Starting phenix.real_space_refine on Fri Sep 11 18:14:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xny_67063/09_2026/9xny_67063.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xny_67063/09_2026/9xny_67063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xny_67063/09_2026/9xny_67063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xny_67063/09_2026/9xny_67063.map" model { file = "/net/cci-nas-00/data/ceres_data/9xny_67063/09_2026/9xny_67063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xny_67063/09_2026/9xny_67063.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 6623 2.51 5 N 1695 2.21 5 O 2071 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10441 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1104, 8489 Classifications: {'peptide': 1104} Link IDs: {'PTRANS': 40, 'TRANS': 1063} Chain breaks: 12 Chain: "F" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 881 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "G" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 743 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 8, 'TRANS': 93} Chain: "B" 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "H" 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: "I" 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: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, '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: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 88 Unusual residues: {'NAG': 5, 'PAM': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.52, per 1000 atoms: 0.24 Number of scatterers: 10441 At special positions: 0 Unit cell: (98.58, 137.64, 157.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 2071 8.00 N 1695 7.00 C 6623 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 148 " distance=2.04 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 373 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 589 " distance=2.03 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 599 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 830 " distance=2.03 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 931 " distance=2.03 Simple disulfide: pdb=" SG CYS A1122 " - pdb=" SG CYS A1133 " distance=2.03 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1226 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA J 3 " - " MAN J 4 " ALPHA1-6 " BMA J 3 " - " MAN J 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A1401 " - " ASN A 726 " " NAG A1402 " - " ASN A 781 " " NAG A1403 " - " ASN A 743 " " NAG A1404 " - " ASN A 787 " " NAG A1405 " - " ASN A1009 " " NAG B 1 " - " ASN A 216 " " NAG C 1 " - " ASN A 324 " " NAG D 1 " - " ASN A 344 " " NAG E 1 " - " ASN A 688 " " NAG H 1 " - " ASN A 514 " " NAG I 1 " - " ASN A 873 " " NAG J 1 " - " ASN A 264 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 268.5 milliseconds 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 20 sheets defined 19.8% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 233 through 241 removed outlier: 3.682A pdb=" N SER A 238 " --> pdb=" O CYS A 234 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 removed outlier: 3.701A pdb=" N ILE A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'A' and resid 807 through 814 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 828 through 852 removed outlier: 3.832A pdb=" N ILE A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 860 Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 917 through 922 removed outlier: 3.921A pdb=" N SER A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASN A 922 " --> pdb=" O LYS A 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 917 through 922' Processing helix chain 'A' and resid 928 through 935 Processing helix chain 'A' and resid 946 through 960 Processing helix chain 'A' and resid 973 through 986 removed outlier: 3.896A pdb=" N ALA A 977 " --> pdb=" O PRO A 973 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 985 " --> pdb=" O ARG A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1014 Processing helix chain 'A' and resid 1030 through 1045 removed outlier: 3.514A pdb=" N GLN A1045 " --> pdb=" O VAL A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1055 Processing helix chain 'A' and resid 1056 through 1058 No H-bonds generated for 'chain 'A' and resid 1056 through 1058' Processing helix chain 'A' and resid 1066 through 1074 Processing helix chain 'A' and resid 1075 through 1123 Processing helix chain 'A' and resid 1216 through 1218 No H-bonds generated for 'chain 'A' and resid 1216 through 1218' Processing helix chain 'F' and resid 106 through 110 removed outlier: 3.569A pdb=" N ALA F 110 " --> pdb=" O THR F 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'G' and resid 99 through 103 removed outlier: 3.605A pdb=" N ASP G 102 " --> pdb=" O GLN G 99 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU G 103 " --> pdb=" O ALA G 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 99 through 103' Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 51 removed outlier: 3.653A pdb=" N ALA A 45 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.595A pdb=" N GLY A 79 " --> pdb=" O VAL A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 270 through 286 removed outlier: 7.616A pdb=" N VAL A 273 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL A 453 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER A 275 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A 