Starting phenix.real_space_refine on Thu May 15 20:30:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t2v_40989/05_2025/8t2v_40989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t2v_40989/05_2025/8t2v_40989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t2v_40989/05_2025/8t2v_40989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t2v_40989/05_2025/8t2v_40989.map" model { file = "/net/cci-nas-00/data/ceres_data/8t2v_40989/05_2025/8t2v_40989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t2v_40989/05_2025/8t2v_40989.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 7 9.91 5 Mg 1 5.21 5 S 101 5.16 5 C 8225 2.51 5 N 2209 2.21 5 O 2591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13134 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7247 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 946, 7239 Classifications: {'peptide': 946} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 882} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 946, 7239 Classifications: {'peptide': 946} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 882} Chain breaks: 2 bond proxies already assigned to first conformer: 7403 Chain: "B" Number of atoms: 5502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5502 Classifications: {'peptide': 718} Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 682} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Unusual residues: {' CA': 5, 'NAG': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 79 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 2, 'NAG': 1} Classifications: {'undetermined': 6, 'water': 6} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.31, per 1000 atoms: 0.78 Number of scatterers: 13134 At special positions: 0 Unit cell: (103.68, 166.32, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 7 19.99 S 101 16.00 Mg 1 11.99 O 2591 8.00 N 2209 7.00 C 8225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.04 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.11 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.07 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 484 " distance=2.06 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 545 " distance=2.05 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 608 " distance=2.06 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 687 " distance=2.05 Simple disulfide: pdb=" SG CYS A 826 " - pdb=" SG CYS A 890 " distance=2.06 Simple disulfide: pdb=" SG CYS A 880 " - pdb=" SG CYS A 885 " distance=2.04 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 23 " distance=2.02 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 435 " distance=2.06 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 38 " distance=2.07 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 49 " distance=2.07 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.02 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.12 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.07 Simple disulfide: pdb=" SG CYS B 406 " - pdb=" SG CYS B 433 " distance=2.04 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 457 " distance=2.06 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 460 " distance=2.06 Simple disulfide: pdb=" SG CYS B 460 " - pdb=" SG CYS B 471 " distance=2.06 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 471 " distance=2.05 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 503 " distance=2.06 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 501 " distance=2.05 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 506 " distance=2.04 Simple disulfide: pdb=" SG CYS B 508 " - pdb=" SG CYS B 521 " distance=2.07 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 544 " distance=2.05 Simple disulfide: pdb=" SG CYS B 528 " - pdb=" SG CYS B 542 " distance=2.05 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 547 " distance=2.04 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 558 " distance=2.05 Simple disulfide: pdb=" SG CYS B 560 " - pdb=" SG CYS B 583 " distance=2.06 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 581 " distance=2.05 Simple disulfide: pdb=" SG CYS B 575 " - pdb=" SG CYS B 586 " distance=2.02 Simple disulfide: pdb=" SG CYS B 588 " - pdb=" SG CYS B 598 " distance=2.08 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 604 " distance=2.05 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 655 " distance=2.08 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 635 " distance=2.06 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 631 " distance=2.06 Simple disulfide: pdb=" SG CYS B 663 " - pdb=" SG CYS B 687 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " BETA1-6 " BMA F 3 " - " BMA F 5 " " BMA H 3 " - " BMA H 4 " NAG-ASN " NAG A1105 " - " ASN A 249 " " NAG A1106 " - " ASN A 680 " " NAG A1107 " - " ASN A 570 " " NAG A1108 " - " ASN A 15 " " NAG B 801 " - " ASN B 654 " " NAG C 1 " - " ASN A 931 " " NAG D 1 " - " ASN B 559 " " NAG E 1 " - " ASN B 320 " " NAG F 1 " - " ASN B 371 " " NAG G 1 " - " ASN B 99 " " NAG H 1 " - " ASN B 452 " Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 2.3 seconds 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 30 sheets defined 16.1% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.904A pdb=" N TYR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 259 through 264 removed outlier: 3.605A