Starting phenix.real_space_refine on Sat Aug 23 17:18:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t2v_40989/08_2025/8t2v_40989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t2v_40989/08_2025/8t2v_40989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t2v_40989/08_2025/8t2v_40989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t2v_40989/08_2025/8t2v_40989.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t2v_40989/08_2025/8t2v_40989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t2v_40989/08_2025/8t2v_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-2.0-5787/lib/python3.9/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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Unusual residues: {' CA': 5, 'NAG': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 79 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 2, 'NAG': 1} Classifications: {'undetermined': 6, 'water': 6} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.90, per 1000 atoms: 0.37 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: 1.32 Conformation dependent library (CDL) restraints added in 904.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.72 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: 2.72 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2227 1.30 - 1.44: 3331 1.44 - 1.57: 7712 1.57 - 1.71: 1 1.71 - 1.85: 128 Bond restraints: 13399 Sorted by residual: bond pdb=" C GLY A 423 " pdb=" O GLY A 423 " ideal model delta sigma weight residual 1.233 1.186 0.047 7.00e-03 2.04e+04 4.49e+01 bond pdb=" C PRO A 433 " pdb=" O PRO A 433 " ideal model delta sigma weight residual 1.233 1.159 0.074 1.16e-02 7.43e+03 4.03e+01 bond pdb=" C SER A 420 " pdb=" O SER A 420 " ideal model delta sigma weight residual 1.235 1.165 0.070 1.14e-02 7.69e+03 3.81e+01 bond pdb=" CA SER B 211 " pdb=" CB SER B 211 " ideal model delta sigma weight residual 1.534 1.458 0.076 1.34e-02 5.57e+03 3.25e+01 bond pdb=" N GLY A 641 " pdb=" CA GLY A 641 " ideal model delta sigma weight residual 1.442 1.483 -0.041 7.70e-03 1.69e+04 2.85e+01 ... (remaining 13394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 13964 2.25 - 4.50: 3793 4.50 - 6.74: 439 6.74 - 8.99: 25 8.99 - 11.24: 3 Bond angle restraints: 18224 Sorted by residual: angle pdb=" C PRO A 403 " pdb=" CA PRO A 403 " pdb=" CB PRO A 403 " ideal model delta sigma weight residual 111.56 102.38 9.18 1.09e+00 8.42e-01 7.09e+01 angle pdb=" CA GLY A 387 " pdb=" C GLY A 387 " pdb=" O GLY A 387 " ideal model delta sigma weight residual 122.22 116.88 5.34 6.50e-01 2.37e+00 6.76e+01 angle pdb=" CA GLY B 555 " pdb=" C GLY B 555 " pdb=" O GLY B 555 " ideal model delta sigma weight residual 122.22 117.90 4.32 6.50e-01 2.37e+00 4.41e+01 angle pdb=" N PRO A 403 " pdb=" CA PRO A 403 " pdb=" CB PRO A 403 " ideal model delta sigma weight residual 103.30 108.50 -5.20 8.00e-01 1.56e+00 4.22e+01 angle pdb=" CA GLY B 518 " pdb=" C GLY B 518 " pdb=" O GLY B 518 " ideal model delta sigma weight residual 122.22 118.22 4.00 6.50e-01 2.37e+00 3.80e+01 ... (remaining 18219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.38: 7726 24.38 - 48.75: 632 48.75 - 73.12: 138 73.12 - 97.50: 61 97.50 - 121.87: 19 Dihedral angle restraints: 8576 sinusoidal: 3814 harmonic: 4762 Sorted by residual: dihedral pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " pdb=" SG CYS B 38 " pdb=" CB CYS B 38 " ideal model delta sinusoidal sigma weight residual -86.00 -176.18 90.18 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS B 549 " pdb=" SG CYS B 549 " pdb=" SG CYS B 558 " pdb=" CB CYS B 558 " ideal model delta sinusoidal sigma weight residual 93.00 -179.32 -87.68 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS B 601 " pdb=" SG CYS B 601 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -164.75 78.75 1 1.00e+01 1.00e-02 7.73e+01 ... (remaining 8573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 1863 0.147 - 0.293: 238 0.293 - 0.440: 3 0.440 - 0.587: 1 0.587 - 0.733: 1 Chirality restraints: 2106 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.23e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.88e+01 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.74e+01 ... (remaining 2103 