451 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN A 277 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA A 449 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU A 279 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL A 447 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL A 281 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN A 445 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 440 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASP A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 414 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 286 removed outlier: 7.616A pdb=" N VAL A 273 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL A 453 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER A 275 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A 451 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN A 277 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA A 449 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU A 279 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL A 447 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL A 281 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN A 445 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 450 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE A 461 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLU A 452 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 298 removed outlier: 7.007A pdb=" N HIS A 338 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL A 422 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 336 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE A 424 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER A 334 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE A 335 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 349 through 350 removed outlier: 4.473A pdb=" N TYR A 371 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A 389 " --> pdb=" O CYS A 373 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 483 through 488 removed outlier: 3.945A pdb=" N GLY A 715 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 499 through 502 removed outlier: 3.504A pdb=" N GLY A 659 " --> pdb=" O TYR A 652 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL A 694 " --> pdb=" O THR A 666 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU A 684 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 531 through 536 removed outlier: 3.954A pdb=" N ALA A 531 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 549 " --> pdb=" O THR A 629 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS A 587 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLY A 625 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 585 " --> pdb=" O GLY A 625 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 531 through 536 removed outlier: 3.954A pdb=" N ALA A 531 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 549 " --> pdb=" O THR A 629 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU A 603 " --> pdb=" O PHE A 615 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N SER A 617 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE A 601 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR A 619 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N CYS A 599 " --> pdb=" O TYR A 619 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 749 through 750 Processing sheet with id=AB4, first strand: chain 'A' and resid 780 through 798 removed outlier: 6.962A pdb=" N ASN A 781 " --> pdb=" O ILE A1167 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE A1167 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N SER A 783 " --> pdb=" O ASP A1165 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASP A1165 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE A1163 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN A 787 " --> pdb=" O GLY A1161 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A1141 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A1158 " --> pdb=" O HIS A1139 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N HIS A1139 " --> pdb=" O LEU A1158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 780 through 798 removed outlier: 6.962A pdb=" N ASN A 781 " --> pdb=" O ILE A1167 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE A1167 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N SER A 783 " --> pdb=" O ASP A1165 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASP A1165 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE A1163 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN A 787 " --> pdb=" O GLY A1161 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE A1167 " --> pdb=" O THR A1191 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR A1191 " --> pdb=" O ILE A1167 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A1189 " --> pdb=" O ILE A1169 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 804 through 806 Processing sheet with id=AB7, first strand: chain 'A' and resid 1171 through 1174 Processing sheet with id=AB8, first strand: chain 'F' and resid 22 through 26 removed outlier: 3.703A pdb=" N VAL F 37 " --> pdb=" O MET F 102 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU F 100 " --> pdb=" O LEU F 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 77 through 79 removed outlier: 6.627A pdb=" N TRP F 55 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY F 69 