pdb=" N THR A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.594A pdb=" N GLN A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 991 removed outlier: 3.832A pdb=" N VAL A 969 " --> pdb=" O PRO A 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 20 removed outlier: 4.353A pdb=" N SER B 20 " --> pdb=" O CYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 removed outlier: 3.823A pdb=" N ASP B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.582A pdb=" N VAL B 80 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 124 through 130 removed outlier: 3.581A pdb=" N TRP B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 169 through 175 removed outlier: 3.522A pdb=" N GLU B 174 " --> pdb=" O GLU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 207 removed outlier: 4.411A pdb=" N PHE B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 281 through 286 removed outlier: 4.532A pdb=" N THR B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B 286 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 302 removed outlier: 3.669A pdb=" N LYS B 302 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 323 removed outlier: 4.502A pdb=" N ASN B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 352 Processing helix chain 'B' and resid 435 through 441 removed outlier: 3.537A pdb=" N ALA B 441 " --> pdb=" O GLN B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 449 Processing helix chain 'B' and resid 493 through 498 Processing helix chain 'B' and resid 535 through 539 Processing helix chain 'B' and resid 573 through 578 Processing helix chain 'B' and resid 606 through 610 Processing helix chain 'B' and resid 611 through 621 removed outlier: 3.722A pdb=" N CYS B 617 " --> pdb=" O GLU B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 718 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.580A pdb=" N ASP A 434 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A 424 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 27 removed outlier: 4.734A pdb=" N VAL A 53 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 100 Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 364 removed outlier: 5.850A pdb=" N ASP A 373 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AB2, first strand: chain 'A' and resid 521 through 523 removed outlier: 5.513A pdb=" N VAL A 454 " --> pdb=" O HIS A 587 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 465 through 466 Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB5, first strand: chain 'A' and resid 612 through 619 removed outlier: 4.104A pdb=" N ARG A 661 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 674 through 678 removed outlier: 6.664A pdb=" N ALA A 647 " --> pdb=" O LEU A 689 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 748 through 755 removed outlier: 7.141A pdb=" N PHE A 908 " --> pdb=" O ILE A 815 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ILE A 815 " --> pdb=" O PHE A 908 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 758 through 760 removed outlier: 6.524A pdb=" N LEU A 759 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 922 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N GLN A 925 " --> pdb=" O PRO A 804 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN A 795 " --> pdb=" O GLU A 894 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU A 894 " --> pdb=" O ASN A 795 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 758 through 760 removed outlier: 6.524A pdb=" N LEU A 759 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 922 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 878 " --> pdb=" O GLN A 925 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N HIS A 927 " --> pdb=" O VAL A 878 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AC2, first strand: chain 'B' and resid 63 through 65 removed outlier: 5.160A pdb=" N VAL B 63 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA B 89 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AC4, first strand: chain 'B' and resid 190 through 197 removed outlier: 4.904A pdb=" N HIS B 192 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA B 155 " --> pdb=" O HIS B 192 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU B 196 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE B 151 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 310 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 355 Processing sheet with id=AC6, first strand: chain 'B' and resid 454 through 456 Processing sheet with id=AC7, first strand: chain 'B' and resid 500 through 502 Processing sheet with id=AC8, first strand: chain 'B' and resid 516 through 517 Processing sheet with id=AC9, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AD1, first strand: chain 'B' and resid 553 through 554 Processing sheet with id=AD2, first strand: chain 'B' and resid 580 through 582 Processing sheet with id=AD3, first strand: chain 'B' and resid 638 through 640 removed outlier: 3.523A pdb=" N ILE B 678 " --> pdb=" O TYR B 670 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.50 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2227 1.30 - 1.44: 3331 1.44 - 1.57: 7712 1.57 - 1.71: 1 1.71 - 1.85: 128 Bond restraints: 13399 Sorted by residual: bond pdb=" C GLY A 423 " pdb=" O GLY A 423 " ideal model delta sigma weight residual 1.233 1.186 0.047 7.00e-03 