Starting phenix.real_space_refine on Tue Aug 26 02:59:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnk_38505/08_2025/8xnk_38505.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnk_38505/08_2025/8xnk_38505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xnk_38505/08_2025/8xnk_38505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnk_38505/08_2025/8xnk_38505.map" model { file = "/net/cci-nas-00/data/ceres_data/8xnk_38505/08_2025/8xnk_38505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnk_38505/08_2025/8xnk_38505.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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 135 5.16 5 C 18372 2.51 5 N 4758 2.21 5 O 5513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28779 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: 7799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7799 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 55, 'TRANS': 942} Chain breaks: 7 Chain: "C" Number of atoms: 7784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7784 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 53, 'TRANS': 940} Chain breaks: 8 Chain: "D" Number of atoms: 7917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7917 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 54, 'TRANS': 957} Chain breaks: 7 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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=0.63 ... (18 atoms not shown) pdb=" NE2BHIS A 34 " occ=0.37 Time building chain proxies: 6.60, per 1000 atoms: 0.23 Number of scatterers: 28779 At special positions: 0 Unit cell: (124.432, 138.168, 236.744, 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 135 16.00 O 5513 8.00 N 4758 7.00 C 18372 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, 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=2.03 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=2.04 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 379 " - pdb=" SG CYS C 432 " 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=2.04 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 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=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.04 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 90 " " NAG A 703 " - " ASN A 103 " " NAG A 704 " - " ASN A 432 " " NAG A 705 " - " ASN A 546 " " NAG A 706 " - " ASN A 322 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B1098 " " NAG B1305 " - " ASN B1134 " " NAG B1306 " - " ASN B 331 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " " NAG D1301 " - " ASN D 717 " " NAG D1302 " - " ASN D 801 " " NAG D1303 " - " ASN D 61 " " NAG D1304 " - " ASN D 122 " " NAG D1305 " - " ASN D 165 " " NAG D1306 " - " ASN D 282 " " NAG D1307 " - " ASN D 709 " " NAG D1308 " - " ASN D1098 " " NAG D1309 " - " ASN D1134 " Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 707 " pdb="ZN ZN A 707 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 707 " - pdb=" NE2 HIS A 374 " 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6768 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 47 sheets defined 31.2% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.668A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP A 38 " --> pdb=" O AHIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.535A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 102 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: 4.181A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.536A 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 218 through 252 removed outlier: 3.778A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.761A 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 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 389 through 393 Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.512A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.702A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.138A 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 485 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 509 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.428A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.842A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (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 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.533A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.697A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.921A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.080A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.746A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.511A 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 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.316A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.810A 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 365 through 371 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.698A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.805A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 