA1-6 : bond 0.00749 / 0.39 ( 2) link_BETA1-6 : angle 1.68384 / 0.76 ( 6) link_NAG-ASN : bond 0.00528 / 0.29 ( 11) link_NAG-ASN : angle 3.10251 / 1.87 ( 33) *********************** 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 84 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 44 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9330 (OUTLIER) cc_final: 0.7334 (t80) REVERT: A 402 ARG cc_start: 0.2921 (OUTLIER) cc_final: -0.1514 (mtm-85) REVERT: A 489 MET cc_start: 0.9180 (pmm) cc_final: 0.8806 (pmm) REVERT: A 915 TYR cc_start: 0.9238 (m-10) cc_final: 0.9024 (m-80) REVERT: A 924 LEU cc_start: 0.9493 (tp) cc_final: 0.9108 (pp) REVERT: B 568 MET cc_start: 0.9394 (tpp) cc_final: 0.9160 (tpp) outliers start: 40 outliers final: 32 residues processed: 81 average time/residue: 0.0839 time to fit residues: 10.8270 Evaluate side-chains 78 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 44 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 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 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 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 244 HIS 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 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 109 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 155 optimal weight: 9.9990 chunk 106 optimal weight: 0.3980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.073976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.047702 restraints weight = 99711.538| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 6.14 r_work: 0.2803 rms_B_bonded: 5.57 restraints_weight: 2.0000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 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 = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2303 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= 0.138 Angle : 0.698 12.563 18372 Z= 0.331 Chirality : 0.045 0.355 2106 Planarity : 0.005 0.121 2354 Dihedral : 5.823 59.449 1824 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.34 % Favored : 93.48 % Rotamer: Outliers : 2.54 % Allowed : 21.35 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.21), residues: 1657 helix: 0.68 (0.39), residues: 181 sheet: 0.05 (0.22), residues: 568 loop : -1.12 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 530 TYR 0.012 0.001 TYR A 288 PHE 0.012 0.001 PHE B 248 TRP 0.011 0.001 TRP A 839 HIS 0.002 0.001 HIS B 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (13399) covalent geometry : angle 0.67883 / 0.33 (18224) SS BOND : bond 0.00210 / 0.12 ( 38) SS BOND : angle 1.04102 / 0.86 ( 76) hydrogen bonds : bond 0.03049 / 2.03 ( 468) hydrogen bonds : angle 5.58909 / 3.92 ( 1226) link_BETA1-3 : bond 0.00859 / 0.45 ( 1) link_BETA1-3 : angle 2.16912 / 0.88 ( 3) link_BETA1-4 : bond 0.00726 / 0.39 ( 10) link_BETA1-4 : angle 2.23899 / 1.42 ( 30) link_BETA1-6 : bond 0.00735 / 0.38 ( 2) link_BETA1-6 : angle 1.65157 / 0.74 ( 6) link_NAG-ASN : bond 0.00528 / 0.29 ( 11) link_NAG-ASN : angle 2.99878 / 1.81 ( 33) *********************** 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 82 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 46 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9323 (OUTLIER) cc_final: 0.7552 (t80) REVERT: A 402 ARG cc_start: 0.3023 (OUTLIER) cc_final: -0.1565 (mtm-85) REVERT: A 489 MET cc_start: 0.9217 (pmm) cc_final: 0.8824 (pmm) REVERT: A 915 TYR cc_start: 0.9260 (m-10) cc_final: 0.9027 (m-80) REVERT: A 924 LEU cc_start: 0.9490 (tp) cc_final: 0.9105 (pp) REVERT: B 180 MET cc_start: 0.9331 (pmm) cc_final: 0.9000 (pmm) outliers start: 36 outliers final: 32 residues processed: 79 average time/residue: 0.0969 time to fit residues: 12.0422 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 : 0.494 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 22 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 42 