2.04e+04 4.49e+01 bond pdb=" C PRO A 433 " pdb=" O PRO A 433 " ideal model delta sigma weight residual 1.233 1.159 0.074 1.16e-02 7.43e+03 4.03e+01 bond pdb=" C SER A 420 " pdb=" O SER A 420 " ideal model delta sigma weight residual 1.235 1.165 0.070 1.14e-02 7.69e+03 3.81e+01 bond pdb=" CA SER B 211 " pdb=" CB SER B 211 " ideal model delta sigma weight residual 1.534 1.458 0.076 1.34e-02 5.57e+03 3.25e+01 bond pdb=" N GLY A 641 " pdb=" CA GLY A 641 " ideal model delta sigma weight residual 1.442 1.483 -0.041 7.70e-03 1.69e+04 2.85e+01 ... (remaining 13394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 13964 2.25 - 4.50: 3793 4.50 - 6.74: 439 6.74 - 8.99: 25 8.99 - 11.24: 3 Bond angle restraints: 18224 Sorted by residual: angle pdb=" C PRO A 403 " pdb=" CA PRO A 403 " pdb=" CB PRO A 403 " ideal model delta sigma weight residual 111.56 102.38 9.18 1.09e+00 8.42e-01 7.09e+01 angle pdb=" CA GLY A 387 " pdb=" C GLY A 387 " pdb=" O GLY A 387 " ideal model delta sigma weight residual 122.22 116.88 5.34 6.50e-01 2.37e+00 6.76e+01 angle pdb=" CA GLY B 555 " pdb=" C GLY B 555 " pdb=" O GLY B 555 " ideal model delta sigma weight residual 122.22 117.90 4.32 6.50e-01 2.37e+00 4.41e+01 angle pdb=" N PRO A 403 " pdb=" CA PRO A 403 " pdb=" CB PRO A 403 " ideal model delta sigma weight residual 103.30 108.50 -5.20 8.00e-01 1.56e+00 4.22e+01 angle pdb=" CA GLY B 518 " pdb=" C GLY B 518 " pdb=" O GLY B 518 " ideal model delta sigma weight residual 122.22 118.22 4.00 6.50e-01 2.37e+00 3.80e+01 ... (remaining 18219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.38: 7726 24.38 - 48.75: 632 48.75 - 73.12: 138 73.12 - 97.50: 61 97.50 - 121.87: 19 Dihedral angle restraints: 8576 sinusoidal: 3814 harmonic: 4762 Sorted by residual: dihedral pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " pdb=" SG CYS B 38 " pdb=" CB CYS B 38 " ideal model delta sinusoidal sigma weight residual -86.00 -176.18 90.18 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS B 549 " pdb=" SG CYS B 549 " pdb=" SG CYS B 558 " pdb=" CB CYS B 558 " ideal model delta sinusoidal sigma weight residual 93.00 -179.32 -87.68 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS B 601 " pdb=" SG CYS B 601 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -164.75 78.75 1 1.00e+01 1.00e-02 7.73e+01 ... (remaining 8573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 1863 0.147 - 0.293: 238 0.293 - 0.440: 3 0.440 - 0.587: 1 0.587 - 0.733: 1 Chirality restraints: 2106 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.23e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.88e+01 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.74e+01 ... (remaining 2103 not shown) Planarity restraints: 2365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.145 2.00e-02 2.50e+03 1.25e-01 1.96e+02 pdb=" C7 NAG C 1 " -0.097 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.127 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.178 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 308 " -0.077 2.00e-02 2.50e+03 4.86e-02 4.13e+01 pdb=" CG PHE B 308 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE B 308 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE B 308 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 PHE B 308 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 308 " -0.027 2.00e-02 2.50e+03 pdb=" CZ PHE B 308 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1106 " 0.064 2.00e-02 2.50e+03 5.44e-02 3.70e+01 pdb=" C7 NAG A1106 " -0.032 2.00e-02 2.50e+03 pdb=" C8 NAG A1106 " 0.053 2.00e-02 2.50e+03 pdb=" N2 NAG A1106 " -0.082 2.00e-02 2.50e+03 pdb=" O7 NAG A1106 " -0.003 2.00e-02 2.50e+03 ... (remaining 2362 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 75 2.38 - 3.01: 7251 3.01 - 3.64: 19663 3.64 - 4.27: 28595 4.27 - 4.90: 46954 Nonbonded interactions: 102538 Sorted by model distance: nonbonded pdb=" OE1 GLU B 220 " pdb="CA CA B 805 " model vdw 1.751 2.510 nonbonded pdb=" OE1 GLU A 243 " pdb="CA CA A1102 " model vdw 1.789 2.510 nonbonded pdb=" OE2 GLU A 252 " pdb="CA CA A1102 " model vdw 1.794 2.510 nonbonded pdb=" OE2 GLU A 642 " pdb="CA CA A1109 " model vdw 1.822 2.510 nonbonded pdb="MG MG B 804 " pdb=" O HOH B 902 " model vdw 1.906 2.170 ... (remaining 102533 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 35.420 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.092 13461 Z= 1.140 Angle : 1.973 45.462 18372 Z= 1.332 Chirality : 0.095 0.733 2106 Planarity : 0.009 0.152 2354 Dihedral : 20.167 121.873 5414 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.97 % Allowed : 9.06 % Favored : 89.98 % Rotamer: Outliers : 5.50 % Allowed : 17.48 % Favored : 77.03 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.20), residues: 1657 helix: -0.68 (0.37), residues: 162 sheet: -0.46 (0.23), residues: 478 loop : -1.94 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.008 TRP A 100 HIS 0.018 0.003 HIS A 112 PHE 0.081 0.010 PHE B 308 TYR 0.064 0.010 TYR A 288 ARG 0.020 0.002 ARG A 320 Details of bonding type rmsd link_NAG-ASN : bond 0.01681 ( 11) link_NAG-ASN : angle 4.36011 ( 33) link_BETA1-4 : bond 0.01973 ( 10) link_BETA1-4 : angle 8.93797 ( 30) hydrogen bonds : bond 0.15041 ( 468) hydrogen bonds : angle 7.72635 ( 1226) link_BETA1-6 : bond 0.01139 ( 2) link_BETA1-6 : angle 5.82030 ( 6) SS BOND : bond 0.03287 ( 38) SS BOND : angle 