Starting phenix.real_space_refine on Sat Jun 28 15:48:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xn5_38498/06_2025/8xn5_38498.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xn5_38498/06_2025/8xn5_38498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xn5_38498/06_2025/8xn5_38498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xn5_38498/06_2025/8xn5_38498.map" model { file = "/net/cci-nas-00/data/ceres_data/8xn5_38498/06_2025/8xn5_38498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xn5_38498/06_2025/8xn5_38498.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4872 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 137 5.16 5 C 18604 2.51 5 N 4804 2.21 5 O 5603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29149 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4872 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} bond proxies already assigned to first conformer: 4987 Chain: "B" Number of atoms: 7900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7900 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 55, 'TRANS': 955} Chain breaks: 7 Chain: "C" Number of atoms: 7924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7924 Classifications: {'peptide': 1013} Link IDs: {'PTRANS': 55, 'TRANS': 957} Chain breaks: 7 Chain: "D" Number of atoms: 7948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 7948 Classifications: {'peptide': 1016} Link IDs: {'PTRANS': 55, 'TRANS': 960} Chain breaks: 7 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} 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 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 34 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 34 " occ=0.50 Time building chain proxies: 18.51, per 1000 atoms: 0.64 Number of scatterers: 29149 At special positions: 0 Unit cell: (148.672, 134.128, 227.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 137 16.00 O 5603 8.00 N 4804 7.00 C 18604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.02 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.04 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " 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 NAG-ASN " NAG A 701 " - " ASN A 53 " " NAG A 702 " - " ASN A 103 " " NAG A 703 " - " ASN A 432 " " NAG A 704 " - " ASN A 546 " " NAG A 705 " - " ASN A 322 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B 717 " " NAG B1310 " - " ASN B 801 " " NAG B1311 " - " ASN B 709 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 801 " " NAG C1311 " - " ASN C 717 " " NAG D1301 " - " ASN D 717 " " NAG D1302 " - " ASN D 801 " " NAG D1303 " - " ASN D 122 " " NAG D1304 " - " ASN D 165 " " NAG D1305 " - " ASN D 282 " " NAG D1306 " - " ASN D 709 " " NAG D1307 " - " ASN D1098 " " NAG D1308 " - " ASN D1134 " " NAG D1309 " - " ASN D 616 " Time building additional restraints: 7.29 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 706 " pdb="ZN ZN A 706 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 706 " - pdb=" NE2 HIS A 374 " 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6838 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 49 sheets defined 32.2% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.985A pdb=" N ASP A 38 " --> pdb=" O AHIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.693A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.072A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.605A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.644A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.646A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.511A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.078A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.185A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.579A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 547 through 561 removed outlier: 3.526A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 560 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 155 through 158 removed outlier: 3.645A pdb=" N ARG B 158 " --> pdb=" O SER B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 158' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.618A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.759A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.846A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.580A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.051A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.674A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.711A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.301A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.617A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.760A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.877A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.894A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.083A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.615A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.534A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.592A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 383 through 387 Processing helix chain 'D' and resid 404 through 408 removed outlier: 3.760A pdb=" N SER D 408 " --> pdb=" O ASN D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'D' and resid 737 through 744 Processing helix chain 'D' and resid 746 through 757 removed outlier: 3.588A pdb=" N LEU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY D 757 " --> pdb=" O LEU D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 783 Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 897 through 909 Processing helix chain 'D' and resid 912 through 919 removed outlier: 3.991A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.855A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 Processing helix chain 'D' and resid 976 through 984 Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.117A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 134 removed outlier: 6.967A pdb=" N GLU A 140 