827 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.128A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 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 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.706A 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 removed outlier: 3.532A pdb=" N PHE D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.697A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 744 Processing helix chain 'D' and resid 746 through 757 removed outlier: 3.503A pdb=" N SER D 750 " --> pdb=" O SER D 746 " (cutoff:3.500A) removed outlier: 3.806A 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 910 Processing helix chain 'D' and resid 912 through 919 removed outlier: 4.077A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.853A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 3.953A 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 1033 removed outlier: 4.621A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1118 No H-bonds generated for 'chain 'D' and resid 1116 through 1118' Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 134 removed outlier: 3.574A pdb=" N ASN A 134 " --> pdb=" O GLU A 140 " (cutoff:3.500A) removed outlier: 6.886A 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: 6.507A 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: 6.164A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.196A pdb=" N SER B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.137A 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: 6.280A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.204A 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: 3.725A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.719A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 126 through 129 Processing sheet with id=AA9, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.672A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.200A 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: 4.107A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.444A 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: 3.864A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (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 Processing sheet with id=AB5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.004A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.477A 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 Processing sheet with id=AB7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.660A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.816A 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: 6.660A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.183A 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: 4.494A 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: 5.698A 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: 3.576A pdb=" N THR C 25 " --> pdb=" O HIS C 66 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.182A pdb=" N PHE C 43 " --> pdb=" O ARG D 567 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY D 566 " --> pdb=" O ASP D 574 " (cutoff:3.500A) removed outlier: 5.326A 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: 3.855A 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: 4.059A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.699A 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: 6.765A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.083A 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: 3.865A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (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 Processing sheet with id=AD3, first strand: chain 'C' and resid 654 through 655 Processing sheet with id=AD4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.540A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.519A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 788 through 789 removed outlier: 5.610A pdb=" N ILE C 788 " --> pdb=" O ASN D 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 1120 through 1121 Processing sheet with id=AD8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'D' and resid 26 through 30 removed outlier: 7.957A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 227 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.816A 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: 4.164A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASN D 121 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLU D 132 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N CYS D 166 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.498A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.561A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY D 431 " --> pdb=" O TYR D 380 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'D' and resid 654 through 655 Processing sheet with id=AE8, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.666A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.666A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA D1078 " --> pdb=" O PHE D1095 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.561A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1120 through 1121 1261 hydrogen bonds defined for protein. 