2.44728 ( 76) link_BETA1-3 : bond 0.00230 ( 1) link_BETA1-3 : angle 3.26883 ( 3) covalent geometry : bond 0.01573 (13399) covalent geometry : angle 1.92879 (18224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 51 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.9255 (OUTLIER) cc_final: 0.9002 (m-30) REVERT: A 400 ARG cc_start: 0.1721 (OUTLIER) cc_final: 0.0346 (tpt170) REVERT: A 402 ARG cc_start: 0.3222 (OUTLIER) cc_final: 0.2560 (mtm-85) REVERT: A 549 MET cc_start: 0.8201 (mmm) cc_final: 0.7715 (mmm) REVERT: A 779 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8344 (tppt) REVERT: A 924 LEU cc_start: 0.9707 (OUTLIER) cc_final: 0.9478 (tp) REVERT: B 534 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.5473 (mp0) outliers start: 78 outliers final: 38 residues processed: 124 average time/residue: 0.2583 time to fit residues: 47.1222 Evaluate side-chains 89 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 45 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 692 PRO Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 642 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS B 313 ASN B 438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.074380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.047995 restraints weight = 116001.502| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 6.63 r_work: 0.2759 rms_B_bonded: 5.93 restraints_weight: 2.0000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 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 = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 13461 Z= 0.159 Angle : 0.815 18.519 18372 Z= 0.385 Chirality : 0.050 0.394 2106 Planarity : 0.006 0.140 2354 Dihedral : 15.169 111.282 2499 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.74 % Favored : 93.90 % Rotamer: Outliers : 2.47 % Allowed : 18.11 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.20), residues: 1657 helix: 0.51 (0.41), residues: 170 sheet: -0.19 (0.22), residues: 544 loop : -1.47 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 262 HIS 0.005 0.001 HIS A 587 PHE 0.011 0.001 PHE B 248 TYR 0.020 0.002 TYR B 318 ARG 0.007 0.001 ARG B 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00767 ( 11) link_NAG-ASN : angle 4.32200 ( 33) link_BETA1-4 : bond 0.00802 ( 10) link_BETA1-4 : angle 3.40315 ( 30) hydrogen bonds : bond 0.03905 ( 468) hydrogen bonds : angle 6.25407 ( 1226) link_BETA1-6 : bond 0.01172 ( 2) link_BETA1-6 : angle 2.91608 ( 6) SS BOND : bond 0.00304 ( 38) SS BOND : angle 1.08958 ( 76) link_BETA1-3 : bond 0.00173 ( 1) link_BETA1-3 : angle 4.01688 ( 3) covalent geometry : bond 0.00366 (13399) covalent geometry : angle 0.77908 (18224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 44 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.2778 (OUTLIER) cc_final: -0.0683 (mtm-85) REVERT: A 549 MET cc_start: 0.7934 (mmm) cc_final: 0.7630 (mmm) REVERT: B 357 LEU cc_start: 0.9000 (mt) cc_final: 0.8744 (mt) REVERT: B 534 GLU cc_start: 0.4497 (OUTLIER) cc_final: 0.2472 (mp0) outliers start: 35 outliers final: 19 residues processed: 76 average time/residue: 0.2380 time to fit residues: 28.6901 Evaluate side-chains 65 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 534 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 21 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 ASN B 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.072046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.046746 restraints weight = 64854.657| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 5.01 r_work: 0.2752 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 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 = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 13461 Z= 0.289 Angle : 0.829 11.726 18372 Z= 0.400 Chirality : 0.050 0.404 2106 Planarity : 0.006 0.135 2354 Dihedral : 13.138 102.467 2433 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.15 % Favored : 91.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.21), residues: 1657 helix: 0.64 (0.41), residues: 171 sheet: -0.28 (0.22), residues: 557 loop : -1.47 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 839 HIS 0.006 0.001 HIS B 280 PHE 0.020 0.002 PHE A 289 TYR 0.014 0.002 TYR A 448 ARG 0.014 0.001 ARG B 530 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 11) link_NAG-ASN : angle 4.00632 ( 33) link_BETA1-4 : bond 0.00752 ( 10) link_BETA1-4 : angle 3.34925 ( 30) hydrogen bonds : bond 0.04221 ( 468) hydrogen bonds : angle 6.23830 ( 1226) link_BETA1-6 : bond 0.00930 ( 2) link_BETA1-6 : angle 2.71478 ( 6) SS BOND : bond 0.00429 ( 38) SS BOND : angle 1.18003 ( 76) link_BETA1-3 : bond 0.00747 ( 1) link_BETA1-3 : angle 3.55237 ( 3) covalent geometry : bond 0.00648 (13399) covalent geometry : angle 0.79705 (18224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 45 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9431 (OUTLIER) cc_final: 0.7104 (t80) REVERT: A 400 ARG cc_start: 0.3313 (OUTLIER) cc_final: -0.1592 (mmm-85) REVERT: A 402 ARG cc_start: 0.3367 (OUTLIER) cc_final: -0.1718 (mtm-85) REVERT: A 489 MET cc_start: 0.9167 (pmm) cc_final: 0.8954 (pmm) REVERT: A 549 MET cc_start: 0.7900 (mmm) cc_final: 0.7649 (mmm) REVERT: A 924 LEU cc_start: 0.9446 (tp) cc_final: 0.9044 (pp) REVERT: B 142 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8772 (tpt) REVERT: B 534 