not shown) Planarity restraints: 2365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.145 2.00e-02 2.50e+03 1.25e-01 1.96e+02 pdb=" C7 NAG C 1 " -0.097 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.127 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.178 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 308 " -0.077 2.00e-02 2.50e+03 4.86e-02 4.13e+01 pdb=" CG PHE B 308 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE B 308 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE B 308 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 PHE B 308 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 308 " -0.027 2.00e-02 2.50e+03 pdb=" CZ PHE B 308 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1106 " 0.064 2.00e-02 2.50e+03 5.44e-02 3.70e+01 pdb=" C7 NAG A1106 " -0.032 2.00e-02 2.50e+03 pdb=" C8 NAG A1106 " 0.053 2.00e-02 2.50e+03 pdb=" N2 NAG A1106 " -0.082 2.00e-02 2.50e+03 pdb=" O7 NAG A1106 " -0.003 2.00e-02 2.50e+03 ... (remaining 2362 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 75 2.38 - 3.01: 7251 3.01 - 3.64: 19663 3.64 - 4.27: 28595 4.27 - 4.90: 46954 Nonbonded interactions: 102538 Sorted by model distance: nonbonded pdb=" OE1 GLU B 220 " pdb="CA CA B 805 " model vdw 1.751 2.510 nonbonded pdb=" OE1 GLU A 243 " pdb="CA CA A1102 " model vdw 1.789 2.510 nonbonded pdb=" OE2 GLU A 252 " pdb="CA CA A1102 " model vdw 1.794 2.510 nonbonded pdb=" OE2 GLU A 642 " pdb="CA CA A1109 " model vdw 1.822 2.510 nonbonded pdb="MG MG B 804 " pdb=" O HOH B 902 " model vdw 1.906 2.170 ... (remaining 102533 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.680 Find NCS groups from input model: 0.090 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.092 13461 Z= 1.140 Angle : 1.973 45.462 18372 Z= 1.332 Chirality : 0.095 0.733 2106 Planarity : 0.009 0.152 2354 Dihedral : 20.167 121.873 5414 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.97 % Allowed : 9.06 % Favored : 89.98 % Rotamer: Outliers : 5.50 % Allowed : 17.48 % Favored : 77.03 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.01573 (13399) covalent geometry : angle 1.92879 (18224) SS BOND : bond 0.03287 ( 38) SS BOND : angle 2.44728 ( 76) hydrogen bonds : bond 0.15041 ( 468) hydrogen bonds : angle 7.72635 ( 1226) link_BETA1-3 : bond 0.00230 ( 1) link_BETA1-3 : angle 3.26883 ( 3) link_BETA1-4 : bond 0.01973 ( 10) link_BETA1-4 : angle 8.93797 ( 30) link_BETA1-6 : bond 0.01139 ( 2) link_BETA1-6 : angle 5.82030 ( 6) link_NAG-ASN : bond 0.01681 ( 11) link_NAG-ASN : angle 4.36011 ( 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 : 0.512 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: 0.1266 time to fit residues: 22.9808 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 : 0.509 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.074168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048546 restraints weight = 71055.577| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 5.40 r_work: 0.2799 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 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 = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 13461 Z= 0.165 Angle : 0.820 19.098 18372 Z= 0.387 Chirality : 0.049 0.396 2106 Planarity : 0.006 0.140 2354 Dihedral : 15.122 111.227 2497 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.80 % Favored : 93.84 % Rotamer: Outliers : 2.54 % Allowed : 17.90 % Favored : 79.56 % 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 aren not related in a simple way. whole: -1.23 (0.20), residues: 1657 helix: 0.50 (0.41), residues: 170 sheet: -0.22 (0.22), residues: 550 loop : -1.47 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 216 TYR 0.021 0.002 TYR B 318 PHE 0.011 0.001 PHE A 419 TRP 0.017 0.002 TRP A 262 HIS 0.004 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00380 (13399) covalent geometry : angle 0.78380 (18224) SS BOND : bond 0.00297 ( 38) SS BOND : angle 1.08751 ( 76) hydrogen bonds : bond 0.03904 ( 468) hydrogen bonds : angle 6.26539 ( 1226) link_BETA1-3 : bond 0.00142 ( 1) link_BETA1-3 : angle 4.03947 ( 3) link_BETA1-4 : bond 0.00874 ( 10) link_BETA1-4 : angle 3.41173 ( 30) link_BETA1-6 : bond 0.00976 ( 2) link_BETA1-6 : angle 