3592 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: 6.77 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4692 1.31 - 1.44: 8232 1.44 - 1.57: 16358 1.57 - 1.70: 0 1.70 - 1.82: 183 Bond restraints: 29465 Sorted by residual: bond pdb=" CA SER D 31 " pdb=" CB SER D 31 " ideal model delta sigma weight residual 1.524 1.462 0.062 1.22e-02 6.72e+03 2.60e+01 bond pdb=" N THR C 333 " pdb=" CA THR C 333 " ideal model delta sigma weight residual 1.458 1.503 -0.045 9.00e-03 1.23e+04 2.51e+01 bond pdb=" C SER D 31 " pdb=" O SER D 31 " ideal model delta sigma weight residual 1.233 1.175 0.057 1.21e-02 6.83e+03 2.26e+01 bond pdb=" N PRO D 491 " pdb=" CD PRO D 491 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.13e+01 bond pdb=" N PRO B 491 " pdb=" CD PRO B 491 " ideal model delta sigma weight residual 1.473 1.537 -0.064 1.40e-02 5.10e+03 2.10e+01 ... (remaining 29460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 39575 2.66 - 5.32: 462 5.32 - 7.97: 37 7.97 - 10.63: 3 10.63 - 13.29: 2 Bond angle restraints: 40079 Sorted by residual: angle pdb=" O PHE C 329 " pdb=" C PHE C 329 " pdb=" N PRO C 330 " ideal model delta sigma weight residual 121.71 114.65 7.06 6.40e-01 2.44e+00 1.22e+02 angle pdb=" CA PHE C 329 " pdb=" C PHE C 329 " pdb=" N PRO C 330 " ideal model delta sigma weight residual 117.71 125.28 -7.57 9.20e-01 1.18e+00 6.76e+01 angle pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" N PRO B 521 " ideal model delta sigma weight residual 117.68 122.57 -4.89 7.10e-01 1.98e+00 4.74e+01 angle pdb=" C THR D 523 " pdb=" CA THR D 523 " pdb=" CB THR D 523 " ideal model delta sigma weight residual 110.42 97.13 13.29 1.99e+00 2.53e-01 4.46e+01 angle pdb=" C GLU D 516 " pdb=" CA GLU D 516 " pdb=" CB GLU D 516 " ideal model delta sigma weight residual 111.51 103.70 7.81 1.38e+00 5.25e-01 3.20e+01 ... (remaining 40074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 16445 17.91 - 35.83: 1218 35.83 - 53.74: 193 53.74 - 71.65: 59 71.65 - 89.56: 21 Dihedral angle restraints: 17936 sinusoidal: 7427 harmonic: 10509 Sorted by residual: dihedral pdb=" CD ARG D 498 " pdb=" NE ARG D 498 " pdb=" CZ ARG D 498 " pdb=" NH1 ARG D 498 " ideal model delta sinusoidal sigma weight residual 0.00 62.89 -62.89 1 1.00e+01 1.00e-02 5.23e+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 -140.74 54.74 1 1.00e+01 1.00e-02 4.06e+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 -140.00 54.00 1 1.00e+01 1.00e-02 3.96e+01 ... (remaining 17933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.176: 4549 0.176 - 0.353: 16 0.353 - 0.529: 2 0.529 - 0.706: 1 0.706 - 0.882: 1 Chirality restraints: 4569 Sorted by residual: chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.95e+01 chirality pdb=" C1 NAG D1309 " pdb=" ND2 ASN D1134 " pdb=" C2 NAG D1309 " pdb=" O5 NAG D1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" C1 NAG D1305 " pdb=" ND2 ASN D 165 " pdb=" C2 NAG D1305 " pdb=" O5 NAG D1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.15e+00 ... (remaining 4566 not shown) Planarity restraints: 5175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1304 " -0.294 2.00e-02 2.50e+03 2.51e-01 7.85e+02 pdb=" C7 NAG B1304 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG B1304 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG B1304 " 0.436 2.00e-02 2.50e+03 pdb=" O7 NAG B1304 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1306 " -0.278 2.00e-02 2.50e+03 2.34e-01 6.82e+02 pdb=" C7 NAG C1306 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG C1306 " -0.182 2.00e-02 2.50e+03 pdb=" N2 NAG C1306 " 0.396 2.00e-02 2.50e+03 pdb=" O7 NAG C1306 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " -0.258 2.00e-02 2.50e+03 2.16e-01 5.85e+02 pdb=" C7 NAG B1301 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " 0.363 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " -0.001 2.00e-02 2.50e+03 ... (remaining 5172 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 276 2.63 - 3.20: 25619 3.20 - 3.77: 43395 3.77 - 4.33: 61564 4.33 - 4.90: 101494 Nonbonded interactions: 232348 Sorted by model distance: nonbonded pdb=" CD GLU A 402 " pdb="ZN ZN A 707 " model vdw 2.067 2.460 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 707 " model vdw 2.094 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 707 " model vdw 2.096 2.230 nonbonded pdb=" OG SER D 116 " pdb=" O CYS D 131 " model vdw 2.203 3.040 nonbonded pdb=" ND2 ASN B 317 " pdb=" OD2 ASP D 737 " model vdw 2.227 3.120 ... (remaining 232343 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 26 through 66 or resid 83 through 142 or resid 167 through \ 244 or resid 260 through 516 or resid 529 through 1306)) selection = (chain 'C' and (resid 26 through 66 or resid 83 through 142 or resid 167 through \ 244 or resid 260 through 1306)) selection = (chain 'D' and (resid 26 through 142 or resid 167 through 244 or resid 260 throu \ gh 516 or resid 529 through 676 or resid 689 through 827 or resid 854 through 13 \ 06)) } 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=0.37 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: 11.