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.194A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.466A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.933A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.586A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.764A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 169 through 172 removed outlier: 4.912A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 134 through 135 removed outlier: 6.297A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.787A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.252A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.527A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.680A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.997A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.574A pdb=" N LYS D 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.636A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.636A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.519A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.812A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AC3, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AC4, first strand: chain 'C' and resid 25 through 30 removed outlier: 8.104A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.923A pdb=" N PHE C 43 " --> pdb=" O ARG D 567 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLY D 566 " --> pdb=" O ASP D 574 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.786A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.340A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.846A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.526A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.680A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.083A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.496A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 788 through 789 removed outlier: 5.644A pdb=" N ILE C 788 " --> pdb=" O ASN D 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 1120 through 1121 Processing sheet with id=AD9, first strand: chain 'D' and resid 26 through 30 removed outlier: 8.351A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.943A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.650A pdb=" N LEU D 141 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.564A pdb=" N LEU D 241 " --> pdb=" O GLY D 103 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN D 121 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL D 126 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL D 171 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE D 128 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU D 169 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL D 130 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASN D 165 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLN D 134 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ALA D 163 " --> pdb=" O GLN D 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 311 through 319 removed outlier: 7.042A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.527A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 376 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 391 through 392 removed outlier: 3.548A pdb=" N VAL D 524 " --> pdb=" O PHE D 392 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.680A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 654 through 655 Processing sheet with id=AF1, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.723A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.513A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1120 through 1121 Processing sheet with id=AF4, first strand: chain 'D' and resid 1094 through 1097 1270 hydrogen bonds defined for protein. 3589 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: 13.20 Time building geometry restraints manager: 8.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6253 1.33 - 1.45: 7166 1.45 - 1.58: 16240 1.58 - 1.70: 0 1.70 - 1.82: 185 Bond restraints: 29844 Sorted by residual: bond pdb=" N LEU D 335 " pdb=" CA LEU D 335 " ideal model delta sigma weight residual 1.454 1.504 -0.050 1.18e-02 7.18e+03 1.81e+01 bond pdb=" C ASN A 33 " pdb=" N BHIS A 34 " ideal model delta sigma weight residual 1.335 1.393 -0.058 1.38e-02 5.25e+03 1.79e+01 bond pdb=" N ASN C 331 " pdb=" CA ASN C 331 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.29e-02 6.01e+03 1.26e+01 bond pdb=" N GLY D 526 " pdb=" CA GLY D 526 " ideal model delta sigma weight residual 1.434 1.471 -0.037 1.22e-02 6.72e+03 9.32e+00 bond pdb=" N VAL D 615 " pdb=" CA VAL D 615 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.28e-02 6.10e+03 9.16e+00 ... (remaining 29839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 39970 2.26 - 4.52: 573 4.52 - 6.78: 47 6.78 - 9.04: 7 9.04 - 11.30: 3 Bond angle restraints: 40600 Sorted by residual: angle pdb=" C ILE A 21 " pdb=" N GLU A 22 " pdb=" CA GLU A 22 " ideal model delta sigma weight residual 120.29 109.84 10.45 1.42e+00 4.96e-01 5.41e+01 angle pdb=" N ALA C 668 " pdb=" CA ALA C 668 " pdb=" C ALA C 668 " ideal model delta sigma weight residual 108.63 98.63 10.00 1.60e+00 3.91e-01 3.91e+01 angle pdb=" N LYS C 528 " pdb=" CA LYS C 528 " pdb=" C LYS C 528 " ideal model delta sigma weight residual 110.80 99.50 11.30 2.13e+00 2.20e-01 2.82e+01 angle pdb=" C ASN C 334 " pdb=" N LEU C 335 " pdb=" CA LEU C 335 " ideal model delta sigma weight residual 120.71 113.31 7.40 1.42e+00 4.96e-01 2.71e+01 angle pdb=" C ASN B 334 " pdb=" N LEU B 335 " pdb=" CA LEU B 335 " ideal model delta sigma weight residual 122.73 131.16 -8.43 1.62e+00 3.81e-01 2.71e+01 ... (remaining 40595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.10: 17345 23.10 - 46.21: 764 46.21 - 69.31: 104 69.31 - 92.42: 29 92.42 - 115.52: 17 Dihedral angle restraints: 18259 sinusoidal: 7642 harmonic: 10617 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -144.46 58.46 1 1.00e+01 1.00e-02 