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE F 53 " --> pdb=" O GLY F 69 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL F 56 " --> pdb=" O TYR F 114 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR F 114 " --> pdb=" O VAL F 56 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 22 through 24 Processing sheet with id=AC2, first strand: chain 'G' and resid 65 through 68 removed outlier: 5.847A pdb=" N LEU G 66 " --> pdb=" O GLN G 57 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLN G 57 " --> pdb=" O LEU G 66 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET G 68 " --> pdb=" O TRP G 55 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER G 54 " --> pdb=" O LYS G 109 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1161 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3288 1.34 - 1.47: 2796 1.47 - 1.59: 4511 1.59 - 1.71: 0 1.71 - 1.83: 68 Bond restraints: 10663 Sorted by residual: bond pdb=" C GLU A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.44e+00 bond pdb=" CA ASN A 743 " pdb=" CB ASN A 743 " ideal model delta sigma weight residual 1.534 1.564 -0.029 2.47e-02 1.64e+03 1.38e+00 bond pdb=" N GLU A1224 " pdb=" CA GLU A1224 " ideal model delta sigma weight residual 1.460 1.477 -0.018 1.54e-02 4.22e+03 1.33e+00 bond pdb=" C ALA A 43 " pdb=" N PRO A 44 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.96e-01 bond pdb=" CB ASN A 743 " pdb=" CG ASN A 743 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.39e-01 ... (remaining 10658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 14131 1.66 - 3.32: 301 3.32 - 4.97: 47 4.97 - 6.63: 4 6.63 - 8.29: 3 Bond angle restraints: 14486 Sorted by residual: angle pdb=" C VAL A 638 " pdb=" N THR A 639 " pdb=" CA THR A 639 " ideal model delta sigma weight residual 121.54 127.50 -5.96 1.91e+00 2.74e-01 9.73e+00 angle pdb=" C ILE A1223 " pdb=" N GLU A1224 " pdb=" CA GLU A1224 " ideal model delta sigma weight residual 122.46 126.84 -4.38 1.41e+00 5.03e-01 9.67e+00 angle pdb=" CA CYS A1173 " pdb=" CB CYS A1173 " pdb=" SG CYS A1173 " ideal model delta sigma weight residual 114.40 120.05 -5.65 2.30e+00 1.89e-01 6.03e+00 angle pdb=" CA LEU A 341 " pdb=" CB LEU A 341 " pdb=" CG LEU A 341 " ideal model delta sigma weight residual 116.30 124.59 -8.29 3.50e+00 8.16e-02 5.61e+00 angle pdb=" CA TYR G 69 " pdb=" CB TYR G 69 " pdb=" CG TYR G 69 " ideal model delta sigma weight residual 113.90 118.15 -4.25 1.80e+00 3.09e-01 5.59e+00 ... (remaining 14481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 6125 17.38 - 34.76: 345 34.76 - 52.14: 51 52.14 - 69.53: 26 69.53 - 86.91: 8 Dihedral angle restraints: 6555 sinusoidal: 2765 harmonic: 3790 Sorted by residual: dihedral pdb=" CB CYS A 283 " pdb=" SG CYS A 283 " pdb=" SG CYS A 307 " pdb=" CB CYS A 307 " ideal model delta sinusoidal sigma weight residual 93.00 169.71 -76.71 1 1.00e+01 1.00e-02 7.39e+01 dihedral pdb=" CB CYS A 744 " pdb=" SG CYS A 744 " pdb=" SG CYS A 757 " pdb=" CB CYS A 757 " ideal model delta sinusoidal sigma weight residual 93.00 24.07 68.93 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS A 196 " pdb=" SG CYS A 196 " pdb=" SG CYS A 202 " pdb=" CB CYS A 202 " ideal model delta sinusoidal sigma weight residual -86.00 -146.47 60.47 1 1.00e+01 1.00e-02 4.87e+01 ... (remaining 6552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1337 0.051 - 0.101: 275 0.101 - 0.152: 89 0.152 - 0.202: 4 0.202 - 0.253: 2 Chirality restraints: 1707 Sorted by residual: chirality pdb=" C1 NAG A1404 " pdb=" ND2 ASN A 787 " pdb=" C2 NAG A1404 " pdb=" O5 NAG A1404 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE A1140 " pdb=" CA ILE A1140 " pdb=" CG1 ILE A1140 " pdb=" CG2 ILE A1140 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA TYR G 69 " pdb=" N TYR G 69 " pdb=" C TYR G 69 " pdb=" CB TYR G 69 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.96e-01 ... (remaining 1704 not shown) Planarity restraints: 1846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG G 74 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.30e+00 pdb=" N PRO G 75 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO G 75 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 75 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 731 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO A 732 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 732 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 732 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 101 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO A 102 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " 0.028 5.00e-02 4.00e+02 ... (remaining 1843 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.04: 6031 3.04 - 3.50: 9552 3.50 - 3.97: 16534 3.97 - 4.43: 18608 4.43 - 4.90: 30667 Nonbonded interactions: 81392 Sorted by model distance: nonbonded pdb=" O2 BMA E 3 " pdb=" O3 BMA E 3 " model vdw 2.570 2.432 nonbonded pdb=" O5 MAN J 4 " pdb=" O6 MAN J 4 " model vdw 2.592 2.432 nonbonded pdb=" N THR G 113 " pdb=" O THR G 113 " model vdw 2.620 2.496 nonbonded pdb=" N THR A 503 " pdb=" O THR A 503 " model vdw 2.628 2.496 nonbonded pdb=" N SER A 177 " pdb=" O SER A 177 " model vdw 2.629 2.496 ... (remaining 81387 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'H' selection = chain 'I' } 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: 1.730 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.750 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 