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 28.130 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 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 : 0.006 0.209 29533 Z= 0.288 Angle : 0.726 21.005 40240 Z= 0.412 Chirality : 0.051 0.882 4569 Planarity : 0.011 0.441 5146 Dihedral : 13.065 89.563 11057 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.83 % Favored : 96.11 % Rotamer: Outliers : 0.19 % Allowed : 0.35 % Favored : 99.46 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.14), residues: 3551 helix: 1.75 (0.16), residues: 1040 sheet: 0.83 (0.19), residues: 659 loop : -0.71 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.027 0.002 TYR D 380 PHE 0.043 0.002 PHE C 906 TRP 0.032 0.002 TRP C 886 HIS 0.012 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00558 (29465) covalent geometry : angle 0.68124 (40079) SS BOND : bond 0.00283 ( 37) SS BOND : angle 1.29388 ( 74) hydrogen bonds : bond 0.13652 ( 1244) hydrogen bonds : angle 6.70404 ( 3592) metal coordination : bond 0.20676 ( 2) link_NAG-ASN : bond 0.01185 ( 29) link_NAG-ASN : angle 5.31564 ( 87) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 361 time to evaluate : 1.226 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: symmetry clash REVERT: A 292 ASP cc_start: 0.4986 (t70) cc_final: 0.4704 (p0) REVERT: A 332 MET cc_start: -0.1457 (ptm) cc_final: -0.1699 (pp-130) REVERT: D 58 PHE cc_start: 0.8366 (m-10) cc_final: 0.8083 (m-10) REVERT: D 133 PHE cc_start: 0.6932 (m-80) cc_final: 0.6442 (m-80) REVERT: D 390 LEU cc_start: 0.9292 (mt) cc_final: 0.9078 (mt) REVERT: D 392 PHE cc_start: 0.8938 (m-80) cc_final: 0.8690 (m-80) REVERT: D 425 LEU cc_start: 0.8884 (mt) cc_final: 0.8617 (tp) REVERT: D 904 TYR cc_start: 0.7548 (m-80) cc_final: 0.7106 (m-10) outliers start: 6 outliers final: 3 residues processed: 367 average time/residue: 0.7835 time to fit residues: 330.4419 Evaluate side-chains 166 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 745 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A A 42 GLN A 89 GLN A 194 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 901 GLN B 965 GLN B1074 ASN B1088 HIS C 331 ASN C 762 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN D 30 ASN D 207 HIS D 540 ASN D 965 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.142218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090936 restraints weight = 118640.127| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 4.60 r_work: 0.2938 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29533 Z= 0.151 Angle : 0.626 15.564 40240 Z= 0.315 Chirality : 0.046 0.473 4569 Planarity : 0.004 0.052 5146 Dihedral : 6.134 98.926 4475 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.14 % Allowed : 7.82 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.14), residues: 3551 helix: 2.14 (0.16), residues: 1038 sheet: 1.04 (0.19), residues: 660 loop : -0.51 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 319 TYR 0.022 0.001 TYR C 170 PHE 0.022 0.001 PHE C 133 TRP 0.030 0.001 TRP C 436 HIS 0.007 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00333 (29465) covalent geometry : angle 0.60416 (40079) SS BOND : bond 0.00181 ( 37) SS BOND : angle 0.82042 ( 74) hydrogen bonds : bond 0.04535 ( 1244) hydrogen bonds : angle 5.20944 ( 3592) metal coordination : bond 0.00499 ( 2) link_NAG-ASN : bond 0.00675 ( 29) link_NAG-ASN : angle 3.54962 ( 87) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 1.196 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: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7847 (pt0) REVERT: A 111 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8551 (t0) REVERT: A 249 MET cc_start: 0.4596 (mtt) cc_final: 0.4200 (mmt) REVERT: A 332 MET cc_start: 0.2054 (ptm) cc_final: 0.1237 (pp-130) REVERT: A 360 MET cc_start: 0.4170 (tmt) cc_final: 0.3630 (tmt) REVERT: B 776 LYS cc_start: 0.9339 (ttpt) cc_final: 0.8710 (tttm) REVERT: B 1002 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8769 (mm-40) REVERT: C 571 ASP cc_start: 0.9253 (t0) cc_final: 0.8951 (t0) REVERT: C 957 GLN cc_start: 0.8904 (mt0) cc_final: 0.8688 (tt0) REVERT: C 988 GLU cc_start: 0.9253 (mp0) cc_final: 0.9045 (mp0) REVERT: C 1010 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8861 (mp10) REVERT: D 133 PHE cc_start: 0.7373 (m-80) cc_final: 0.7099 (m-80) REVERT: D 338 PHE cc_start: 0.8569 (m-10) cc_final: 0.8347 (m-10) REVERT: D 425 LEU cc_start: 0.8976 (mt) cc_final: 0.8576 (tp) REVERT: D 740 MET cc_start: 0.9021 (ttt) cc_final: 0.8654 (ttm) REVERT: D 762 GLN