4.58e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -143.77 57.77 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -141.73 55.73 1 1.00e+01 1.00e-02 4.19e+01 ... (remaining 18256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.373: 4645 0.373 - 0.745: 0 0.745 - 1.118: 2 1.118 - 1.490: 1 1.490 - 1.863: 1 Chirality restraints: 4649 Sorted by residual: chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -4.26 1.86 2.00e-01 2.50e+01 8.68e+01 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.15 -1.25 2.00e-01 2.50e+01 3.91e+01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.78e+01 ... (remaining 4646 not shown) Planarity restraints: 5241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1311 " -0.330 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG B1311 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG B1311 " -0.119 2.00e-02 2.50e+03 pdb=" N2 NAG B1311 " 0.512 2.00e-02 2.50e+03 pdb=" O7 NAG B1311 " -0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1310 " -0.306 2.00e-02 2.50e+03 2.65e-01 8.79e+02 pdb=" C7 NAG B1310 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B1310 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG B1310 " 0.472 2.00e-02 2.50e+03 pdb=" O7 NAG B1310 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 703 " -0.306 2.00e-02 2.50e+03 2.63e-01 8.67e+02 pdb=" C7 NAG A 703 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A 703 " -0.001 2.00e-02 2.50e+03 pdb=" N2 NAG A 703 " 0.450 2.00e-02 2.50e+03 pdb=" O7 NAG A 703 " -0.213 2.00e-02 2.50e+03 ... (remaining 5238 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 80 2.49 - 3.09: 20650 3.09 - 3.69: 43285 3.69 - 4.30: 65416 4.30 - 4.90: 108655 Nonbonded interactions: 238086 Sorted by model distance: nonbonded pdb=" OD1 ASN C 331 " pdb=" C1 NAG C1301 " model vdw 1.884 2.776 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 706 " model vdw 2.066 2.230 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.206 3.040 nonbonded pdb=" NH2 ARG B 357 " pdb=" O THR D 167 " model vdw 2.210 3.120 nonbonded pdb=" NE2 GLN C 895 " pdb=" OD1 ASN D1074 " model vdw 2.213 3.120 ... (remaining 238081 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' and (resid 25 through 66 or resid 81 through 1139 or resid 1301 throu \ gh 1309)) selection = (chain 'C' and (resid 25 through 244 or resid 259 through 1139 or resid 1301 thr \ ough 1309)) selection = (chain 'D' and (resid 25 through 244 or resid 259 through 676 or resid 689 throu \ gh 826 or resid 854 through 1139 or resid 1301 through 1309)) } 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=0.50 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: 17.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.220 Construct map_model_manager: 0.020 Extract box with map and model: 1.270 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 77.240 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.140 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:13.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.007 1.023 29922 Z= 0.378 Angle : 0.755 49.290 40788 Z= 0.403 Chirality : 0.060 1.863 4649 Planarity : 0.009 0.286 5205 Dihedral : 13.390 115.521 11301 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.23 % Favored : 96.71 % Rotamer: Outliers : 0.03 % Allowed : 0.47 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.14), residues: 3589 helix: 2.01 (0.16), residues: 1024 sheet: 1.02 (0.19), residues: 629 loop : -0.58 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 886 HIS 0.011 0.001 HIS A 378 PHE 0.026 0.001 PHE D 565 TYR 0.021 0.001 TYR A 385 ARG 0.006 0.000 ARG D 567 Details of bonding type rmsd link_NAG-ASN : bond 0.17084 ( 36) link_NAG-ASN : angle 7.51524 ( 108) hydrogen bonds : bond 0.12422 ( 1251) hydrogen bonds : angle 6.78320 ( 3589) metal coordination : bond 0.28210 ( 2) SS BOND : bond 0.00306 ( 40) SS BOND : angle 1.03877 ( 80) covalent geometry : bond 0.00392 (29844) covalent geometry : angle 0.64806 (40600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 3.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 TRP cc_start: 0.7852 (m-90) cc_final: 0.7377 (m-90) REVERT: B 135 PHE cc_start: 0.6599 (m-80) cc_final: 0.6371 (m-80) REVERT: B 157 PHE cc_start: 0.8973 (t80) cc_final: 0.8711 (t80) REVERT: B 338 PHE cc_start: 0.7969 (m-80) cc_final: 0.7450 (m-80) REVERT: C 571 ASP cc_start: 0.8410 (t0) cc_final: 0.8143 (t0) REVERT: D 365 TYR cc_start: 0.7176 (m-80) cc_final: 0.6917 (m-80) REVERT: D 453 TYR cc_start: 0.7729 (p90) cc_final: 0.6550 (p90) REVERT: D 515 PHE cc_start: 0.8247 (m-80) cc_final: 0.7955 (m-80) REVERT: D 904 TYR cc_start: 0.7889 (m-80) cc_final: 0.7544 (m-10) REVERT: D 950 ASP cc_start: 0.8680 (m-30) cc_final: 0.8462 (m-30) outliers start: 1 outliers final: 2 residues processed: 347 average time/residue: 1.5955 time to fit residues: 639.5074 Evaluate side-chains 164 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 3.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 305 optimal weight: 0.9990 chunk 274 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 185 optimal weight: 0.0770 chunk 146 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A A 194 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 901 GLN B 965 GLN B1005 GLN B1074 ASN C 955 ASN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 GLN ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN D 965 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.125248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.075724 restraints weight = 104396.497| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 4.66 r_work: 0.2828 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29922 Z= 0.179 Angle : 0.665 19.345 40788 Z= 0.326 Chirality : 0.049 1.000 4649 Planarity : 0.005 0.052 5205 Dihedral : 8.282 123.720 4657 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.22 % Allowed : 6.80 % Favored : 91.97 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.14), residues: 3589 helix: 2.26 (0.16), residues: 1036 sheet: 0.94 (0.19), residues: 642 loop : -0.43 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 436 HIS 0.010 0.001 HIS A 378 PHE 0.032 0.002 PHE D 220 TYR 0.023 0.002 TYR D 369 ARG 0.007 0.001 ARG D 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00899 ( 36) link_NAG-ASN : angle 4.45579 ( 108) hydrogen bonds : bond 0.04537 ( 1251) hydrogen bonds : angle 5.52451 ( 3589) metal coordination : bond 0.01337 ( 2) SS BOND : bond 0.00699 ( 40) SS BOND : angle 1.01864 ( 80) covalent geometry : bond 0.00399 (29844) covalent geometry : angle 0.62359 (40600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 3.