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 : 0.003 0.032 10704 Z= 0.122 Angle : 0.602 8.290 14591 Z= 0.307 Chirality : 0.046 0.253 1707 Planarity : 0.005 0.052 1834 Dihedral : 11.431 86.907 4085 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.23), residues: 1293 helix: 1.26 (0.35), residues: 210 sheet: -0.36 (0.28), residues: 379 loop : -0.77 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1073 TYR 0.021 0.001 TYR G 69 PHE 0.013 0.001 PHE A 35 TRP 0.010 0.001 TRP A 439 HIS 0.011 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (10663) covalent geometry : angle 0.58527 / 0.30 (14486) SS BOND : bond 0.00350 / 0.22 ( 18) SS BOND : angle 1.34221 / 0.88 ( 36) hydrogen bonds : bond 0.18933 / 12.55 ( 389) hydrogen bonds : angle 8.60202 / 6.00 ( 1161) link_ALPHA1-3 : bond 0.00998 / 0.53 ( 1) link_ALPHA1-3 : angle 1.13644 / 0.58 ( 3) link_ALPHA1-6 : bond 0.01317 / 0.69 ( 1) link_ALPHA1-6 : angle 1.54681 / 0.84 ( 3) link_BETA1-4 : bond 0.00401 / 0.26 ( 9) link_BETA1-4 : angle 1.53054 / 1.06 ( 27) link_NAG-ASN : bond 0.00313 / 0.19 ( 12) link_NAG-ASN : angle 2.24236 / 1.48 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7717 (t80) cc_final: 0.7409 (t80) REVERT: G 116 ASN cc_start: 0.8831 (t0) cc_final: 0.8550 (t0) outliers start: 0 outliers final: 1 residues processed: 191 average time/residue: 0.4686 time to fit residues: 97.3152 Evaluate side-chains 129 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 0.0050 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 overall best weight: 0.7174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 84 HIS A 110 HIS A 151 ASN A 161 HIS A 170 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN A 988 GLN A1051 GLN F 32 GLN F 96 ASN F 124 ASN G 99 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.103194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.071004 restraints weight = 17897.017| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.69 r_work: 0.2936 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10704 Z= 0.128 Angle : 0.570 6.617 14591 Z= 0.293 Chirality : 0.044 0.240 1707 Planarity : 0.004 0.044 1834 Dihedral : 5.594 54.923 1905 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.88 % Allowed : 7.42 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.24), residues: 1293 helix: 1.66 (0.37), residues: 218 sheet: -0.33 (0.27), residues: 384 loop : -0.68 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 70 TYR 0.027 0.001 TYR G 69 PHE 0.010 0.001 PHE A1141 TRP 0.007 0.001 TRP F 55 HIS 0.003 0.001 HIS G 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (10663) covalent geometry : angle 0.55286 / 0.29 (14486) SS BOND : bond 0.00248 / 0.18 ( 18) SS BOND : angle 1.42748 / 0.91 ( 36) hydrogen bonds : bond 0.04352 / 2.92 ( 389) hydrogen bonds : angle 6.31094 / 4.40 ( 1161) link_ALPHA1-3 : bond 0.00835 / 0.44 ( 1) link_ALPHA1-3 : angle 1.38109 / 0.74 ( 3) link_ALPHA1-6 : bond 0.01122 / 0.59 ( 1) link_ALPHA1-6 : angle 1.26877 / 0.70 ( 3) link_BETA1-4 : bond 0.00312 / 0.20 ( 9) link_BETA1-4 : angle 1.58911 / 1.09 ( 27) link_NAG-ASN : bond 0.00257 / 0.17 ( 12) link_NAG-ASN : angle 2.09747 / 1.40 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7708 (t80) cc_final: 0.7231 (t80) REVERT: A 105 TYR cc_start: 0.8046 (m-80) cc_final: 0.7385 (m-80) REVERT: A 204 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8486 (mtt) REVERT: A 386 LYS cc_start: 0.8513 (mttt) cc_final: 0.8304 (mtpm) REVERT: F 65 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: G 68 MET cc_start: 0.8428 (tpp) cc_final: 0.8155 (mpp) REVERT: G 116 ASN cc_start: 0.9125 (t0) cc_final: 0.8808 (t0) outliers start: 21 outliers final: 6 residues processed: 140 average time/residue: 0.4597 time to fit residues: 70.7066 Evaluate side-chains 125 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 1159 VAL Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain F residue 65 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.4980 chunk 126 optimal weight: 0.4980 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 39 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN A 161 HIS A 170 ASN A 409 ASN ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1045 GLN F 32 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.102119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.069753 restraints weight = 17954.865| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.68 r_work: 0.2906 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10704 Z= 0.133 Angle : 0.545 6.672 14591 Z= 0.281 Chirality : 0.043 0.232 1707 Planarity : 0.004 0.037 1834 Dihedral : 5.622 54.060 1905 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.06 % Allowed : 8.05 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.24), residues: 1293 helix: 2.07 (0.37), residues: 209 sheet: -0.31 (0.26), residues: 402 loop : -0.57 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 191 TYR 0.024 0.001 TYR G 69 PHE 0.011 0.001 PHE A 296 TRP 0.005 0.001 TRP F 55 HIS 0.003 0.001 HIS F 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10663) covalent geometry : angle 0.52683 / 0.28 (14486) SS BOND : bond 0.00309 / 0.21 ( 18) SS BOND : angle 1.39370 / 0.93 ( 36) hydrogen bonds : bond 0.04009 / 2.69 ( 389) hydrogen bonds : angle 5.79649 / 4.06 ( 1161) link_ALPHA1-3 : bond 0.00699 / 0.37 ( 1) link_ALPHA1-3 : angle 1.43118 / 0.77 ( 3) link_ALPHA1-6 : bond 0.00859 / 0.45 ( 1) link_ALPHA1-6 : angle 1.33617 / 0.74 ( 3) link_BETA1-4 : bond 0.00258 / 0.16 ( 9) link_BETA1-4 : angle 1.61477 / 1.10 ( 27) link_NAG-ASN : bond 0.00249 / 0.16 ( 12) link_NAG-ASN : angle 2.09165 / 1.39 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8214 (m-80) cc_final: 0.7910 (m-80) REVERT: A 172 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8120 (tmm-80) REVERT: A 204 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8464 (mtt) REVERT: A 490 ARG cc_start: 0.7386 (tmt170) cc_final: 0.7076 (tpt90) REVERT: A 1040 GLU cc_start: 0.8882 (tp30) cc_final: 0.8642 (tp30) REVERT: F 22 LYS cc_start: 0.8817 (mtmm) cc_final: 0.8187 (tmmt) REVERT: F 65 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: F 92 ASP cc_start: 0.8112 (t0) cc_final: 0.7417 (t0) REVERT: G 68 MET cc_start: 0.8407 (tpp) cc_final: 0.8151 (mpp) REVERT: G 81 ARG cc_start: 0.8517 (ptp90) cc_final: 0.7964 (ptp90) REVERT: G 112 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8340 (mttt) REVERT: G 116 ASN cc_start: 0.9124 (t0) cc_final: 0.8802 (t0) outliers start: 23 outliers final: 11 residues processed: 136 average time/residue: 0.4430 time to fit residues: 66.2918 Evaluate side-chains 131 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain A residue 1159 VAL Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 22 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 49 optimal weight: 0.1980 chunk 48 optimal weight: 0.0970 chunk 123 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 9 optimal weight: 0.0870 chunk 46 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 HIS A 151 ASN A 161 HIS A 170 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1045 GLN F 32 GLN G 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.103472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.071296 restraints weight = 17992.140| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.68 r_work: 0.2939 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10704 Z= 0.098 Angle : 0.513 8.572 14591 Z= 0.261 Chirality : 0.042 0.225 1707 Planarity : 0.004 0.043 1834 Dihedral : 5.372 55.390 1905 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.79 % Allowed : 9.39 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.24), residues: 1293 helix: 2.24 (0.37), residues: 208 sheet: -0.16 (0.26), residues: 401 loop : -0.54 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 191 TYR 0.020 0.001 TYR G 69 PHE 0.010 0.001 PHE A 296 TRP 0.005 0.001 TRP F 66 HIS 0.002 0.001 HIS F 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (10663) covalent geometry : angle 0.49929 / 0.26 (14486) SS BOND : bond 0.00408 / 0.29 ( 18) SS BOND : angle 0.99278 / 0.67 ( 36) hydrogen bonds : bond 0.03545 / 2.41 ( 389) hydrogen bonds : angle 5.39757 / 3.81 ( 1161) link_ALPHA1-3 : bond 0.00812 / 0.43 ( 1) link_ALPHA1-3 : angle 1.17804 / 0.62 ( 3) link_ALPHA1-6 : bond 0.00899 / 0.47 ( 1) link_ALPHA1-6 : angle 1.31027 / 0.73 ( 3) link_BETA1-4 : bond 0.00294 / 0.18 ( 9) link_BETA1-4 : angle 1.46395 / 1.01 ( 27) link_NAG-ASN : bond 0.00219 / 0.14 ( 12) link_NAG-ASN : angle 1.90525 / 1.26 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8213 (m-80) cc_final: 0.7867 (m-80) REVERT: A 158 MET cc_start: 0.8401 (mtm) cc_final: 0.7936 (mtm) REVERT: A 164 VAL cc_start: 0.9102 (t) cc_final: 0.8747 (m) REVERT: A 172 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8206 (tmm-80) REVERT: A 1040 GLU cc_start: 0.8891 (tp30) cc_final: 0.8639 (tp30) REVERT: F 65 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7903 (tt0) REVERT: F 92 ASP cc_start: 0.8278 (t0) cc_final: 0.7758 (t0) REVERT: G 81 ARG cc_start: 0.8558 (ptp90) cc_final: 0.7975 (ptp90) REVERT: G 112 LYS cc_start: 0.8775 (mtmt) cc_final: 0.8353 (mttt) REVERT: G 116 ASN cc_start: 0.9104 (t0) cc_final: 0.8764 (t0) outliers start: 20 outliers final: 8 residues processed: 134 average time/residue: 0.4391 time to fit residues: 64.5730 Evaluate side-chains 122 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 7 optimal weight: 0.0870 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN A 161 HIS A 170 ASN ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1149 GLN F 32 GLN G 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.102570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.070024 restraints weight = 17865.205| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.70 r_work: 0.2949 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10704 Z= 0.122 Angle : 0.540 8.561 14591 Z= 0.274 Chirality : 0.043 0.219 1707 Planarity : 0.004 0.046 1834 Dihedral : 5.369 53.955 1903 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.15 % Allowed : 10.11 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.24), residues: 1293 helix: 2.30 (0.37), residues: 208 sheet: -0.13 (0.26), residues: 395 loop : -0.57 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 191 TYR 0.019 0.001 TYR G 69 PHE 0.011 0.001 PHE A 296 TRP 0.003 0.001 TRP A 259 HIS 0.004 0.001 HIS F 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (10663) covalent geometry : angle 0.52508 / 0.27 (14486) SS BOND : bond 0.00274 / 0.17 ( 18) SS BOND : angle 1.14947 / 0.82 ( 36) hydrogen bonds : bond 0.03690 / 2.51 ( 389) hydrogen bonds : angle 5.29564 / 3.74 ( 1161) link_ALPHA1-3 : bond 0.00712 / 0.37 ( 1) link_ALPHA1-3 : angle 1.38650 / 0.74 ( 3) link_ALPHA1-6 : bond 0.00975 / 0.51 ( 1) link_ALPHA1-6 : angle 1.34413 / 0.75 ( 3) link_BETA1-4 : bond 0.00262 / 0.17 ( 9) link_BETA1-4 : angle 