2.98619 ( 6) link_NAG-ASN : bond 0.00730 ( 11) link_NAG-ASN : angle 4.33530 ( 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 : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 ARG cc_start: 0.2509 (OUTLIER) cc_final: -0.0853 (mmt90) REVERT: A 402 ARG cc_start: 0.2740 (OUTLIER) cc_final: 0.0208 (mtm-85) REVERT: A 549 MET cc_start: 0.7930 (mmm) cc_final: 0.7639 (mmm) REVERT: B 357 LEU cc_start: 0.8990 (mt) cc_final: 0.8730 (mt) REVERT: B 534 GLU cc_start: 0.4228 (OUTLIER) cc_final: 0.2247 (mp0) outliers start: 36 outliers final: 18 residues processed: 78 average time/residue: 0.1189 time to fit residues: 14.1627 Evaluate side-chains 65 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 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 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: 5.9990 chunk 79 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 126 optimal weight: 0.0070 chunk 90 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 GLN B 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.072808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.046816 restraints weight = 94493.861| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 5.95 r_work: 0.2733 rms_B_bonded: 5.56 restraints_weight: 2.0000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 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 = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 13461 Z= 0.226 Angle : 0.791 12.125 18372 Z= 0.378 Chirality : 0.049 0.400 2106 Planarity : 0.006 0.135 2354 Dihedral : 13.317 103.928 2436 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.07 % Favored : 92.63 % Rotamer: Outliers : 3.03 % Allowed : 18.96 % Favored : 78.01 % 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 aren not related in a simple way. whole: -1.08 (0.21), residues: 1657 helix: 0.70 (0.41), residues: 171 sheet: -0.17 (0.22), residues: 549 loop : -1.36 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 530 TYR 0.025 0.002 TYR A 915 PHE 0.016 0.002 PHE A 289 TRP 0.018 0.002 TRP A 839 HIS 0.004 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00513 (13399) covalent geometry : angle 0.75754 (18224) SS BOND : bond 0.00359 ( 38) SS BOND : angle 1.06978 ( 76) hydrogen bonds : bond 0.03948 ( 468) hydrogen bonds : angle 6.08103 ( 1226) link_BETA1-3 : bond 0.00771 ( 1) link_BETA1-3 : angle 3.53457 ( 3) link_BETA1-4 : bond 0.00792 ( 10) link_BETA1-4 : angle 3.35752 ( 30) link_BETA1-6 : bond 0.00917 ( 2) link_BETA1-6 : angle 2.72928 ( 6) link_NAG-ASN : bond 0.00551 ( 11) link_NAG-ASN : angle 4.03123 ( 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 88 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 45 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9370 (OUTLIER) cc_final: 0.7298 (t80) REVERT: A 402 ARG cc_start: 0.3471 (OUTLIER) cc_final: -0.1079 (mtm-85) REVERT: A 489 MET cc_start: 0.9163 (pmm) cc_final: 0.8948 (pmm) REVERT: A 549 MET cc_start: 0.7924 (mmm) cc_final: 0.7672 (mmm) REVERT: A 915 TYR cc_start: 0.9264 (m-80) cc_final: 0.9033 (m-80) REVERT: A 924 LEU cc_start: 0.9414 (tp) cc_final: 0.8977 (pp) REVERT: B 534 GLU cc_start: 0.4786 (OUTLIER) cc_final: 0.1007 (mp0) REVERT: B 568 MET cc_start: 0.9385 (tpp) cc_final: 0.9160 (tpt) outliers start: 43 outliers final: 33 residues processed: 84 average time/residue: 0.1005 time to fit residues: 13.6534 Evaluate side-chains 81 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 45 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 498 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 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 429 VAL Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 655 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 42 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 99 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 GLN B 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.073273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.047611 restraints weight = 80397.256| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 5.44 r_work: 0.2769 rms_B_bonded: 5.14 restraints_weight: 2.0000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 13461 Z= 0.168 Angle : 0.741 18.461 18372 Z= 