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 MET cc_start: 0.4722 (mtp) cc_final: 0.3416 (tpp) REVERT: B 157 PHE cc_start: 0.9356 (t80) cc_final: 0.9094 (t80) REVERT: B 979 ASP cc_start: 0.8689 (m-30) cc_final: 0.8454 (t0) REVERT: C 762 GLN cc_start: 0.9156 (mt0) cc_final: 0.8735 (mt0) REVERT: D 200 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7950 (t80) REVERT: D 233 ILE cc_start: 0.8030 (pt) cc_final: 0.7578 (pp) REVERT: D 453 TYR cc_start: 0.8186 (p90) cc_final: 0.7894 (p90) REVERT: D 515 PHE cc_start: 0.8479 (m-80) cc_final: 0.8165 (m-80) REVERT: D 895 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8601 (pt0) REVERT: D 984 LEU cc_start: 0.9168 (mt) cc_final: 0.8300 (mm) REVERT: D 994 ASP cc_start: 0.9192 (m-30) cc_final: 0.8845 (t0) REVERT: D 1113 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8598 (mt0) outliers start: 39 outliers final: 9 residues processed: 187 average time/residue: 1.4793 time to fit residues: 325.3484 Evaluate side-chains 139 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 1113 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 295 optimal weight: 2.9990 chunk 201 optimal weight: 40.0000 chunk 66 optimal weight: 0.0000 chunk 271 optimal weight: 10.0000 chunk 309 optimal weight: 6.9990 chunk 228 optimal weight: 0.2980 chunk 213 optimal weight: 0.6980 chunk 332 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 277 optimal weight: 1.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN A 601 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.125931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.075879 restraints weight = 117273.138| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 4.46 r_work: 0.2881 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29922 Z= 0.121 Angle : 0.594 20.160 40788 Z= 0.289 Chirality : 0.045 0.451 4649 Planarity : 0.004 0.044 5205 Dihedral : 6.788 93.543 4653 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.13 % Allowed : 7.75 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.14), residues: 3589 helix: 2.40 (0.16), residues: 1037 sheet: 0.99 (0.19), residues: 647 loop : -0.32 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 436 HIS 0.009 0.001 HIS A 378 PHE 0.017 0.001 PHE C 135 TYR 0.026 0.001 TYR D 904 ARG 0.005 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00772 ( 36) link_NAG-ASN : angle 4.26790 ( 108) hydrogen bonds : bond 0.04043 ( 1251) hydrogen bonds : angle 5.21654 ( 3589) metal coordination : bond 0.00097 ( 2) SS BOND : bond 0.00139 ( 40) SS BOND : angle 0.93978 ( 80) covalent geometry : bond 0.00260 (29844) covalent geometry : angle 0.55121 (40600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 2.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.5276 (tpp) cc_final: 0.5011 (tpp) REVERT: A 366 MET cc_start: 0.4567 (tpt) cc_final: 0.4289 (mmm) REVERT: A 432 ASN cc_start: 0.6011 (OUTLIER) cc_final: 0.5485 (p0) REVERT: A 579 MET cc_start: 0.3781 (mtp) cc_final: 0.2973 (mmm) REVERT: B 157 PHE cc_start: 0.9515 (t80) cc_final: 0.9297 (t80) REVERT: B 571 ASP cc_start: 0.8882 (t0) cc_final: 0.8667 (t0) REVERT: B 780 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8828 (mm-30) REVERT: B 979 ASP cc_start: 0.8646 (m-30) cc_final: 0.8403 (t0) REVERT: C 762 GLN cc_start: 0.9163 (mt0) cc_final: 0.8753 (mt0) REVERT: C 950 ASP cc_start: 0.8897 (m-30) cc_final: 0.8663 (m-30) REVERT: D 197 ILE cc_start: 0.8464 (mp) cc_final: 0.8241 (pp) REVERT: D 200 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7960 (t80) REVERT: D 233 ILE cc_start: 0.8061 (pt) cc_final: 0.7645 (pp) REVERT: D 453 TYR cc_start: 0.8306 (p90) cc_final: 0.7931 (p90) REVERT: D 518 LEU cc_start: 0.8570 (mt) cc_final: 0.8363 (mm) REVERT: D 569 ILE cc_start: 0.9332 (mp) cc_final: 0.9093 (tp) REVERT: D 756 TYR cc_start: 0.8836 (m-80) cc_final: 0.8478 (m-80) REVERT: D 895 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8467 (pt0) REVERT: D 994 ASP cc_start: 0.9183 (m-30) cc_final: 0.8834 (t0) REVERT: D 1113 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8576 (mt0) outliers start: 36 outliers final: 9 residues processed: 163 average time/residue: 1.3782 time to fit residues: 267.3290 Evaluate side-chains 145 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 3.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 1113 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 262 optimal weight: 0.9980 chunk 350 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 271 optimal weight: 7.9990 chunk 32 optimal weight: 30.0000 chunk 80 optimal weight: 0.9980 chunk 309 optimal weight: 7.9990 chunk 340 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS B 360 ASN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.123763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.073353 restraints weight = 94316.555| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 4.04 r_work: 0.2798 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 29922 Z= 0.253 Angle : 0.648 20.539 40788 Z= 0.318 Chirality : 0.046 0.455 4649 Planarity : 0.004 0.042 5205 Dihedral : 6.216 87.852 4653 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.66 % Allowed : 8.28 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.14), residues: 3589 helix: 2.31 (0.16), residues: 1029 sheet: 0.76 (0.19), residues: 688 loop : -0.32 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 104 