1.56379 / 1.07 ( 27) link_NAG-ASN : bond 0.00217 / 0.14 ( 12) link_NAG-ASN : angle 1.96372 / 1.30 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8237 (m-80) cc_final: 0.7871 (m-80) REVERT: A 158 MET cc_start: 0.8435 (mtm) cc_final: 0.7960 (mtm) REVERT: A 164 VAL cc_start: 0.9115 (t) cc_final: 0.8753 (m) REVERT: A 204 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8433 (mtt) REVERT: A 214 MET cc_start: 0.8855 (tpp) cc_final: 0.8566 (ttt) REVERT: A 490 ARG cc_start: 0.7530 (tmt170) cc_final: 0.7171 (tpt90) REVERT: A 952 MET cc_start: 0.9021 (mtp) cc_final: 0.8798 (mtm) REVERT: A 1040 GLU cc_start: 0.8904 (tp30) cc_final: 0.8647 (tp30) REVERT: F 65 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: F 102 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.7820 (mtm) REVERT: G 81 ARG cc_start: 0.8582 (ptp90) cc_final: 0.7975 (ptp90) REVERT: G 112 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8397 (mttt) REVERT: G 116 ASN cc_start: 0.9091 (t0) cc_final: 0.8748 (t0) outliers start: 24 outliers final: 16 residues processed: 126 average time/residue: 0.4719 time to fit residues: 65.2507 Evaluate side-chains 130 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain A residue 1159 VAL Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 29 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 43 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 128 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 HIS A 151 ASN A 161 HIS A 170 ASN ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 GLN A1033 HIS F 32 GLN G 99 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.099751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.066838 restraints weight = 18143.862| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.66 r_work: 0.2844 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10704 Z= 0.242 Angle : 0.624 8.584 14591 Z= 0.319 Chirality : 0.046 0.233 1707 Planarity : 0.004 0.057 1834 Dihedral : 6.026 52.782 1903 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.06 % Allowed : 10.02 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.23), residues: 1293 helix: 2.10 (0.37), residues: 209 sheet: -0.21 (0.26), residues: 404 loop : -0.65 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 191 TYR 0.020 0.002 TYR A 676 PHE 0.019 0.002 PHE A 411 TRP 0.009 0.001 TRP A 259 HIS 0.005 0.001 HIS F 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 (10663) covalent geometry : angle 0.60576 / 0.31 (14486) SS BOND : bond 0.00348 / 0.23 ( 18) SS BOND : angle 1.27005 / 0.93 ( 36) hydrogen bonds : bond 0.04433 / 2.98 ( 389) hydrogen bonds : angle 5.46544 / 3.83 ( 1161) link_ALPHA1-3 : bond 0.00344 / 0.18 ( 1) link_ALPHA1-3 : angle 1.68401 / 0.93 ( 3) link_ALPHA1-6 : bond 0.00601 / 0.32 ( 1) link_ALPHA1-6 : angle 1.29650 / 0.73 ( 3) link_BETA1-4 : bond 0.00279 / 0.22 ( 9) link_BETA1-4 : angle 1.84246 / 1.21 ( 27) link_NAG-ASN : bond 0.00468 / 0.30 ( 12) link_NAG-ASN : angle 2.33638 / 1.55 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8260 (m-80) cc_final: 0.7708 (m-80) REVERT: A 158 MET cc_start: 0.8417 (mtm) cc_final: 0.7910 (mtm) REVERT: A 164 VAL cc_start: 0.9103 (t) cc_final: 0.8691 (m) REVERT: A 204 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8437 (mtt) REVERT: A 490 ARG cc_start: 0.7579 (tmt170) cc_final: 0.7231 (tpt90) REVERT: A 602 ASP cc_start: 0.8854 (m-30) cc_final: 0.8634 (m-30) REVERT: A 1040 GLU cc_start: 0.8874 (tp30) cc_final: 0.8622 (tp30) REVERT: F 65 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: F 92 ASP cc_start: 0.8300 (t0) cc_final: 0.8081 (t0) REVERT: F 102 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.7976 (mtm) REVERT: G 112 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8446 (mttt) REVERT: G 116 ASN cc_start: 0.9081 (t0) cc_final: 0.8759 (t160) outliers start: 23 outliers final: 13 residues processed: 128 average time/residue: 0.4610 time to fit residues: 64.8048 Evaluate side-chains 127 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain A residue 1173 CYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 22 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 52 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN A 161 HIS A 170 ASN A 270 HIS A 988 GLN F 32 GLN G 24 GLN G 99 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.100103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.067320 restraints weight = 17948.467| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.66 r_work: 0.2853 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10704 Z= 0.184 Angle : 0.587 8.541 14591 Z= 0.299 Chirality : 0.045 0.242 1707 Planarity : 0.004 0.048 1834 Dihedral : 6.094 53.303 1903 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.15 % Allowed : 10.91 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.23), residues: 1293 helix: 2.09 (0.37), residues: 209 sheet: -0.14 (0.26), residues: 405 loop : -0.65 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 191 TYR 0.019 0.001 TYR A 984 PHE 0.016 0.001 PHE A 411 TRP 0.005 0.001 TRP A 259 HIS 0.004 0.001 HIS F 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (10663) covalent geometry : angle 0.56939 / 0.30 (14486) SS BOND : bond 0.00293 / 0.20 ( 18) SS BOND : angle 1.20704 / 0.85 ( 36) hydrogen bonds : bond 0.04171 / 2.82 ( 389) hydrogen bonds : angle 5.38281 / 3.78 ( 1161) link_ALPHA1-3 : bond 0.00554 / 0.29 ( 1) link_ALPHA1-3 : angle 1.54227 / 0.84 ( 3) link_ALPHA1-6 : bond 