GLU cc_start: 0.5157 (OUTLIER) cc_final: 0.0991 (mp0) REVERT: B 590 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7500 (tm-30) outliers start: 43 outliers final: 30 residues processed: 84 average time/residue: 0.2455 time to fit residues: 32.2804 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 : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 655 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 126 optimal weight: 0.4980 chunk 91 optimal weight: 0.0370 chunk 102 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.074029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048245 restraints weight = 79250.246| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 5.63 r_work: 0.2793 rms_B_bonded: 5.53 restraints_weight: 2.0000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 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 = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 13461 Z= 0.128 Angle : 0.730 18.042 18372 Z= 0.342 Chirality : 0.047 0.379 2106 Planarity : 0.005 0.131 2354 Dihedral : 11.688 95.123 2432 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.10 % Favored : 93.72 % Rotamer: Outliers : 2.26 % Allowed : 20.51 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.21), residues: 1657 helix: 0.55 (0.39), residues: 179 sheet: -0.06 (0.22), residues: 554 loop : -1.19 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 839 HIS 0.003 0.001 HIS A 587 PHE 0.012 0.001 PHE B 248 TYR 0.013 0.001 TYR A 288 ARG 0.003 0.000 ARG B 666 Details of bonding type rmsd link_NAG-ASN : bond 0.00604 ( 11) link_NAG-ASN : angle 3.77724 ( 33) link_BETA1-4 : bond 0.00769 ( 10) link_BETA1-4 : angle 3.34749 ( 30) hydrogen bonds : bond 0.03199 ( 468) hydrogen bonds : angle 5.76207 ( 1226) link_BETA1-6 : bond 0.01033 ( 2) link_BETA1-6 : angle 2.17388 ( 6) SS BOND : bond 0.00211 ( 38) SS BOND : angle 0.92986 ( 76) link_BETA1-3 : bond 0.00868 ( 1) link_BETA1-3 : angle 3.76527 ( 3) covalent geometry : bond 0.00294 (13399) covalent geometry : angle 0.69684 (18224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 47 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9313 (OUTLIER) cc_final: 0.7526 (t80) REVERT: A 402 ARG cc_start: 0.2168 (OUTLIER) cc_final: -0.1304 (mtm-85) REVERT: A 489 MET cc_start: 0.9213 (pmm) cc_final: 0.8929 (pmm) REVERT: A 549 MET cc_start: 0.8001 (mmm) cc_final: 0.7750 (mmm) REVERT: A 880 CYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7195 (p) REVERT: A 917 ARG cc_start: 0.9218 (ptp90) cc_final: 0.8916 (ptt90) REVERT: A 924 LEU cc_start: 0.9462 (tp) cc_final: 0.9025 (pp) REVERT: B 165 MET cc_start: 0.8660 (mtm) cc_final: 0.8374 (mtm) REVERT: B 180 MET cc_start: 0.9344 (pmm) cc_final: 0.9060 (pmm) REVERT: B 335 MET cc_start: 0.9097 (mmm) cc_final: 0.8721 (tpt) REVERT: B 357 LEU cc_start: 0.8963 (mt) cc_final: 0.8698 (mt) outliers start: 32 outliers final: 23 residues processed: 77 average time/residue: 0.2329 time to fit residues: 28.1373 Evaluate side-chains 72 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 46 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 957 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 655 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 48 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 82 optimal weight: 0.2980 chunk 153 optimal weight: 9.9990 chunk 120 optimal weight: 0.0270 overall best weight: 1.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.073149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.047087 restraints weight = 93579.514| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 6.04 r_work: 0.2755 rms_B_bonded: 5.43 restraints_weight: 2.0000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 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 = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 13461 Z= 0.168 Angle : 0.727 14.516 18372 Z= 0.342 Chirality : 0.046 0.385 2106 Planarity : 0.005 0.127 2354 Dihedral : 10.928 91.527 2426 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.82 % Favored : 92.93 % Rotamer: Outliers : 3.24 % Allowed : 19.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.21), residues: 1657 helix: 0.61 (0.40), residues: 179 sheet: -0.02 (0.22), residues: 571 loop : -1.22 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 929 HIS 0.003 0.001 HIS B 280 PHE 0.021 0.001 PHE A 930 TYR 0.012 0.001 TYR A 448 ARG 0.009 0.000 ARG B 530 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 11) link_NAG-ASN : angle 3.64995 ( 33) link_BETA1-4 : bond 0.00678 ( 10) link_BETA1-4 : angle 3.32279 ( 30) hydrogen bonds : bond 0.03291 ( 468) hydrogen bonds : angle 5.73507 ( 1226) link_BETA1-6 : bond 0.01019 ( 2) link_BETA1-6 : angle 1.90440 ( 6) SS BOND : bond 0.00255 ( 38) SS BOND : angle 0.87440 ( 76) link_BETA1-3 : bond 0.00533 ( 1) link_BETA1-3 : angle 3.39466 ( 3) covalent geometry : bond 0.00386 (13399) covalent geometry : angle 0.69595 (18224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 45 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9347 (OUTLIER) cc_final: 0.7246 (t80) REVERT: A 402 ARG cc_start: 0.3245 (OUTLIER) cc_final: -0.1334 (mtm-85) REVERT: A 489 MET cc_start: 0.9167 (pmm) cc_final: 0.8813 (pmm) REVERT: A 549 MET cc_start: 0.8010 (mmm) cc_final: 0.7773 (mmm) REVERT: A 880 CYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7232 (p) REVERT: A 917 ARG