HIS 0.010 0.001 HIS A 378 PHE 0.025 0.002 PHE D 515 TYR 0.042 0.002 TYR D 904 ARG 0.009 0.001 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00765 ( 36) link_NAG-ASN : angle 4.32527 ( 108) hydrogen bonds : bond 0.04411 ( 1251) hydrogen bonds : angle 5.30832 ( 3589) metal coordination : bond 0.00086 ( 2) SS BOND : bond 0.00212 ( 40) SS BOND : angle 0.94233 ( 80) covalent geometry : bond 0.00583 (29844) covalent geometry : angle 0.60875 (40600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 135 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.5093 (tpp) cc_final: 0.4649 (tpp) REVERT: A 360 MET cc_start: 0.3916 (ttt) cc_final: 0.3491 (mtm) REVERT: A 366 MET cc_start: 0.4686 (tpt) cc_final: 0.4440 (mmm) REVERT: A 383 MET cc_start: 0.9097 (ptt) cc_final: 0.8833 (pmm) REVERT: A 579 MET cc_start: 0.4494 (mtp) cc_final: 0.3302 (tpp) REVERT: B 157 PHE cc_start: 0.9407 (t80) cc_final: 0.9163 (t80) REVERT: B 332 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7249 (mt) REVERT: B 979 ASP cc_start: 0.8695 (m-30) cc_final: 0.8443 (t0) REVERT: C 762 GLN cc_start: 0.9185 (mt0) cc_final: 0.8792 (mt0) REVERT: C 950 ASP cc_start: 0.8934 (m-30) cc_final: 0.8691 (m-30) REVERT: C 1092 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8438 (pm20) REVERT: D 197 ILE cc_start: 0.8540 (mp) cc_final: 0.8255 (pp) REVERT: D 200 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7890 (t80) REVERT: D 233 ILE cc_start: 0.8058 (pt) cc_final: 0.7622 (pp) REVERT: D 453 TYR cc_start: 0.8451 (p90) cc_final: 0.7926 (p90) REVERT: D 523 THR cc_start: 0.8677 (p) cc_final: 0.8152 (t) REVERT: D 569 ILE cc_start: 0.9282 (mp) cc_final: 0.9045 (tp) REVERT: D 950 ASP cc_start: 0.9120 (m-30) cc_final: 0.8918 (m-30) REVERT: D 994 ASP cc_start: 0.9196 (m-30) cc_final: 0.8906 (t0) outliers start: 53 outliers final: 18 residues processed: 172 average time/residue: 1.3137 time to fit residues: 271.4021 Evaluate side-chains 148 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 562 PHE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain D residue 1096 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 149 optimal weight: 0.6980 chunk 270 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 chunk 206 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 319 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 289 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 252 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.123847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.073389 restraints weight = 103131.574| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 4.04 r_work: 0.2807 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 29922 Z= 0.206 Angle : 0.605 20.858 40788 Z= 0.297 Chirality : 0.045 0.392 4649 Planarity : 0.004 0.041 5205 Dihedral : 5.969 81.117 4653 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.54 % Allowed : 8.78 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.14), residues: 3589 helix: 2.36 (0.16), residues: 1036 sheet: 0.72 (0.19), residues: 674 loop : -0.28 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 436 HIS 0.009 0.001 HIS A 378 PHE 0.026 0.001 PHE B 133 TYR 0.038 0.001 TYR D 904 ARG 0.008 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 36) link_NAG-ASN : angle 4.20868 ( 108) hydrogen bonds : bond 0.04122 ( 1251) hydrogen bonds : angle 5.21782 ( 3589) metal coordination : bond 0.00081 ( 2) SS BOND : bond 0.00227 ( 40) SS BOND : angle 1.12875 ( 80) covalent geometry : bond 0.00470 (29844) covalent geometry : angle 0.56405 (40600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 128 time to evaluate : 3.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.5020 (tpp) cc_final: 0.4596 (tpp) REVERT: A 360 MET cc_start: 0.3863 (ttt) cc_final: 0.3426 (mtm) REVERT: A 366 MET cc_start: 0.4573 (tpt) cc_final: 0.4263 (mmm) REVERT: A 383 MET cc_start: 0.9083 (ptt) cc_final: 0.8855 (pmm) REVERT: A 432 ASN cc_start: 0.5850 (OUTLIER) cc_final: 0.5252 (p0) REVERT: A 579 MET cc_start: 0.4473 (mtp) cc_final: 0.3221 (tpp) REVERT: B 133 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.6782 (m-80) REVERT: B 157 PHE cc_start: 0.9470 (t80) cc_final: 0.9228 (t80) REVERT: B 332 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7354 (mt) REVERT: B 780 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8841 (mm-30) REVERT: B 979 ASP cc_start: 0.8690 (m-30) cc_final: 0.8439 (t0) REVERT: B 1116 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8729 (p) REVERT: C 166 CYS cc_start: 0.6670 (OUTLIER) cc_final: 0.6105 (p) REVERT: C 314 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8533 (tm-30) REVERT: C 762 GLN cc_start: 0.9170 (mt0) cc_final: 0.8761 (mt0) REVERT: C 950 ASP cc_start: 0.8937 (m-30) cc_final: 0.8704 (m-30) REVERT: C 1092 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8482 (pm20) REVERT: D 157 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.7460 (p90) REVERT: D 197 ILE cc_start: 0.8592 (mp) cc_final: 0.8290 (pp) REVERT: D 200 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7871 (t80) REVERT: D 233 ILE cc_start: 0.8101 (pt) cc_final: 0.7690 (pp) REVERT: D 453 TYR cc_start: 0.8465 (p90) cc_final: 0.7920 (p90) REVERT: D 523 THR cc_start: 0.8727 (p) cc_final: 0.8229 (t) REVERT: D 569 ILE cc_start: 0.9260 (mp) cc_final: 0.9043 (tp) REVERT: D 740 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8693 (ttp) REVERT: D 994 ASP cc_start: 0.9184 (m-30) cc_final: 0.8899 (t0) outliers start: 49 outliers final: 20 residues processed: 164 average time/residue: 1.2932 time to fit residues: 257.2095 Evaluate side-chains 155 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 562 PHE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 1096 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 208 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 291 optimal weight: 0.0670 chunk 227 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 259 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.124277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.073995 