0.00886 / 0.47 ( 1) link_ALPHA1-6 : angle 1.36017 / 0.75 ( 3) link_BETA1-4 : bond 0.00246 / 0.17 ( 9) link_BETA1-4 : angle 1.71485 / 1.14 ( 27) link_NAG-ASN : bond 0.00365 / 0.23 ( 12) link_NAG-ASN : angle 2.24941 / 1.50 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8205 (m-80) cc_final: 0.7786 (m-80) REVERT: A 158 MET cc_start: 0.8371 (mtm) cc_final: 0.7867 (mtm) REVERT: A 164 VAL cc_start: 0.9103 (t) cc_final: 0.8684 (m) REVERT: A 204 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8415 (mtt) REVERT: A 1040 GLU cc_start: 0.8873 (tp30) cc_final: 0.8611 (tp30) REVERT: F 65 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: G 81 ARG cc_start: 0.8613 (ptp90) cc_final: 0.8218 (ptp90) REVERT: G 112 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8445 (mttt) REVERT: G 116 ASN cc_start: 0.9103 (t0) cc_final: 0.8790 (t160) outliers start: 24 outliers final: 15 residues processed: 127 average time/residue: 0.4873 time to fit residues: 67.9585 Evaluate side-chains 128 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain A residue 1173 CYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain G residue 22 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 119 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 HIS A 151 ASN A 161 HIS A 270 HIS F 32 GLN G 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.100440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.067734 restraints weight = 17853.314| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.64 r_work: 0.2865 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10704 Z= 0.156 Angle : 0.578 8.507 14591 Z= 0.294 Chirality : 0.044 0.241 1707 Planarity : 0.004 0.048 1834 Dihedral : 6.037 53.652 1903 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.06 % Allowed : 11.18 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.23), residues: 1293 helix: 2.16 (0.37), residues: 209 sheet: -0.10 (0.26), residues: 400 loop : -0.65 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 191 TYR 0.016 0.001 TYR A 676 PHE 0.014 0.001 PHE A 411 TRP 0.004 0.001 TRP A 439 HIS 0.004 0.001 HIS F 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (10663) covalent geometry : angle 0.56122 / 0.29 (14486) SS BOND : bond 0.00260 / 0.18 ( 18) SS BOND : angle 1.12581 / 0.80 ( 36) hydrogen bonds : bond 0.04009 / 2.72 ( 389) hydrogen bonds : angle 5.29514 / 3.72 ( 1161) link_ALPHA1-3 : bond 0.00653 / 0.34 ( 1) link_ALPHA1-3 : angle 1.47818 / 0.80 ( 3) link_ALPHA1-6 : bond 0.00943 / 0.50 ( 1) link_ALPHA1-6 : angle 1.37475 / 0.77 ( 3) link_BETA1-4 : bond 0.00228 / 0.15 ( 9) link_BETA1-4 : angle 1.65417 / 1.11 ( 27) link_NAG-ASN : bond 0.00309 / 0.19 ( 12) link_NAG-ASN : angle 2.18756 / 1.46 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8242 (m-80) cc_final: 0.7890 (m-80) REVERT: A 158 MET cc_start: 0.8366 (mtm) cc_final: 0.7862 (mtm) REVERT: A 164 VAL cc_start: 0.9125 (t) cc_final: 0.8713 (m) REVERT: A 204 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8407 (mtt) REVERT: A 490 ARG cc_start: 0.7588 (tmt170) cc_final: 0.7250 (tpt90) REVERT: A 1040 GLU cc_start: 0.8906 (tp30) cc_final: 0.8612 (tp30) REVERT: F 22 LYS cc_start: 0.8888 (mtmm) cc_final: 0.8291 (tmmt) REVERT: F 65 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: F 102 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8082 (mpt) REVERT: G 81 ARG cc_start: 0.8621 (ptp90) cc_final: 0.8209 (ptp90) REVERT: G 112 LYS cc_start: 0.8845 (mtmt) cc_final: 0.8444 (mttt) REVERT: G 116 ASN cc_start: 0.9067 (t0) cc_final: 0.8743 (t0) outliers start: 23 outliers final: 16 residues processed: 123 average time/residue: 0.4688 time to fit residues: 63.3257 Evaluate side-chains 126 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain A residue 1173 CYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 29 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 chunk 121 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN A 161 HIS A 270 HIS F 32 GLN G 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.101324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.068805 restraints weight = 17897.911| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.66 r_work: 0.2889 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10704 Z= 0.121 Angle : 0.558 8.733 14591 Z= 0.283 Chirality : 0.043 0.237 1707 Planarity : 0.004 0.050 1834 Dihedral : 5.799 54.525 1903 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.79 % Allowed : 11.72 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.23), residues: 1293 helix: 2.26 (0.37), residues: 209 sheet: -0.13 (0.26), residues: 402 loop : -0.62 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 86 TYR 0.016 0.001 TYR G 69 PHE 0.011 0.001 PHE A 539 TRP 0.005 0.001 TRP A 439 HIS 0.002 0.001 HIS A1155 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (10663) covalent geometry : angle 0.54397 / 0.28 (14486) SS BOND : bond 0.00219 / 0.15 ( 18) SS BOND : angle 1.04747 / 0.75 ( 36) hydrogen bonds : bond 0.03710 / 2.52 ( 389) hydrogen bonds : angle 5.16146 / 3.63 ( 1161) link_ALPHA1-3 : bond 0.01094 / 0.58 ( 1) link_ALPHA1-3 : angle 1.49234 / 0.80 ( 3) link_ALPHA1-6 : bond 0.00897 / 0.47 ( 1) link_ALPHA1-6 : angle 1.31632 / 0.74 ( 3) link_BETA1-4 : bond 0.00269 / 0.17 ( 9) link_BETA1-4 : angle 1.52808 / 1.05 ( 27) link_NAG-ASN : bond 0.00250 / 0.15 ( 12) link_NAG-ASN : angle 2.03941 / 1.37 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8249 (m-80) cc_final: 