cc_start: 0.9231 (ptp90) cc_final: 0.8926 (ptt90) REVERT: A 924 LEU cc_start: 0.9490 (tp) cc_final: 0.9089 (pp) REVERT: B 142 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8635 (tpt) REVERT: B 165 MET cc_start: 0.8868 (mtm) cc_final: 0.8597 (mtm) outliers start: 46 outliers final: 26 residues processed: 86 average time/residue: 0.2271 time to fit residues: 30.7342 Evaluate side-chains 75 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 45 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 957 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 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 368 LEU 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 Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 1 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 131 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.073455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.047768 restraints weight = 73363.331| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 5.31 r_work: 0.2787 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 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 = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2235 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= 0.145 Angle : 0.716 13.842 18372 Z= 0.337 Chirality : 0.046 0.376 2106 Planarity : 0.005 0.125 2354 Dihedral : 10.289 91.235 2426 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.34 % Favored : 93.48 % Rotamer: Outliers : 2.82 % Allowed : 20.65 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.21), residues: 1657 helix: 0.62 (0.40), residues: 178 sheet: 0.10 (0.22), residues: 568 loop : -1.17 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 839 HIS 0.020 0.001 HIS A 787 PHE 0.012 0.001 PHE B 248 TYR 0.012 0.001 TYR A 288 ARG 0.005 0.000 ARG A 683 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 11) link_NAG-ASN : angle 3.49540 ( 33) link_BETA1-4 : bond 0.00694 ( 10) link_BETA1-4 : angle 3.28733 ( 30) hydrogen bonds : bond 0.03193 ( 468) hydrogen bonds : angle 5.66502 ( 1226) link_BETA1-6 : bond 0.01076 ( 2) link_BETA1-6 : angle 1.74266 ( 6) SS BOND : bond 0.00220 ( 38) SS BOND : angle 1.03734 ( 76) link_BETA1-3 : bond 0.00678 ( 1) link_BETA1-3 : angle 3.24059 ( 3) covalent geometry : bond 0.00334 (13399) covalent geometry : angle 0.68531 (18224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 45 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9322 (OUTLIER) cc_final: 0.7295 (t80) REVERT: A 402 ARG cc_start: 0.2793 (OUTLIER) cc_final: -0.1523 (mtm-85) REVERT: A 489 MET cc_start: 0.9149 (pmm) cc_final: 0.8757 (pmm) REVERT: A 549 MET cc_start: 0.7988 (mmm) cc_final: 0.7728 (mmm) REVERT: A 880 CYS cc_start: 0.7355 (OUTLIER) cc_final: 0.7065 (p) REVERT: A 917 ARG cc_start: 0.9251 (ptp90) cc_final: 0.8966 (ptt90) REVERT: A 924 LEU cc_start: 0.9498 (tp) cc_final: 0.9124 (pp) REVERT: B 142 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8561 (tpt) REVERT: B 180 MET cc_start: 0.9477 (pmm) cc_final: 0.9249 (pmm) REVERT: B 568 MET cc_start: 0.9399 (tpp) cc_final: 0.9188 (tpp) outliers start: 40 outliers final: 30 residues processed: 82 average time/residue: 0.2306 time to fit residues: 29.7844 Evaluate side-chains 78 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 44 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 957 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 655 CYS Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 43 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.073415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.048133 restraints weight = 62972.697| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 5.02 r_work: 0.2803 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 13461 Z= 0.142 Angle : 0.703 12.749 18372 Z= 0.331 Chirality : 0.046 0.371 2106 Planarity : 0.005 0.123 2354 Dihedral : 9.656 89.295 2425 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.40 % Favored : 93.42 % Rotamer: Outliers : 3.24 % Allowed : 20.65 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1657 helix: 0.60 (0.39), residues: 180 sheet: 0.15 (0.22), residues: 568 loop : -1.11 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 929 HIS 0.002 0.001 HIS B 509 PHE 0.012 0.001 PHE B 248 TYR 0.012 0.001 TYR A 288 ARG 0.006 0.000 ARG B 530 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 11) link_NAG-ASN : angle 3.46629 ( 33) link_BETA1-4 : bond 0.00678 ( 10) link_BETA1-4 : angle 3.19442 ( 30) hydrogen bonds : bond 0.03065 ( 468) hydrogen bonds : angle 5.56765 ( 1226) link_BETA1-6 : bond 0.01031 ( 2) link_BETA1-6 : angle 1.68912 ( 6) SS BOND : bond 0.00227 ( 38) SS BOND : angle 1.11420 ( 76) link_BETA1-3 : bond 0.00652 ( 1) link_BETA1-3 : angle 2.92901 ( 3) covalent geometry : bond 0.00327 (13399) covalent geometry : angle 0.67239 (18224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 43 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9305 (OUTLIER) cc_final: 0.7336 (t80) REVERT: A 400 ARG cc_start: 0.2926 (OUTLIER) cc_final: -0.1947 (mmm-85) REVERT: A 402 ARG cc_start: 0.3009 (OUTLIER) cc_final: -0.2000 (mtm-85) REVERT: A 549 MET cc_start: 0.7997 (mmm) cc_final: 0.7754 (mmm) REVERT: A 880 CYS cc_start: 0.7327 (OUTLIER) cc_final: 0.7007 (p) REVERT: A 917 ARG cc_start: 0.9283 (ptp90) cc_final: 0.9014 (ptt90) REVERT: A 924 LEU cc_start: 0.9520 (tp) cc_final: 0.9141 (pp) REVERT: B 142 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8554 (tpt) REVERT: B 180 MET cc_start: 0.9450 (pmm) cc_final: 0.9187 (pmm) outliers start: 46 outliers final: 35 residues processed: 84 average time/residue: 0.2464 time to fit residues: 31.4312 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 : 1.365 ------------------------------------------------------------------------------- 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 402 ARG Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 957 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 149 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 83 optimal weight: 50.