cc_start: 0.9212 (mt0) cc_final: 0.8947 (mp10) outliers start: 36 outliers final: 14 residues processed: 192 average time/residue: 0.7034 time to fit residues: 159.5420 Evaluate side-chains 153 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 973 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 276 optimal weight: 1.9990 chunk 321 optimal weight: 0.9980 chunk 281 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 50 optimal weight: 30.0000 chunk 181 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1083 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.140067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.089037 restraints weight = 118848.345| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.07 r_work: 0.2928 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29533 Z= 0.167 Angle : 0.589 13.098 40240 Z= 0.297 Chirality : 0.045 0.493 4569 Planarity : 0.004 0.046 5146 Dihedral : 5.625 94.603 4473 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.39 % Allowed : 8.84 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.14), residues: 3551 helix: 2.27 (0.16), residues: 1035 sheet: 0.94 (0.19), residues: 690 loop : -0.41 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 995 TYR 0.025 0.001 TYR B 453 PHE 0.021 0.001 PHE B 338 TRP 0.022 0.001 TRP C 436 HIS 0.007 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00377 (29465) covalent geometry : angle 0.56385 (40079) SS BOND : bond 0.00207 ( 37) SS BOND : angle 1.45861 ( 74) hydrogen bonds : bond 0.04241 ( 1244) hydrogen bonds : angle 5.02032 ( 3592) metal coordination : bond 0.00201 ( 2) link_NAG-ASN : bond 0.00671 ( 29) link_NAG-ASN : angle 3.52023 ( 87) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 1.231 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 190 MET cc_start: 0.2812 (pp-130) cc_final: 0.2345 (ptm) REVERT: A 249 MET cc_start: 0.3482 (mtt) cc_final: 0.3113 (mmt) REVERT: A 332 MET cc_start: 0.1459 (ptm) cc_final: 0.0736 (pp-130) REVERT: A 360 MET cc_start: 0.4577 (tmt) cc_final: 0.4081 (tmt) REVERT: B 177 MET cc_start: 0.7800 (ppp) cc_final: 0.7469 (ppp) REVERT: B 515 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.8077 (p90) REVERT: B 1002 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8811 (mm-40) REVERT: C 129 LYS cc_start: 0.8501 (mtmm) cc_final: 0.8186 (mppt) REVERT: C 571 ASP cc_start: 0.9292 (t0) cc_final: 0.9069 (t0) REVERT: C 957 GLN cc_start: 0.8904 (mt0) cc_final: 0.8689 (tt0) REVERT: C 988 GLU cc_start: 0.9244 (mp0) cc_final: 0.9015 (mp0) REVERT: C 1010 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8888 (mp10) REVERT: D 133 PHE cc_start: 0.7417 (m-80) cc_final: 0.7115 (m-80) REVERT: D 220 PHE cc_start: 0.7227 (t80) cc_final: 0.6951 (t80) REVERT: D 338 PHE cc_start: 0.8746 (m-10) cc_final: 0.8449 (m-80) REVERT: D 353 TRP cc_start: 0.8918 (p-90) cc_final: 0.8461 (p-90) REVERT: D 425 LEU cc_start: 0.9059 (mt) cc_final: 0.8649 (tp) REVERT: D 762 GLN cc_start: 0.9216 (mt0) cc_final: 0.8959 (mm-40) REVERT: D 912 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8849 (p) REVERT: D 1096 VAL cc_start: 0.9391 (OUTLIER) cc_final: 0.9148 (m) outliers start: 44 outliers final: 18 residues processed: 172 average time/residue: 0.7001 time to fit residues: 143.2463 Evaluate side-chains 157 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain D residue 1096 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 289 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 294 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 200 optimal weight: 40.0000 chunk 197 optimal weight: 6.9990 chunk 12 optimal weight: 0.0970 chunk 356 optimal weight: 0.7980 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 535 HIS A 556 ASN B 641 ASN C 914 ASN C 965 GLN D 339 HIS D 703 ASN D 955 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.139468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.087145 restraints weight = 108974.843| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 4.38 r_work: 0.2848 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- 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 = 0.21 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 = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 29533 Z= 0.242 Angle : 0.608 13.553 40240 Z= 0.307 Chirality : 0.046 0.549 4569 Planarity : 0.004 0.075 5146 Dihedral : 5.374 87.828 4471 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.71 % Allowed : 9.91 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.14), residues: 3551 helix: 2.30 (0.16), residues: 1023 sheet: 0.70 (0.19), residues: 703 loop : -0.41 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 466 TYR 0.029 0.001 TYR B 904 PHE 0.025 0.002 PHE C 906 TRP 0.022 0.002 TRP C 436 HIS 0.011 0.001 HIS D 339 Details of bonding type rmsd covalent geometry : bond 0.00555 (29465) covalent geometry : angle 0.58584 (40079) SS BOND : bond 0.00265 ( 37) SS BOND : angle 1.34027 ( 74) hydrogen bonds : bond 0.04338 ( 1244) hydrogen bonds : angle 5.05184 ( 3592) metal coordination : bond 0.00049 ( 2) link_NAG-ASN : bond 0.00604 ( 29) link_NAG-ASN : angle 3.40356 ( 87) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 136 time to evaluate : 1.456 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 249 MET cc_start: 0.5204 (mtt) cc_final: 0.4820 (mmt) REVERT: A 332 MET cc_start: 0.3049 (ptm) cc_final: 0.2165 (pp-130) REVERT: A 360 MET cc_start: 0.4964 (tmt) cc_final: 0.4423 (tmt) REVERT: B 101 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.6736 (pp) REVERT: B 200 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.8493 (t80) REVERT: B 309 GLU cc_start: 0.8683 (mp0) cc_final: 0.8430 (pm20) REVERT: B 392 PHE cc_start: 0.8875 (m-10) cc_final: 0.8537 (m-10) REVERT: B 394 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8104 (p0) REVERT: B 762 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8468 (mm-40) REVERT: B 1002 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8904 (mm-40) REVERT: C 740 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8453 (tpp) REVERT: C 957 GLN cc_start: 0.8908 (mt0) cc_final: 0.8698 (tt0) REVERT: C 988 GLU cc_start: 0.9257 (mp0) cc_final: 0.9018 (mp0) REVERT: C 1010 GLN cc_start: 0.9302 (OUTLIER) cc_final: 0.8943 (mp10) REVERT: D 133 PHE cc_start: 0.7539 (m-80) cc_final: 0.7300 (m-80) REVERT: D 314 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8600 (tm-30) REVERT: D 338 PHE cc_start: 0.8803 (m-10) cc_final: 0.8498 (m-80) REVERT: D 425 LEU cc_start: 0.9057 (mt) cc_final: 0.8694 (tp) REVERT: D 740 MET cc_start: 0.9020 (ttt) cc_final: 0.8741 (ttm) REVERT: D 780 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8898 (mm-30) REVERT: D 904 TYR cc_start: 0.8627 (m-10) cc_final: 0.8383 (m-10) REVERT: D 1019 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8511 (ttt-90) outliers start: 54 outliers final: 21 residues processed: 171 average time/residue: 0.6861 time to fit residues: 139.7140 Evaluate side-chains 156 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 531 THR 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 973 ILE Chi-restraints excluded: chain D residue 1019 ARG Chi-restraints excluded: chain D residue 1096 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 33 optimal weight: 30.0000 chunk 354 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 268 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 134 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** B 505 HIS B 856 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN D 505 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.139681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.088678 restraints weight = 95296.438| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.63 r_work: 0.2895 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29533 Z= 0.186 Angle : 0.567 13.548 40240 Z= 0.286 Chirality : 0.045 0.511 4569 Planarity : 0.004 0.042 5146 Dihedral : 5.241 96.912 4471 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.18 % Rotamer: Outliers : 1.55 % Allowed : 10.23 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.14), residues: 3551 helix: 2.38 (0.16), residues: 1023 sheet: 0.69 (0.19), residues: 694 loop : -0.37 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 214 TYR 0.017 0.001 TYR D1067 PHE 0.019 0.001 PHE D 220 TRP 0.025 0.001 TRP D 353 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00424 (29465) covalent geometry : angle 0.54464 (40079) SS BOND : bond 0.00248 ( 37) SS BOND : angle 1.09247 ( 74) hydrogen bonds : bond 0.04031 ( 1244) hydrogen bonds : angle 4.93905 ( 3592) metal coordination : bond 0.00050 ( 2) link_NAG-ASN : bond 0.00626 ( 29) link_NAG-ASN : angle 3.32105 ( 87) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.3514 (mtt) cc_final: 0.3154 (mmt) REVERT: A 323 MET cc_start: 0.0079 (tpt) cc_final: -0.0884 (tpt) REVERT: A 332 MET cc_start: 0.1630 (ptm) cc_final: 0.0883 (pp-130) REVERT: A 360 MET cc_start: 0.5142 (tmt) cc_final: 0.4644 (tmt) REVERT: A 383 MET cc_start: 0.6162 (mtt) cc_final: 0.5647 (pp-130) REVERT: B 200 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.8510 (t80) REVERT: B 392 PHE cc_start: 0.8788 (m-10) cc_final: 0.8396 (m-10) REVERT: B 762 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8456 (mm-40) REVERT: B 1002 GLN cc_start: 0.9214 (mm-40) cc_final: 0.8871 (mm-40) REVERT: C 957 GLN cc_start: 0.8878 (tt0) cc_final: 0.8660 (tt0) REVERT: C 988 GLU cc_start: 0.9258 (mp0) cc_final: 0.9033 (mp0) REVERT: C 1010 GLN cc_start: 0.9264 (OUTLIER) cc_final: 0.8898 (mp10) REVERT: D 133 PHE cc_start: 0.7521 (m-80) cc_final: 0.7291 (m-80) REVERT: D 314 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8626 (tm-30) REVERT: D 338 PHE cc_start: 0.8960 (m-10) cc_final: 0.8645 (m-80) REVERT: D 393 THR cc_start: 0.7707 (OUTLIER) cc_final: 0.7278 (p) REVERT: D 425 LEU cc_start: 0.9221 (mt) cc_final: 0.8812 (tp) REVERT: D 740 MET cc_start: 0.8977 (ttt) cc_final: 0.8684 (ttm) REVERT: D 780 