0.7929 (m-80) REVERT: A 124 ARG cc_start: 0.7529 (ptp90) cc_final: 0.7289 (mtm-85) REVERT: A 158 MET cc_start: 0.8393 (mtm) cc_final: 0.7925 (mtm) REVERT: A 164 VAL cc_start: 0.9105 (t) cc_final: 0.8713 (m) REVERT: A 204 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8391 (mtt) REVERT: A 490 ARG cc_start: 0.7540 (tmt170) cc_final: 0.7181 (tpt90) REVERT: A 1040 GLU cc_start: 0.8900 (tp30) cc_final: 0.8628 (tp30) REVERT: F 22 LYS cc_start: 0.8834 (mtmm) cc_final: 0.8313 (tmmt) REVERT: F 38 ARG cc_start: 0.8904 (ttt90) cc_final: 0.8447 (ttt-90) REVERT: F 65 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: F 109 ASP cc_start: 0.8036 (t0) cc_final: 0.7601 (t0) REVERT: G 81 ARG cc_start: 0.8579 (ptp90) cc_final: 0.8205 (ptp90) REVERT: G 112 LYS cc_start: 0.8828 (mtmt) cc_final: 0.8422 (mttt) REVERT: G 116 ASN cc_start: 0.9082 (t0) cc_final: 0.8742 (t0) outliers start: 20 outliers final: 15 residues processed: 123 average time/residue: 0.5084 time to fit residues: 68.3887 Evaluate side-chains 125 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain A residue 1173 CYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 29 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 HIS A 151 ASN A 161 HIS A 270 HIS F 32 GLN G 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.100067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.067270 restraints weight = 17820.787| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.64 r_work: 0.2857 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10704 Z= 0.208 Angle : 0.597 8.765 14591 Z= 0.304 Chirality : 0.045 0.237 1707 Planarity : 0.004 0.049 1834 Dihedral : 6.064 52.798 1903 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.88 % Allowed : 11.72 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.23), residues: 1293 helix: 2.19 (0.37), residues: 209 sheet: -0.12 (0.26), residues: 401 loop : -0.62 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 191 TYR 0.019 0.001 TYR A 984 PHE 0.017 0.001 PHE A 411 TRP 0.006 0.001 TRP A 259 HIS 0.005 0.001 HIS F 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (10663) covalent geometry : angle 0.58074 / 0.30 (14486) SS BOND : bond 0.00307 / 0.21 ( 18) SS BOND : angle 1.18830 / 0.85 ( 36) hydrogen bonds : bond 0.04114 / 2.78 ( 389) hydrogen bonds : angle 5.26877 / 3.69 ( 1161) link_ALPHA1-3 : bond 0.00331 / 0.17 ( 1) link_ALPHA1-3 : angle 1.58121 / 0.86 ( 3) link_ALPHA1-6 : bond 0.00842 / 0.44 ( 1) link_ALPHA1-6 : angle 1.37035 / 0.76 ( 3) link_BETA1-4 : bond 0.00247 / 0.17 ( 9) link_BETA1-4 : angle 1.71602 / 1.14 ( 27) link_NAG-ASN : bond 0.00388 / 0.24 ( 12) link_NAG-ASN : angle 2.22442 / 1.49 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8293 (m-80) cc_final: 0.7923 (m-80) REVERT: A 158 MET cc_start: 0.8394 (mtm) cc_final: 0.7961 (mtm) REVERT: A 164 VAL cc_start: 0.9105 (t) cc_final: 0.8681 (m) REVERT: A 171 ASP cc_start: 0.8098 (t0) cc_final: 0.7463 (p0) REVERT: A 204 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8407 (mtt) REVERT: A 490 ARG cc_start: 0.7568 (tmt170) cc_final: 0.7255 (tpt90) REVERT: A 1040 GLU cc_start: 0.8908 (tp30) cc_final: 0.8635 (tp30) REVERT: F 22 LYS cc_start: 0.8859 (mtmm) cc_final: 0.8301 (tmmt) REVERT: F 65 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8135 (tp30) REVERT: F 109 ASP cc_start: 0.8032 (t0) cc_final: 0.7811 (t0) REVERT: G 81 ARG cc_start: 0.8634 (ptp90) cc_final: 0.8192 (ptp90) REVERT: G 112 LYS cc_start: 0.8869 (mtmt) cc_final: 0.8464 (mttt) REVERT: G 116 ASN cc_start: 0.9072 (t0) cc_final: 0.8736 (t0) outliers start: 21 outliers final: 14 residues processed: 121 average time/residue: 0.4762 time to fit residues: 63.3347 Evaluate side-chains 123 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain A residue 1173 CYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 29 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN A 161 HIS A 270 HIS F 32 GLN G 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.101134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.068637 restraints weight = 17828.135| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.65 r_work: 0.2886 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10704 Z= 0.124 Angle : 0.561 8.847 14591 Z= 0.284 Chirality : 0.044 0.237 1707 Planarity : 0.004 0.051 1834 Dihedral : 5.877 54.474 1903 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.61 % Allowed : 12.16 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.24), residues: 1293 helix: 2.30 (0.37), residues: 209 sheet: -0.12 (0.26), residues: 402 loop : -0.59 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 191 TYR 0.020 0.001 TYR A 984 PHE 0.013 0.001 PHE A 539 TRP 0.005 0.001 TRP A 439 HIS 0.004 0.001 HIS F 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (10663) covalent geometry : angle 0.54706 / 0.28 (14486) SS BOND : bond 0.00239 / 0.16 ( 18) SS BOND : angle 1.04286 / 0.75 ( 36) hydrogen bonds : bond 0.03735 / 2.54 ( 389) hydrogen bonds : angle 5.12426 / 3.59 ( 1161) link_ALPHA1-3 : bond 0.00866 / 0.46 ( 1) link_ALPHA1-3 : angle 1.31764 / 0.71 ( 3) link_ALPHA1-6 : bond 0.00963 / 0.51 ( 1) link_ALPHA1-6 : angle 1.36668 / 0.77 ( 3) link_BETA1-4 : bond 0.00262 / 0.16 ( 9) link_BETA1-4 : angle 1.52743 / 1.04 ( 27) link_NAG-ASN : bond 0.00248 / 0.15 ( 12) link_NAG-ASN : angle 2.02708 / 1.36 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6406.16 seconds wall clock time: 109 minutes 19.65 seconds (6559.65 seconds total)