0.349 Chirality : 0.047 0.389 2106 Planarity : 0.005 0.131 2354 Dihedral : 11.981 96.933 2431 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.52 % Favored : 93.30 % Rotamer: Outliers : 2.82 % Allowed : 20.16 % Favored : 77.03 % 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 aren not related in a simple way. whole: -0.94 (0.21), residues: 1657 helix: 0.82 (0.40), residues: 172 sheet: -0.11 (0.22), residues: 557 loop : -1.25 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 683 TYR 0.018 0.001 TYR A 915 PHE 0.022 0.001 PHE A 930 TRP 0.014 0.002 TRP A 839 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00386 (13399) covalent geometry : angle 0.70793 (18224) SS BOND : bond 0.00251 ( 38) SS BOND : angle 0.93607 ( 76) hydrogen bonds : bond 0.03424 ( 468) hydrogen bonds : angle 5.83052 ( 1226) link_BETA1-3 : bond 0.00817 ( 1) link_BETA1-3 : angle 3.69853 ( 3) link_BETA1-4 : bond 0.00712 ( 10) link_BETA1-4 : angle 3.32318 ( 30) link_BETA1-6 : bond 0.01004 ( 2) link_BETA1-6 : angle 2.31255 ( 6) link_NAG-ASN : bond 0.00528 ( 11) link_NAG-ASN : angle 3.80336 ( 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 83 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 43 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9337 (OUTLIER) cc_final: 0.7396 (t80) REVERT: A 402 ARG cc_start: 0.2920 (OUTLIER) cc_final: -0.0991 (mtm-85) REVERT: A 489 MET cc_start: 0.9202 (pmm) cc_final: 0.8894 (pmm) REVERT: A 549 MET cc_start: 0.7981 (mmm) cc_final: 0.7717 (mmm) REVERT: A 880 CYS cc_start: 0.7367 (OUTLIER) cc_final: 0.7111 (p) REVERT: A 924 LEU cc_start: 0.9483 (tp) cc_final: 0.9074 (pp) REVERT: B 180 MET cc_start: 0.9292 (pmm) cc_final: 0.9055 (pmm) REVERT: B 590 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7528 (tm-30) outliers start: 40 outliers final: 26 residues processed: 80 average time/residue: 0.0933 time to fit residues: 11.7638 Evaluate side-chains 73 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 43 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 916 GLN 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 227 MET 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 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: 20.0000 chunk 23 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.072461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.046688 restraints weight = 72372.598| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 5.37 r_work: 0.2752 rms_B_bonded: 5.21 restraints_weight: 2.0000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 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 = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 13461 Z= 0.249 Angle : 0.773 14.582 18372 Z= 0.368 Chirality : 0.047 0.392 2106 Planarity : 0.006 0.128 2354 Dihedral : 11.351 93.705 2426 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.43 % Favored : 92.33 % Rotamer: Outliers : 3.17 % Allowed : 20.01 % Favored : 76.81 % 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 aren not related in a simple way. whole: -1.00 (0.21), residues: 1657 helix: 0.80 (0.41), residues: 171 sheet: -0.13 (0.22), residues: 571 loop : -1.32 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 530 TYR 0.013 0.001 TYR A 448 PHE 0.016 0.002 PHE A 289 TRP 0.013 0.002 TRP A 929 HIS 0.004 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00556 (13399) covalent geometry : angle 0.74265 (18224) SS BOND : bond 0.00330 ( 38) SS BOND : angle 0.93610 ( 76) hydrogen bonds : bond 0.03620 ( 468) hydrogen bonds : angle 5.91227 ( 1226) link_BETA1-3 : bond 0.00381 ( 1) link_BETA1-3 : angle 3.42261 ( 3) link_BETA1-4 : bond 0.00757 ( 10) link_BETA1-4 : angle 3.37296 ( 30) link_BETA1-6 : bond 0.01058 ( 2) link_BETA1-6 : angle 2.03862 ( 6) link_NAG-ASN : bond 0.00513 ( 11) link_NAG-ASN : angle 3.71126 ( 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 91 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 46 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9398 (OUTLIER) cc_final: 0.7047 (t80) REVERT: A 402 ARG cc_start: 0.3269 (OUTLIER) cc_final: -0.1274 (mtm-85) REVERT: A 489 MET cc_start: 0.9210 (pmm) cc_final: 0.8877 (pmm) REVERT: A 549 MET cc_start: 0.7982 (mmm) cc_final: 0.7756 (mmm) REVERT: A 880 CYS cc_start: 0.7398 (OUTLIER) cc_final: 0.7194 (p) REVERT: A 915 TYR cc_start: 0.9208 (m-80) cc_final: 0.8945 (m-80) REVERT: A 924 LEU cc_start: 0.9506 (tp) cc_final: 0.9108 (pp) REVERT: B 590 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7535 (tm-30) outliers start: 45 outliers final: 33 residues processed: 88 average time/residue: 0.0878 time to fit residues: 12.2910 Evaluate side-chains 83 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 46 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 957 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 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 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 406 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 118 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.073579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.047568 restraints weight = 93640.653| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 6.03 r_work: 0.2769 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 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 = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 13461 Z= 0.138 Angle : 0.721 13.968 18372 Z= 0.339 Chirality : 0.046 0.375 2106 Planarity : 0.005 0.125 2354 Dihedral : 10.627 91.915 2426 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.22 % Favored : 93.60 % Rotamer: Outliers : 3.03 % Allowed : 20.65 % 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 aren not related in a simple way. whole: -0.78 (0.21), residues: 1657 helix: 0.79 (0.40), residues: 174 sheet: 0.03 (0.22), residues: 567 loop : -1.14 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 683 TYR 0.013 0.001 TYR A 288 PHE 0.012 0.001 PHE B 248 TRP 0.012 0.001 TRP A 839 HIS 0.003 0.001 HIS B 509 Details of bonding type rmsd covalent geometry : bond 0.00319 (13399) covalent geometry : angle 0.69018 (18224) SS BOND : bond 0.00219 ( 38) SS BOND : angle 0.93586 ( 76) hydrogen bonds : bond 0.03148 ( 468) hydrogen bonds : angle 5.69229 ( 1226) link_BETA1-3 : bond 0.00653 ( 1) link_BETA1-3 : angle 3.49149 ( 3) link_BETA1-4 : bond 0.00696 ( 10) link_BETA1-4 : angle 3.31447 ( 30) link_BETA1-6 : bond 0.01058 ( 2) link_BETA1-6 : angle 1.82991 ( 6) link_NAG-ASN : bond 0.00541 ( 11) link_NAG-ASN : angle 3.55614 ( 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 89 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 46 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9331 (OUTLIER) cc_final: 0.7345 (t80) REVERT: A 400 ARG cc_start: 0.2746 (OUTLIER) cc_final: -0.2096 (mmm-85) REVERT: A 402 ARG cc_start: 0.2669 (OUTLIER) cc_final: -0.2101 (mtm-85) REVERT: A 489 MET cc_start: 0.9190 (pmm) cc_final: 0.8837 (pmm) REVERT: A 549 MET cc_start: 0.8001 (mmm) cc_final: 0.7767 (mmm) REVERT: A 915 TYR cc_start: 0.9247 (m-10) cc_final: 0.9029 (m-80) REVERT: A 924 LEU cc_start: 0.9499 (tp) cc_final: 0.9104 (pp) outliers start: 43 outliers final: 29 residues processed: 86 average time/residue: 0.0975 time to fit residues: 12.8202 Evaluate side-chains 77 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 45 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 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 679 GLU 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 104 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.071503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.046113 restraints weight = 72640.011| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 5.26 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 13461 Z= 0.345 Angle : 0.852 13.019 18372 Z= 0.410 Chirality : 0.049 0.390 2106 Planarity : 0.006 0.126 2354 Dihedral : 10.491 95.078 2426 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.03 % Favored : 91.79 % Rotamer: Outliers : 3.31 % Allowed : 20.72 % Favored : 75.97 % 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 aren not related in a simple way. whole: -1.11 (0.21), residues: 1657 helix: 0.68 (0.40), residues: 172 sheet: -0.17 (0.22), residues: 564 loop : -1.40 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 530 TYR 0.015 0.002 TYR A 448 PHE 0.021 0.002 PHE A 289 TRP 0.015 0.002 TRP A 839 HIS 0.006 0.001 HIS B 509 Details of bonding