optimal weight: 0.4980 chunk 108 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 921 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.073222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.049662 restraints weight = 73879.797| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 5.14 r_work: 0.2800 rms_B_bonded: 5.14 restraints_weight: 2.0000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 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 = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 13461 Z= 0.192 Angle : 0.724 12.341 18372 Z= 0.346 Chirality : 0.045 0.361 2106 Planarity : 0.005 0.121 2354 Dihedral : 5.875 59.570 1823 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.88 % Favored : 92.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.21), residues: 1657 helix: 0.84 (0.40), residues: 175 sheet: -0.02 (0.22), residues: 571 loop : -1.19 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 530 TYR 0.011 0.001 TYR A 288 PHE 0.015 0.001 PHE A 289 TRP 0.010 0.001 TRP A 839 HIS 0.003 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (13399) covalent geometry : angle 0.70547 / 0.34 (18224) SS BOND : bond 0.00289 / 0.18 ( 38) SS BOND : angle 1.04268 / 0.84 ( 76) hydrogen bonds : bond 0.03266 / 2.17 ( 468) hydrogen bonds : angle 5.66356 / 3.97 ( 1226) link_BETA1-3 : bond 0.00785 / 0.41 ( 1) link_BETA1-3 : angle 2.08473 / 0.84 ( 3) link_BETA1-4 : bond 0.00653 / 0.36 ( 10) link_BETA1-4 : angle 2.20751 / 1.43 ( 30) link_BETA1-6 : bond 0.00677 / 0.36 ( 2) link_BETA1-6 : angle 1.66363 / 0.75 ( 6) link_NAG-ASN : bond 0.00509 / 0.26 ( 11) link_NAG-ASN : angle 3.07759 / 1.84 ( 33) *********************** 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 85 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 46 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9342 (OUTLIER) cc_final: 0.7144 (t80) REVERT: A 400 ARG cc_start: 0.3271 (OUTLIER) cc_final: -0.1016 (tpt170) REVERT: A 402 ARG cc_start: 0.3195 (OUTLIER) cc_final: -0.1468 (mpp80) REVERT: A 915 TYR cc_start: 0.9242 (m-10) cc_final: 0.9027 (m-80) REVERT: A 924 LEU cc_start: 0.9477 (tp) cc_final: 0.9139 (pp) REVERT: B 180 MET cc_start: 0.9346 (pmm) cc_final: 0.9061 (pmm) outliers start: 39 outliers final: 32 residues processed: 82 average time/residue: 0.1041 time to fit residues: 13.2872 Evaluate side-chains 81 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 46 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 358 SER Chi-restraints excluded: chain A residue 400 ARG 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 839 TRP 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 163 optimal weight: 30.0000 chunk 119 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 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 = 0.3787 r_free = 0.3787 target = 0.073619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.049634 restraints weight = 80140.631| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 5.48 r_work: 0.2799 rms_B_bonded: 5.38 restraints_weight: 2.0000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 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 = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 13461 Z= 0.158 Angle : 0.705 13.107 18372 Z= 0.336 Chirality : 0.045 0.352 2106 Planarity : 0.005 0.119 2354 Dihedral : 5.770 58.582 1823 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.70 % Favored : 93.12 % Rotamer: Outliers : 2.47 % Allowed : 21.42 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.21), residues: 1657 helix: 0.87 (0.40), residues: 175 sheet: 0.00 (0.22), residues: 569 loop : -1.14 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 530 TYR 0.012 0.001 TYR A 288 PHE 0.012 0.001 PHE A 289 TRP 0.011 0.001 TRP B 238 HIS 0.003 0.001 HIS B 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (13399) covalent geometry : angle 0.68721 / 0.33 (18224) SS BOND : bond 0.00235 / 0.14 ( 38) SS BOND : angle 0.97560 / 0.79 ( 76) hydrogen bonds : bond 0.03086 / 2.05 ( 468) hydrogen bonds : angle 5.59887 / 3.92 ( 1226) link_BETA1-3 : bond 0.00861 / 0.45 ( 1) link_BETA1-3 : angle 2.06458 / 0.85 ( 3) link_BETA1-4 : bond 0.00676 / 0.37 ( 10) link_BETA1-4 : angle 2.16314 / 1.39 ( 30) link_BETA1-6 : bond 0.00694 / 0.36 ( 2) link_BETA1-6 : angle 1.62141 / 0.73 ( 6) link_NAG-ASN : bond 0.00518 / 0.28 ( 11) link_NAG-ASN : angle 2.97176 / 1.78 ( 33) ********************** 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 81 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 46 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9341 (OUTLIER) cc_final: 0.7310 (t80) REVERT: A 400 ARG cc_start: 0.3170 (OUTLIER) cc_final: -0.1599 (mmm-85) REVERT: A 402 ARG cc_start: 0.3241 (OUTLIER) cc_final: -0.2018 (mtm-85) REVERT: A 489 MET cc_start: 0.9208 (pmm) cc_final: 0.9007 (pmm) REVERT: A 902 MET cc_start: 0.8071 (tpp) cc_final: 0.7716 (tpt) REVERT: A 915 TYR cc_start: 0.9258 (m-10) cc_final: 0.9046 (m-80) REVERT: A 924 LEU cc_start: 0.9479 (tp) cc_final: 0.9127 (pp) REVERT: B 180 MET cc_start: 0.9343 (pmm) cc_final: 0.9050 (pmm) REVERT: B 433 CYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7919 (m) outliers start: 35 outliers final: 30 residues processed: 77 average time/residue: 0.1172 time to fit residues: 13.8257 Evaluate side-chains 80 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 46 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 358 SER Chi-restraints excluded: chain A residue 400 ARG 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 839 TRP 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 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 256 ILE Chi-restraints excluded: chain B residue 262 LEU 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 433 CYS 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 687 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 93 optimal weight: 50.0000 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 GLN ** 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 = 0.3814 r_free = 0.3814 target = 0.074668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.051186 restraints weight = 73087.390| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 5.30 r_work: 0.2843 rms_B_bonded: 5.15 restraints_weight: 2.0000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 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 = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2576 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= 0.117 Angle : 0.695 13.253 18372 Z= 0.327 Chirality : 0.045 0.348 2106 Planarity : 0.005 0.117 2354 Dihedral : 5.493 57.902 1822 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.58 % Favored : 93.24 % Rotamer: Outliers : 2.18 % Allowed : 21.63 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.21), residues: 1657 helix: 0.65 (0.40), residues: 181 sheet: 0.12 (0.22), residues: 566 loop : -1.04 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 636 TYR 0.013 0.001 TYR A 288 PHE 0.010 0.001 PHE B 248 TRP 0.014 0.001 TRP B 238 HIS 0.002 0.001 HIS B 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (13399) covalent geometry : angle 0.67777 / 0.32 (18224) SS BOND : bond 0.00183 / 0.12 ( 38) SS BOND : angle 0.91248 / 0.74 ( 76) hydrogen bonds : bond 0.02878 / 1.92 ( 468) hydrogen bonds : angle 5.44223 / 3.81 ( 1226) link_BETA1-3 : bond 0.00933 / 0.49 ( 1) link_BETA1-3 : angle 2.09295 / 0.87 ( 3) link_BETA1-4 : bond 0.00721 / 0.39 ( 10) link_BETA1-4 : angle 2.14092 / 1.36 ( 30) link_BETA1-6 : bond 0.00720 / 0.38 ( 2) link_BETA1-6 : angle 1.57691 / 0.70 ( 6) link_NAG-ASN : bond 0.00560 / 0.32 ( 11) link_NAG-ASN : angle 2.84462 / 1.69 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4462.59 seconds wall clock time: 76 minutes 43.35 seconds (4603.35 seconds total)