restraints weight = 99699.947| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 4.03 r_work: 0.2846 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29922 Z= 0.144 Angle : 0.576 20.839 40788 Z= 0.281 Chirality : 0.044 0.368 4649 Planarity : 0.004 0.040 5205 Dihedral : 5.582 65.710 4653 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.35 % Allowed : 9.19 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.14), residues: 3589 helix: 2.40 (0.16), residues: 1037 sheet: 0.85 (0.19), residues: 661 loop : -0.25 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 436 HIS 0.008 0.001 HIS A 378 PHE 0.023 0.001 PHE B 133 TYR 0.035 0.001 TYR D 904 ARG 0.009 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00665 ( 36) link_NAG-ASN : angle 4.13021 ( 108) hydrogen bonds : bond 0.03820 ( 1251) hydrogen bonds : angle 5.05516 ( 3589) metal coordination : bond 0.00070 ( 2) SS BOND : bond 0.00144 ( 40) SS BOND : angle 0.88889 ( 80) covalent geometry : bond 0.00324 (29844) covalent geometry : angle 0.53486 (40600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.4578 (tpp) cc_final: 0.4108 (tpp) REVERT: A 360 MET cc_start: 0.3905 (ttt) cc_final: 0.3457 (mtm) REVERT: A 366 MET cc_start: 0.4445 (tpt) cc_final: 0.4157 (mmm) REVERT: A 383 MET cc_start: 0.9093 (ptt) cc_final: 0.8854 (pmm) REVERT: A 455 MET cc_start: 0.6726 (tpt) cc_final: 0.4955 (tmm) REVERT: A 480 MET cc_start: 0.5385 (mpm) cc_final: 0.5110 (ppp) REVERT: A 579 MET cc_start: 0.3982 (mtp) cc_final: 0.3647 (ttt) REVERT: B 157 PHE cc_start: 0.9529 (t80) cc_final: 0.9311 (t80) REVERT: B 332 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7300 (mt) REVERT: B 780 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8840 (mm-30) REVERT: B 979 ASP cc_start: 0.8697 (m-30) cc_final: 0.8469 (t0) REVERT: C 166 CYS cc_start: 0.6610 (OUTLIER) cc_final: 0.6080 (p) REVERT: C 314 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8558 (tm-30) REVERT: C 762 GLN cc_start: 0.9150 (mt0) cc_final: 0.8731 (mt0) REVERT: C 950 ASP cc_start: 0.8884 (m-30) cc_final: 0.8654 (m-30) REVERT: D 141 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7478 (pt) REVERT: D 157 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7451 (p90) REVERT: D 197 ILE cc_start: 0.8649 (mp) cc_final: 0.8334 (pp) REVERT: D 200 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.7880 (t80) REVERT: D 233 ILE cc_start: 0.8211 (pt) cc_final: 0.7829 (pp) REVERT: D 453 TYR cc_start: 0.8456 (p90) cc_final: 0.7977 (p90) REVERT: D 523 THR cc_start: 0.8751 (p) cc_final: 0.8291 (t) REVERT: D 984 LEU cc_start: 0.9353 (mm) cc_final: 0.9008 (mp) REVERT: D 994 ASP cc_start: 0.9163 (m-30) cc_final: 0.8886 (t0) outliers start: 43 outliers final: 20 residues processed: 168 average time/residue: 1.3305 time to fit residues: 268.7424 Evaluate side-chains 150 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 562 PHE Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain D residue 1096 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 133 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 121 optimal weight: 0.0770 chunk 185 optimal weight: 10.0000 chunk 196 optimal weight: 30.0000 chunk 124 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 12 optimal weight: 50.0000 chunk 298 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 overall best weight: 2.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN B 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.123281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.072288 restraints weight = 123507.889| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 4.47 r_work: 0.2778 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 29922 Z= 0.260 Angle : 0.635 21.127 40788 Z= 0.310 Chirality : 0.046 0.370 4649 Planarity : 0.004 0.051 5205 Dihedral : 5.569 57.850 4653 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.41 % Allowed : 9.66 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.14), residues: 3589 helix: 2.33 (0.16), residues: 1034 sheet: 0.68 (0.19), residues: 683 loop : -0.28 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 436 HIS 0.009 0.001 HIS A 378 PHE 0.021 0.001 PHE B 133 TYR 0.019 0.001 TYR B 421 ARG 0.012 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00646 ( 36) link_NAG-ASN : angle 4.19627 ( 108) hydrogen bonds : bond 0.04168 ( 1251) hydrogen bonds : angle 5.22561 ( 3589) metal coordination : bond 0.00047 ( 2) SS BOND : bond 0.00197 ( 40) SS BOND : angle 0.93598 ( 80) covalent geometry : bond 0.00601 (29844) covalent geometry : angle 0.59665 (40600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 124 time to evaluate : 3.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: -0.2962 (OUTLIER) cc_final: -0.3221 (ppp) REVERT: A 270 MET cc_start: 0.4402 (tpp) cc_final: 0.3492 (tpp) REVERT: A 366 MET cc_start: 0.4503 (tpt) cc_final: 0.4220 (mmm) REVERT: A 432 ASN cc_start: 0.5772 (OUTLIER) cc_final: 0.5135 (p0) REVERT: A 579 MET cc_start: 0.4358 (mtp) cc_final: 0.3991 (ttt) REVERT: B 332 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7403 (mt) REVERT: B 369 TYR cc_start: 0.8485 (m-80) cc_final: 0.7938 (m-80) REVERT: B 740 MET cc_start: 0.9346 (mmm) cc_final: 0.9033 (tpp) REVERT: B 979 ASP cc_start: 0.8703 (m-30) cc_final: 0.8458 (t0) REVERT: C 166 CYS cc_start: 0.6763 (OUTLIER) cc_final: 0.6497 (p) REVERT: C 314 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8700 (tm-30) REVERT: C 762 GLN cc_start: 0.9190 (mt0) cc_final: 0.8759 (mt0) REVERT: C 950 ASP cc_start: 0.8951 (m-30) cc_final: 0.8721 (m-30) REVERT: D 157 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7461 (p90) REVERT: D 197 ILE cc_start: 0.8678 (mp) cc_final: 0.8329 (pp) REVERT: D 200 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.7776 (t80) REVERT: D 233 ILE cc_start: 0.8221 (pt) cc_final: 0.7833 (pp) REVERT: D 453 TYR cc_start: 0.8581 (p90) cc_final: 0.8009 (p90) REVERT: D 523 THR cc_start: 0.8871 (p) cc_final: 0.8435 (t) outliers start: 45 outliers final: 23 residues processed: 158 average time/residue: 1.3275 time to fit residues: 253.8809 Evaluate side-chains 148 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 562 PHE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain D residue 1096 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 304 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 chunk 316 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 232 optimal weight: 0.7980 chunk 220 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 190 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.123581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.073174 restraints weight = 110699.709| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 4.21 r_work: 0.2807 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29922 Z= 0.176 Angle : 0.607 21.108 40788 Z= 0.296 Chirality : 0.044 0.372 4649 Planarity : 0.004 0.046 5205 Dihedral : 5.361 54.033 4653 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.35 % Allowed : 9.88 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.14), residues: 3589 helix: 2.34 (0.16), residues: 1040 sheet: 0.65 (0.19), residues: 686 loop : -0.27 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 436 HIS 0.010 0.001 HIS A 378 PHE 0.023 0.001 PHE D 497 TYR 0.029 0.001 TYR D 369 ARG 0.013 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00623 ( 36) link_NAG-ASN : angle 4.13145 ( 108) hydrogen bonds : bond 0.03938 ( 1251) hydrogen bonds : angle 5.15088 ( 3589) metal coordination : bond 0.00875 ( 2) SS BOND : bond 0.00154 ( 40) SS BOND : angle 0.86990 ( 80) covalent geometry : bond 0.00402 (29844) covalent geometry : angle 0.56855 (40600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: -0.3085 (OUTLIER) cc_final: -0.3321 (ppp) REVERT: A 270 MET cc_start: 0.4177 (tpp) cc_final: 0.3213 (tpp) REVERT: A 360 MET cc_start: 0.3645 (ttt) cc_final: 0.3245 (mtm) REVERT: A 366 MET cc_start: 0.4652 (tpt) cc_final: 0.4370 (mmm) REVERT: A 432 ASN cc_start: 0.5886 (OUTLIER) cc_final: 0.5280 (p0) REVERT: A 579 MET cc_start: 0.4496 (mtp) cc_final: 0.4148 (ttt) REVERT: B 332 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7395 (mt) REVERT: B 369 TYR cc_start: 0.8511 (m-80) cc_final: 0.7969 (m-80) REVERT: B 740 MET cc_start: 0.9341 (mmm) cc_final: 0.8945 (tpp) REVERT: B 780 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8816 (mm-30) REVERT: B 979 ASP cc_start: 0.8685 (m-30) cc_final: 0.8462 (t0) REVERT: C 166 CYS cc_start: 0.6612 (OUTLIER) cc_final: 0.6387 (p) REVERT: C 314 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8689 (tm-30) REVERT: C 762 GLN cc_start: 0.9174 (mt0) cc_final: 0.8778 (mt0) REVERT: C 794 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.9124 (pp) REVERT: C 950 ASP cc_start: 0.8908 (m-30) cc_final: 0.8677 (m-30) REVERT: D 157 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7423 (p90) REVERT: D 197 ILE cc_start: 0.8730 (mp) cc_final: 0.8396 (pp) REVERT: D 200 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7883 (t80) REVERT: D 233 ILE cc_start: 0.8195 (pt) cc_final: 0.7821 (pp) REVERT: D 453 TYR cc_start: 0.8581 (p90) cc_final: 0.8157 (p90) REVERT: D 455 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8518 (mp) outliers start: 43 outliers final: 22 residues processed: 155 average time/residue: 1.3349 time to fit residues: 248.5755 Evaluate side-chains 150 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 562 PHE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain D residue 1096 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 236 optimal weight: 0.1980 chunk 88 optimal weight: 8.9990 chunk 322 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 291 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 161 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 304 optimal weight: 0.0570 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN D 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.120042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.070143 restraints weight = 127688.295| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 4.11 r_work: 0.2814 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29922 Z= 0.120 Angle : 0.593 20.895 40788 Z= 0.290 Chirality : 0.044 0.368 4649 Planarity : 0.004 0.058 5205 Dihedral : 5.170 53.912 4653 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.22 % Allowed : 10.13 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.14), residues: 3589 helix: 2.40 (0.16), residues: 1029 sheet: 0.74 (0.19), residues: 667 loop : -0.24 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 436 HIS 0.007 0.001 HIS A 378 PHE 0.025 0.001 PHE B 133 TYR 0.019 0.001 TYR D 904 ARG 0.014 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00645 ( 36) link_NAG-ASN : angle 4.05866 ( 108) hydrogen bonds : bond 0.03746 ( 1251) hydrogen bonds : angle 5.06616 ( 3589) metal coordination : bond 0.00110 ( 2) SS BOND : bond 0.00117 ( 40) SS BOND : angle 0.81600 ( 80) covalent geometry : bond 0.00268 (29844) covalent geometry : angle 0.55549 (40600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.4030 (tpp) cc_final: 0.3659 (tpp) REVERT: A 360 MET cc_start: 0.3507 (ttt) cc_final: 0.3104 (mtm) REVERT: A 366 MET cc_start: 0.4669 (tpt) cc_final: 0.4392 (mmm) REVERT: A 432 ASN cc_start: 0.5939 (OUTLIER) cc_final: 0.5335 (p0) REVERT: A 579 MET cc_start: 0.4970 (mtp) cc_final: 0.4467 (ttt) REVERT: B 332 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7395 (mt) REVERT: B 369 TYR cc_start: 0.8499 (m-80) cc_final: 0.7948 (m-80) REVERT: B 740 MET cc_start: 0.9298 (mmm) cc_final: 0.8915 (tpp) REVERT: B 780 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8830 (mm-30) REVERT: B 979 ASP cc_start: 0.8686 (m-30) cc_final: 0.8474 (t0) REVERT: C 166 CYS cc_start: 0.6652 (OUTLIER) cc_final: 0.6430 (p) REVERT: C 314 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8545 (tm-30) REVERT: C 436 TRP cc_start: 0.8012 (p90) cc_final: 0.7662 (p90) REVERT: C 762 GLN