type rmsd covalent geometry : bond 0.00765 (13399) covalent geometry : angle 0.82450 (18224) SS BOND : bond 0.00441 ( 38) SS BOND : angle 1.22351 ( 76) hydrogen bonds : bond 0.04027 ( 468) hydrogen bonds : angle 6.04791 ( 1226) link_BETA1-3 : bond 0.00105 ( 1) link_BETA1-3 : angle 3.40808 ( 3) link_BETA1-4 : bond 0.00629 ( 10) link_BETA1-4 : angle 3.39466 ( 30) link_BETA1-6 : bond 0.00985 ( 2) link_BETA1-6 : angle 1.83430 ( 6) link_NAG-ASN : bond 0.00651 ( 11) link_NAG-ASN : angle 3.68180 ( 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 93 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 46 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9387 (OUTLIER) cc_final: 0.7112 (t80) REVERT: A 400 ARG cc_start: 0.3252 (OUTLIER) cc_final: -0.1780 (mmm-85) REVERT: A 402 ARG cc_start: 0.2816 (OUTLIER) cc_final: -0.2373 (mtm-85) REVERT: A 915 TYR cc_start: 0.9272 (m-10) cc_final: 0.9050 (m-80) REVERT: A 924 LEU cc_start: 0.9527 (tp) cc_final: 0.9129 (pp) REVERT: B 142 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8623 (tpt) REVERT: B 568 MET cc_start: 0.9368 (tpp) cc_final: 0.9158 (tpp) REVERT: B 590 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7674 (tm-30) outliers start: 47 outliers final: 37 residues processed: 89 average time/residue: 0.1160 time to fit residues: 15.6200 Evaluate side-chains 86 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 44 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 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 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 344 ILE Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 406 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 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: 5.9990 chunk 34 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 6 optimal weight: 0.0370 chunk 48 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.0470 chunk 105 optimal weight: 7.9990 chunk 87 optimal weight: 0.0020 chunk 155 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 overall best weight: 0.8168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 GLN A 916 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.073628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.047665 restraints weight = 98138.672| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 6.14 r_work: 0.2767 rms_B_bonded: 5.66 restraints_weight: 2.0000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 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 = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2346 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= 0.127 Angle : 0.731 12.629 18372 Z= 0.344 Chirality : 0.046 0.362 2106 Planarity : 0.005 0.122 2354 Dihedral : 9.755 92.425 2426 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.28 % Favored : 93.54 % Rotamer: Outliers : 2.68 % Allowed : 21.56 % Favored : 75.76 % 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 aren not related in a simple way. whole: -0.84 (0.21), residues: 1657 helix: 0.73 (0.40), residues: 174 sheet: -0.02 (0.22), residues: 567 loop : -1.17 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 917 TYR 0.013 0.001 TYR A 288 PHE 0.011 0.001 PHE B 248 TRP 0.013 0.001 TRP A 839 HIS 0.003 0.001 HIS B 509 Details of bonding type rmsd covalent geometry : bond 0.00293 (13399) covalent geometry : angle 0.70150 (18224) SS BOND : bond 0.00182 ( 38) SS BOND : angle 1.09975 ( 76) hydrogen bonds : bond 0.03077 ( 468) hydrogen bonds : angle 5.67843 ( 1226) link_BETA1-3 : bond 0.00808 ( 1) link_BETA1-3 : angle 3.30107 ( 3) link_BETA1-4 : bond 0.00672 ( 10) link_BETA1-4 : angle 3.19182 ( 30) link_BETA1-6 : bond 0.01073 ( 2) link_BETA1-6 : angle 1.76048 ( 6) link_NAG-ASN : bond 0.00552 ( 11) link_NAG-ASN : angle 3.44682 ( 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 83 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 45 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9349 (OUTLIER) cc_final: 0.7342 (t80) REVERT: A 400 ARG cc_start: 0.2433 (OUTLIER) cc_final: -0.1329 (tpt170) REVERT: A 402 ARG cc_start: 0.2389 (OUTLIER) cc_final: -0.2010 (mtm-85) REVERT: A 489 MET cc_start: 0.9232 (pmm) cc_final: 0.9031 (pmm) REVERT: A 915 TYR cc_start: 