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8759 (mm-30) REVERT: D 1019 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8448 (ttt-90) REVERT: D 1096 VAL cc_start: 0.9425 (OUTLIER) cc_final: 0.9168 (p) outliers start: 49 outliers final: 23 residues processed: 167 average time/residue: 0.5916 time to fit residues: 117.6098 Evaluate side-chains 155 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 1019 ARG Chi-restraints excluded: chain D residue 1043 CYS Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain D residue 1133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 25 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 349 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 325 optimal weight: 0.6980 chunk 273 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 196 optimal weight: 10.0000 chunk 275 optimal weight: 0.0670 overall best weight: 1.3122 ------------------------------------------------------------------------------- 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 524 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.139420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.088081 restraints weight = 97582.331| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.52 r_work: 0.2932 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29533 Z= 0.174 Angle : 0.561 13.349 40240 Z= 0.283 Chirality : 0.045 0.509 4569 Planarity : 0.004 0.072 5146 Dihedral : 5.152 101.289 4471 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.82 % Favored : 97.15 % Rotamer: Outliers : 1.62 % Allowed : 10.64 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.14), residues: 3551 helix: 2.32 (0.16), residues: 1021 sheet: 0.72 (0.19), residues: 689 loop : -0.37 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1091 TYR 0.030 0.001 TYR B 904 PHE 0.017 0.001 PHE D 759 TRP 0.025 0.001 TRP B 104 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00395 (29465) covalent geometry : angle 0.53872 (40079) SS BOND : bond 0.00318 ( 37) SS BOND : angle 1.27742 ( 74) hydrogen bonds : bond 0.03966 ( 1244) hydrogen bonds : angle 4.90501 ( 3592) metal coordination : bond 0.00401 ( 2) link_NAG-ASN : bond 0.00606 ( 29) link_NAG-ASN : angle 3.24304 ( 87) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 124 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.2907 (mtt) cc_final: 0.2673 (mmt) REVERT: A 323 MET cc_start: 0.0027 (tpt) cc_final: -0.0684 (tpt) REVERT: A 332 MET cc_start: 0.0573 (ptm) cc_final: 0.0083 (pp-130) REVERT: A 360 MET cc_start: 0.5470 (tmt) cc_final: 0.5020 (tmt) REVERT: A 383 MET cc_start: 0.5995 (mtt) cc_final: 0.5359 (pp-130) REVERT: B 177 MET cc_start: 0.7855 (ppp) cc_final: 0.7092 (ppp) REVERT: B 200 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8492 (t80) REVERT: B 392 PHE cc_start: 0.8850 (m-10) cc_final: 0.8455 (m-10) REVERT: B 740 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8866 (ttm) REVERT: B 762 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8414 (mm-40) REVERT: B 780 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8346 (mp0) REVERT: B 1002 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8864 (mm-40) REVERT: C 957 GLN cc_start: 0.8869 (tt0) cc_final: 0.8658 (tt0) REVERT: C 988 GLU cc_start: 0.9262 (mp0) cc_final: 0.9032 (mp0) REVERT: C 1010 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.8821 (mp10) REVERT: D 133 PHE cc_start: 0.7500 (m-80) cc_final: 0.7289 (m-80) REVERT: D 314 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8678 (tm-30) REVERT: D 338 PHE cc_start: 0.8999 (m-10) cc_final: 0.8687 (m-80) REVERT: D 353 TRP cc_start: 0.8707 (p-90) cc_final: 0.8108 (p-90) REVERT: D 425 LEU cc_start: 0.9167 (mt) cc_final: 0.8749 (tp) REVERT: D 740 MET cc_start: 0.9005 (ttt) cc_final: 0.8709 (ttm) REVERT: D 780 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8762 (mm-30) REVERT: D 1019 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8464 (ttm-80) REVERT: D 1096 VAL cc_start: 0.9438 (OUTLIER) cc_final: 0.9185 (p) outliers start: 51 outliers final: 29 residues processed: 159 average time/residue: 0.5287 time to fit residues: 101.2065 Evaluate side-chains 155 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 1019 ARG Chi-restraints excluded: chain D residue 1043 CYS Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 220 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 73 optimal weight: 0.0670 chunk 182 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 50 optimal weight: 20.0000 chunk 87 optimal weight: 0.0980 chunk 340 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 334 optimal weight: 0.2980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.140188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.088242 restraints weight = 118768.220| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 4.78 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29533 Z= 0.115 Angle : 0.532 12.756 40240 Z= 0.268 Chirality : 0.044 0.463 4569 Planarity : 0.004 0.042 5146 Dihedral : 4.821 89.256 4471 