cc_start: 0.9166 (mt0) cc_final: 0.8749 (mt0) REVERT: C 794 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9078 (pp) REVERT: D 157 PHE cc_start: 0.7702 (p90) cc_final: 0.7419 (p90) REVERT: D 197 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8388 (pp) REVERT: D 200 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.7893 (t80) REVERT: D 233 ILE cc_start: 0.8202 (pt) cc_final: 0.7832 (pp) REVERT: D 453 TYR cc_start: 0.8598 (p90) cc_final: 0.8163 (p90) REVERT: D 455 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8495 (mp) REVERT: D 519 HIS cc_start: 0.6959 (OUTLIER) cc_final: 0.6589 (m-70) REVERT: D 564 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8106 (pm20) outliers start: 39 outliers final: 17 residues processed: 155 average time/residue: 1.3947 time to fit residues: 260.9585 Evaluate side-chains 149 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 3.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 562 PHE Chi-restraints excluded: chain D residue 564 GLN Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 320 optimal weight: 0.0980 chunk 203 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 252 optimal weight: 1.9990 chunk 276 optimal weight: 0.1980 chunk 152 optimal weight: 2.9990 chunk 266 optimal weight: 0.8980 chunk 288 optimal weight: 5.9990 chunk 348 optimal weight: 3.9990 chunk 308 optimal weight: 0.6980 chunk 4 optimal weight: 20.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.119940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.070755 restraints weight = 109589.181| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.65 r_work: 0.2835 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29922 Z= 0.131 Angle : 0.595 20.910 40788 Z= 0.291 Chirality : 0.044 0.365 4649 Planarity : 0.004 0.069 5205 Dihedral : 5.067 53.894 4653 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.97 % Allowed : 10.54 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 3589 helix: 2.39 (0.16), residues: 1035 sheet: 0.71 (0.19), residues: 679 loop : -0.23 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 436 HIS 0.007 0.001 HIS A 378 PHE 0.021 0.001 PHE B 133 TYR 0.031 0.001 TYR D 904 ARG 0.014 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00626 ( 36) link_NAG-ASN : angle 4.02740 ( 108) hydrogen bonds : bond 0.03744 ( 1251) hydrogen bonds : angle 5.02398 ( 3589) metal coordination : bond 0.00017 ( 2) SS BOND : bond 0.00120 ( 40) SS BOND : angle 0.80064 ( 80) covalent geometry : bond 0.00293 (29844) covalent geometry : angle 0.55743 (40600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 3.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.4135 (tpp) cc_final: 0.3804 (tpp) REVERT: A 360 MET cc_start: 0.3722 (ttt) cc_final: 0.3300 (mtm) REVERT: A 366 MET cc_start: 0.4519 (tpt) cc_final: 0.4250 (mmm) REVERT: A 408 MET cc_start: 0.8053 (mmt) cc_final: 0.7733 (mmp) REVERT: A 579 MET cc_start: 0.4327 (mtp) cc_final: 0.3919 (ttt) REVERT: B 332 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7397 (mt) REVERT: B 369 TYR cc_start: 0.8488 (m-80) cc_final: 0.7907 (m-80) REVERT: B 740 MET cc_start: 0.9290 (mmm) cc_final: 0.8904 (tpp) REVERT: B 780 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8809 (mm-30) REVERT: B 1118 ASP cc_start: 0.9200 (m-30) cc_final: 0.8962 (t0) REVERT: C 314 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8676 (tm-30) REVERT: C 436 TRP cc_start: 0.8019 (p90) cc_final: 0.7611 (p90) REVERT: C 762 GLN cc_start: 0.9175 (mt0) cc_final: 0.8793 (mt0) REVERT: C 794 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9126 (pp) REVERT: D 157 PHE cc_start: 0.7595 (p90) cc_final: 0.7324 (p90) REVERT: D 197 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8380 (pp) REVERT: D 200 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.7841 (t80) REVERT: D 233 ILE cc_start: 0.8136 (pt) cc_final: 0.7823 (pp) REVERT: D 453 TYR cc_start: 0.8660 (p90) cc_final: 0.8057 (p90) REVERT: D 519 HIS cc_start: 0.6959 (OUTLIER) cc_final: 0.6601 (m-70) REVERT: D 564 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8073 (pm20) outliers start: 31 outliers final: 21 residues processed: 144 average time/residue: 1.5506 time to fit residues: 265.4147 Evaluate side-chains 148 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 562 PHE Chi-restraints excluded: chain D residue 564 GLN Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 171 optimal weight: 0.0570 chunk 38 optimal weight: 10.0000 chunk 274 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 343 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 140 optimal weight: 0.0970 chunk 32 optimal weight: 8.9990 chunk 51 optimal weight: 0.3980 chunk 72 optimal weight: 6.9990 chunk 316 optimal weight: 3.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.120076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.070382 restraints weight = 122764.677| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.95 r_work: 0.2826 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 29922 Z= 0.128 Angle : 0.605 20.861 40788 Z= 0.297 Chirality : 0.044 0.363 4649 Planarity : 0.004 0.054 5205 Dihedral : 5.030 53.875 4653 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.00 % Allowed : 10.57 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 3589 helix: 2.36 (0.16), residues: 1035 sheet: 0.75 (0.19), residues: 684 loop : -0.22 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 436 HIS 0.007 0.001 HIS A 378 PHE 0.023 0.001 PHE B 157 TYR 0.030 0.001 TYR D 369 ARG 0.012 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 36) link_NAG-ASN : angle 4.00059 ( 108) hydrogen bonds : bond 0.03725 ( 1251) hydrogen bonds : angle 5.01571 ( 3589) metal coordination : bond 0.00023 ( 2) SS BOND : bond 0.00283 ( 40) SS BOND : angle 1.61048 ( 80) covalent geometry : bond 0.00288 (29844) covalent geometry : angle 0.56537 (40600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29148.49 seconds wall clock time: 499 minutes 12.42 seconds (29952.42 seconds total)