0.9292 (m-80) cc_final: 0.9051 (m-80) REVERT: A 924 LEU cc_start: 0.9487 (tp) cc_final: 0.9104 (pp) REVERT: B 357 LEU cc_start: 0.8988 (mt) cc_final: 0.8744 (mt) outliers start: 38 outliers final: 29 residues processed: 80 average time/residue: 0.0935 time to fit residues: 11.7109 Evaluate side-chains 77 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 45 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 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 230 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 22 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 0.1980 chunk 108 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 921 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.072032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.046466 restraints weight = 73871.821| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 5.34 r_work: 0.2747 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 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 = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 13461 Z= 0.268 Angle : 0.791 12.473 18372 Z= 0.377 Chirality : 0.047 0.378 2106 Planarity : 0.006 0.123 2354 Dihedral : 9.695 93.029 2426 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.61 % Favored : 92.21 % Rotamer: Outliers : 2.82 % Allowed : 21.21 % Favored : 75.97 % 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 aren not related in a simple way. whole: -1.04 (0.21), residues: 1657 helix: 0.72 (0.40), residues: 173 sheet: -0.18 (0.22), residues: 571 loop : -1.33 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 530 TYR 0.013 0.002 TYR A 915 PHE 0.018 0.002 PHE A 289 TRP 0.012 0.002 TRP A 113 HIS 0.004 0.001 HIS B 509 Details of bonding type rmsd covalent geometry : bond 0.00598 (13399) covalent geometry : angle 0.76388 (18224) SS BOND : bond 0.00359 ( 38) SS BOND : angle 1.14414 ( 76) hydrogen bonds : bond 0.03597 ( 468) hydrogen bonds : angle 5.87111 ( 1226) link_BETA1-3 : bond 0.00282 ( 1) link_BETA1-3 : angle 3.23610 ( 3) link_BETA1-4 : bond 0.00624 ( 10) link_BETA1-4 : angle 3.11936 ( 30) link_BETA1-6 : bond 0.00971 ( 2) link_BETA1-6 : angle 1.75641 ( 6) link_NAG-ASN : bond 0.00591 ( 11) link_NAG-ASN : angle 3.52548 ( 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 84 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 44 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9395 (OUTLIER) cc_final: 0.7076 (t80) REVERT: A 400 ARG cc_start: 0.3836 (OUTLIER) cc_final: -0.1978 (mmm-85) REVERT: A 402 ARG cc_start: 0.3434 (OUTLIER) cc_final: -0.2147 (mtm-85) REVERT: A 915 TYR cc_start: 0.9279 (m-10) cc_final: 0.9051 (m-80) REVERT: A 924 LEU cc_start: 0.9522 (tp) cc_final: 0.9157 (pp) REVERT: B 142 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8765 (tpt) REVERT: B 180 MET cc_start: 0.9301 (pmm) cc_final: 0.9028 (pmm) outliers start: 40 outliers final: 35 residues processed: 82 average time/residue: 0.1060 time to fit residues: 13.4190 Evaluate side-chains 83 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 44 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 400 ARG 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 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 230 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 303 ASN 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 406 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 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: 0.0980 chunk 119 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 137 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.073964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048129 restraints weight = 78953.044| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 5.56 r_work: 0.2802 rms_B_bonded: 5.24 restraints_weight: 2.0000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 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 = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2509 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= 0.118 Angle : 0.724 13.130 18372 Z= 0.340 Chirality : 0.046 0.359 2106 Planarity : 0.005 0.119 2354 Dihedral : 9.214 90.424 2426 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.34 % Favored : 93.48 % Rotamer: Outliers : 2.26 % Allowed : 22.13 % Favored : 75.62 % 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 aren not related in a simple way. whole: -0.79 (0.21), residues: 1657 helix: 0.69 (0.40), residues: 175 sheet: 0.02 (0.22), residues: 565 loop : -1.13 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 917 TYR 0.014 0.001 TYR A 288 PHE 0.010 0.001 PHE A 356 TRP 0.015 0.001 TRP B 238 HIS 0.003 0.001 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00273 (13399) covalent geometry : angle 0.69800 (18224) SS BOND : bond 0.00214 ( 38) SS BOND : angle 0.97218 ( 76) hydrogen bonds : bond 0.02952 ( 468) hydrogen bonds : angle 5.56141 ( 1226) link_BETA1-3 : bond 0.00818 ( 1) link_BETA1-3 : angle 2.91483 ( 3) link_BETA1-4 : bond 0.00703 ( 10) link_BETA1-4 : angle 2.94662 ( 30) link_BETA1-6 : bond 0.01083 ( 2) link_BETA1-6 : angle 1.69688 ( 6) link_NAG-ASN : bond 0.00576 ( 11) link_NAG-ASN : angle 3.35601 ( 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 78 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 46 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9306 (OUTLIER) cc_final: 0.7509 (t80) REVERT: A 395 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.7094 (pm20) REVERT: A 402 ARG cc_start: 0.2214 (OUTLIER) cc_final: -0.1951 (mpp80) REVERT: A 915 TYR cc_start: 0.9279 (m-10) cc_final: 0.9045 (m-80) REVERT: A 924 LEU cc_start: 0.9495 (tp) cc_final: 0.9130 (pp) REVERT: A 955 LEU cc_start: 0.9728 (mm) cc_final: 0.9458 (tp) REVERT: B 357 LEU cc_start: 0.8948 (mt) cc_final: 0.8703 (mt) outliers start: 32 outliers final: 26 residues processed: 75 average time/residue: 0.0961 time to fit residues: 11.5754 Evaluate side-chains 74 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 45 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 395 GLN 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 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 230 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 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 604 CYS Chi-restraints excluded: chain B residue 642 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: 2.9990 chunk 52 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 93 optimal weight: 50.0000 chunk 48 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 96 optimal weight: 0.0970 chunk 1 optimal weight: 0.0770 chunk 115 optimal weight: 0.5980 overall best weight: 0.9538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.073677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.048211 restraints weight = 72415.083| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 5.29 r_work: 0.2805 rms_B_bonded: 5.20 restraints_weight: 2.0000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 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 = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2596 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= 0.124 Angle : 0.713 13.198 18372 Z= 0.334 Chirality : 0.046 0.360 2106 Planarity : 0.005 0.118 2354 Dihedral : 8.948 88.453 2425 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.34 % Favored : 93.48 % Rotamer: Outliers : 2.54 % Allowed : 21.63 % Favored : 75.83 % 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 aren not related in a simple way. whole: -0.78 (0.21), residues: 1657 helix: 0.54 (0.39), residues: 181 sheet: 0.04 (0.22), residues: 568 loop : -1.11 (0.22), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 917 TYR 0.012 0.001 TYR A 288 PHE 0.012 0.001 PHE B 248 TRP 0.012 0.001 TRP B 238 HIS 0.002 0.001 HIS B 509 Details of bonding type rmsd covalent geometry : bond 0.00291 (13399) covalent geometry : angle 0.68666 (18224) SS BOND : bond 0.00194 ( 38) SS BOND : angle 1.09218 ( 76) hydrogen bonds : bond 0.02929 ( 468) hydrogen bonds : angle 5.47417 ( 1226) link_BETA1-3 : bond 0.00615 ( 1) link_BETA1-3 : angle 2.70496 ( 3) link_BETA1-4 : bond 0.00674 ( 10) link_BETA1-4 : angle 2.86859 ( 30) link_BETA1-6 : bond 0.00992 ( 2) link_BETA1-6 : angle 1.65551 ( 6) link_NAG-ASN : bond 0.00546 ( 11) link_NAG-ASN : angle 3.34292 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5186.05 seconds wall clock time: 89 minutes 3.86 seconds (5343.86 seconds total)