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.073165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.046970 restraints weight = 100668.470| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 6.20 r_work: 0.2749 rms_B_bonded: 5.66 restraints_weight: 2.0000 r_work (final): 0.2749 ------------------------------------------------------------------------------- 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: 0.8425 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 13461 Z= 0.161 Angle : 0.703 12.340 18372 Z= 0.332 Chirality : 0.046 0.364 2106 Planarity : 0.005 0.121 2354 Dihedral : 9.176 88.635 2425 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.34 % Favored : 93.48 % Rotamer: Outliers : 3.10 % Allowed : 20.72 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.21), residues: 1657 helix: 0.82 (0.40), residues: 174 sheet: 0.12 (0.22), residues: 568 loop : -1.11 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 839 HIS 0.002 0.001 HIS A 587 PHE 0.013 0.001 PHE A 289 TYR 0.011 0.001 TYR A 288 ARG 0.008 0.000 ARG B 530 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 11) link_NAG-ASN : angle 3.52906 ( 33) link_BETA1-4 : bond 0.00644 ( 10) link_BETA1-4 : angle 2.99744 ( 30) hydrogen bonds : bond 0.03130 ( 468) hydrogen bonds : angle 5.58749 ( 1226) link_BETA1-6 : bond 0.01007 ( 2) link_BETA1-6 : angle 1.70967 ( 6) SS BOND : bond 0.00236 ( 38) SS BOND : angle 0.98917 ( 76) link_BETA1-3 : bond 0.00571 ( 1) link_BETA1-3 : angle 2.79407 ( 3) covalent geometry : bond 0.00369 (13399) covalent geometry : angle 0.67370 (18224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 42 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9339 (OUTLIER) cc_final: 0.7097 (t80) REVERT: A 400 ARG cc_start: 0.3059 (OUTLIER) cc_final: -0.1418 (mmm-85) REVERT: A 402 ARG cc_start: 0.3209 (OUTLIER) cc_final: -0.1817 (mpp80) REVERT: A 549 MET cc_start: 0.8018 (mmm) cc_final: 0.7780 (mmm) REVERT: A 880 CYS cc_start: 0.7341 (OUTLIER) cc_final: 0.7020 (p) REVERT: A 917 ARG cc_start: 0.9248 (ptp90) cc_final: 0.8963 (ptt90) REVERT: A 924 LEU cc_start: 0.9534 (tp) cc_final: 0.9166 (pp) REVERT: B 142 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8575 (tpt) REVERT: B 165 MET cc_start: 0.8526 (mtp) cc_final: 0.7974 (mtm) REVERT: B 180 MET cc_start: 0.9488 (pmm) cc_final: 0.9217 (pmm) REVERT: B 409 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8984 (tp30) outliers start: 44 outliers final: 35 residues processed: 83 average time/residue: 0.2529 time to fit residues: 31.9456 Evaluate side-chains 83 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 42 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 402 ARG Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 957 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 655 CYS Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 0.0570 chunk 112 optimal weight: 8.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.073424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.047781 restraints weight = 71064.843| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 5.37 r_work: 0.2793 rms_B_bonded: 5.06 restraints_weight: 2.0000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 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 = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 13461 Z= 0.145 Angle : 0.692 12.217 18372 Z= 0.327 Chirality : 0.045 0.360 2106 Planarity : 0.005 0.120 2354 Dihedral : 8.941 87.386 2425 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.22 % Favored : 93.60 % Rotamer: Outliers : 2.89 % Allowed : 21.21 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1657 helix: 0.65 (0.40), residues: 180 sheet: 0.12 (0.22), residues: 568 loop : -1.10 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 238 HIS 0.002 0.001 HIS B 509 PHE 0.012 0.001 PHE B 248 TYR 0.012 0.001 TYR A 288 ARG 0.005 0.000 ARG B 530 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 11) link_NAG-ASN : angle 3.38843 ( 33) link_BETA1-4 : bond 0.00651 ( 10) link_BETA1-4 : angle 2.88599 ( 30) hydrogen bonds : bond 0.02991 ( 468) hydrogen bonds : angle 5.51980 ( 1226) link_BETA1-6 : bond 0.00972 ( 2) link_BETA1-6 : angle 1.64584 ( 6) SS BOND : bond 0.00218 ( 38) SS BOND : angle 0.91179 ( 76) link_BETA1-3 : bond 0.00595 ( 1) link_BETA1-3 : angle 2.59485 ( 3) covalent geometry : bond 0.00334 (13399) covalent geometry : angle 0.66503 (18224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 42 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9324 (OUTLIER) cc_final: 0.7121 (t80) REVERT: A 400 ARG cc_start: 0.2939 (OUTLIER) cc_final: -0.2023 (mmm-85) REVERT: A 402 ARG cc_start: 0.2886 (OUTLIER) cc_final: -0.2380 (mpp80) REVERT: A 549 MET cc_start: 0.8048 (mmm) cc_final: 0.7814 (mmm) REVERT: A 693 MET cc_start: 0.8635 (ppp) cc_final: 0.8264 (ppp) REVERT: A 880 CYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6825 (p) REVERT: A 902 MET cc_start: 0.8545 (tpp) cc_final: 0.8101 (tpt) REVERT: A 917 ARG cc_start: 0.9236 (ptp90) cc_final: 0.8949 (ptt90) REVERT: A 924 LEU cc_start: 0.9538 (tp) cc_final: 0.9158 (pp) REVERT: B 165 MET cc_start: 0.8499 (mtp) cc_final: 0.7898 (mtm) REVERT: B 180 MET cc_start: 0.9466 (pmm) cc_final: 0.9182 (pmm) outliers start: 41 outliers final: 33 residues processed: 78 average time/residue: 0.2635 time to fit residues: 31.2329 Evaluate side-chains 79 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 42 time to evaluate : 1.449 ------------------------------------------------------------------------------- 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 402 ARG Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 957 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 140 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.072827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.047068 restraints weight = 80084.607| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 5.53 r_work: 0.2769 rms_B_bonded: 5.42 restraints_weight: 2.0000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 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 = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 13461 Z= 0.192 Angle : 0.720 12.957 18372 Z= 0.342 Chirality : 0.046 0.365 2106 Planarity : 0.005 0.119 2354 Dihedral : 8.891 87.487 2424 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.46 % Favored : 93.36 % Rotamer: Outliers : 2.68 % Allowed : 21.42 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.21), residues: 1657 helix: 0.78 (0.40), residues: 174 sheet: 0.04 (0.22), residues: 571 loop : -1.15 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 113 HIS 0.003 0.001 HIS B 280 PHE 0.030 0.002 PHE A 930 TYR 0.011 0.001 TYR A 448 ARG 0.008 0.000 ARG B 530 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 11) link_NAG-ASN : angle 3.38573 ( 33) link_BETA1-4 : bond 0.00609 ( 10) link_BETA1-4 : angle 2.84032 ( 30) hydrogen bonds : bond 0.03222 ( 468) hydrogen bonds : angle 5.62668 ( 1226) link_BETA1-6 : bond 0.00932 ( 2) link_BETA1-6 : angle 1.64297 ( 6) SS BOND : bond 0.00266 ( 38) SS BOND : angle 0.95834 ( 76) link_BETA1-3 : bond 0.00366 ( 1) link_BETA1-3 : angle 2.59691 ( 3) covalent geometry : bond 0.00434 (13399) covalent geometry : angle 0.69528 (18224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 43 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9376 (OUTLIER) cc_final: 0.6971 (t80) REVERT: A 400 ARG cc_start: 0.3096 (OUTLIER) cc_final: -0.1410 (mmm-85) REVERT: A 402 ARG cc_start: 0.3019 (OUTLIER) cc_final: -0.2275 (mtm-85) REVERT: A 549 MET cc_start: 0.8067 (mmm) cc_final: 0.7862 (mmm) REVERT: A 880 CYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6659 (p) REVERT: A 917 ARG cc_start: 0.9239 (ptp90) cc_final: 0.8995 (ptt90) REVERT: A 924 LEU cc_start: 0.9551 (tp) cc_final: 0.9179 (pp) REVERT: B 142 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8618 (tpt) REVERT: B 165 MET cc_start: 0.8499 (mtp) cc_final: 0.7841 (mtm) outliers start: 38 outliers final: 31 residues processed: 78 average time/residue: 0.2579 time to fit residues: 30.5475 Evaluate side-chains 79 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 43 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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 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 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 72 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.074032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.048503 restraints weight = 70644.268| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 5.30 r_work: 0.2816 rms_B_bonded: 5.00 restraints_weight: 2.0000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 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 = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 13461 Z= 0.116 Angle : 0.689 13.488 18372 Z= 0.324 Chirality : 0.045 0.353 2106 Planarity : 0.005 0.117 2354 Dihedral : 8.618 85.588 2424 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.04 % Favored : 93.78 % Rotamer: Outliers : 2.40 % Allowed : 21.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.21), residues: 1657 helix: 0.58 (0.39), residues: 180 sheet: 0.15 (0.22), residues: 568 loop : -1.07 (0.22), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 238 HIS 0.003 0.001 HIS B 509 PHE 0.010 0.001 PHE A 356 TYR 0.012 0.001 TYR A 288 ARG 0.002 0.000 ARG B 636 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 11) link_NAG-ASN : angle 3.30046 ( 33) link_BETA1-4 : bond 0.00639 ( 10) link_BETA1-4 : angle 2.74308 ( 30) hydrogen bonds : bond 0.02863 ( 468) hydrogen bonds : angle 5.43568 ( 1226) link_BETA1-6 : bond 0.00963 ( 2) link_BETA1-6 : angle 1.54824 ( 6) SS BOND : bond 0.00173 ( 38) SS BOND : angle 0.85694 ( 76) link_BETA1-3 : bond 0.00617 ( 1) link_BETA1-3 : angle 2.33904 ( 3) covalent geometry : bond 0.00271 (13399) covalent geometry : angle 0.66466 (18224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10889.15 seconds wall clock time: 187 minutes 27.14 seconds (11247.14 seconds total)