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.82 % Favored : 97.15 % Rotamer: Outliers : 1.33 % Allowed : 11.18 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.14), residues: 3551 helix: 2.38 (0.16), residues: 1024 sheet: 0.83 (0.20), residues: 678 loop : -0.30 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 983 TYR 0.019 0.001 TYR A 385 PHE 0.016 0.001 PHE C 565 TRP 0.025 0.001 TRP B 104 HIS 0.008 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00252 (29465) covalent geometry : angle 0.51101 (40079) SS BOND : bond 0.00241 ( 37) SS BOND : angle 1.11834 ( 74) hydrogen bonds : bond 0.03642 ( 1244) hydrogen bonds : angle 4.74681 ( 3592) metal coordination : bond 0.00240 ( 2) link_NAG-ASN : bond 0.00641 ( 29) link_NAG-ASN : angle 3.06910 ( 87) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.2955 (mtt) cc_final: 0.2682 (mmt) REVERT: A 270 MET cc_start: 0.2901 (ptp) cc_final: 0.2678 (ptp) REVERT: A 332 MET cc_start: 0.0701 (ptm) cc_final: 0.0378 (pp-130) REVERT: A 383 MET cc_start: 0.6004 (mtt) cc_final: 0.5286 (pp-130) REVERT: B 177 MET cc_start: 0.7819 (ppp) cc_final: 0.7079 (ppp) REVERT: B 200 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.8454 (t80) REVERT: B 392 PHE cc_start: 0.8782 (m-10) cc_final: 0.8278 (m-10) REVERT: B 762 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8293 (mm-40) REVERT: B 1002 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8720 (mm-40) REVERT: C 957 GLN cc_start: 0.8520 (tt0) cc_final: 0.8319 (tt0) REVERT: C 1010 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8588 (mp10) REVERT: D 133 PHE cc_start: 0.7489 (m-80) cc_final: 0.6754 (t80) REVERT: D 314 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8409 (tm-30) REVERT: D 338 PHE cc_start: 0.8969 (m-10) cc_final: 0.8732 (m-80) REVERT: D 353 TRP cc_start: 0.8898 (p-90) cc_final: 0.8187 (p-90) REVERT: D 425 LEU cc_start: 0.9270 (mt) cc_final: 0.8908 (tp) REVERT: D 740 MET cc_start: 0.8690 (ttt) cc_final: 0.8428 (ttm) REVERT: D 1019 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8056 (ttm-80) REVERT: D 1096 VAL cc_start: 0.9213 (OUTLIER) cc_final: 0.8982 (p) outliers start: 42 outliers final: 27 residues processed: 160 average time/residue: 0.6212 time to fit residues: 118.5373 Evaluate side-chains 151 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 466 ARG Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 1019 ARG Chi-restraints excluded: chain D residue 1043 CYS 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: 358 random chunks: chunk 134 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 312 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 340 optimal weight: 4.9990 chunk 292 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 230 optimal weight: 0.7980 chunk 142 optimal weight: 0.4980 chunk 258 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.139916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.088554 restraints weight = 130672.822| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 4.23 r_work: 0.2893 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29533 Z= 0.132 Angle : 0.548 12.609 40240 Z= 0.273 Chirality : 0.044 0.476 4569 Planarity : 0.004 0.041 5146 Dihedral : 4.827 103.909 4471 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.01 % Rotamer: Outliers : 1.36 % Allowed : 11.53 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.14), residues: 3551 helix: 2.40 (0.16), residues: 1025 sheet: 0.88 (0.20), residues: 674 loop : -0.28 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 983 TYR 0.027 0.001 TYR B 904 PHE 0.019 0.001 PHE D 592 TRP 0.038 0.001 TRP B 104 HIS 0.008 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00297 (29465) covalent geometry : angle 0.52864 (40079) SS BOND : bond 0.00235 ( 37) SS BOND : angle 1.07690 ( 74) hydrogen bonds : bond 0.03670 ( 1244) hydrogen bonds : angle 4.72922 ( 3592) metal coordination : bond 0.00012 ( 2) link_NAG-ASN : bond 0.00615 ( 29) link_NAG-ASN : angle 3.02922 ( 87) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.3678 (mtt) cc_final: 0.3261 (mmt) REVERT: A 270 MET cc_start: 0.3014 (ptp) cc_final: 0.2793 (ptp) REVERT: A 323 MET cc_start: -0.0001 (tpt) cc_final: -0.1072 (tpt) REVERT: A 332 MET cc_start: 0.1877 (ptm) cc_final: 0.1357 (pp-130) REVERT: A 383 MET cc_start: 0.6026 (mtt) cc_final: 0.5568 (pp-130) REVERT: B 177 MET cc_start: 0.7860 (ppp) cc_final: 0.7144 (ppp) REVERT: B 200 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8524 (t80) REVERT: B 762 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8517 (mm-40) REVERT: B 1002 GLN cc_start: 0.9268 (mm-40) cc_final: 0.8884 (mm-40) REVERT: C 762 GLN cc_start: 0.8949 (mm110) cc_final: 0.8660 (mm-40) REVERT: C 957 GLN cc_start: 0.8892 (tt0) cc_final: 0.8684 (tt0) REVERT: C 1010 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.8870 (mp10) REVERT: D 133 PHE cc_start: 0.7392 (m-80) cc_final: 0.6723 (t80) REVERT: D 314 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8702 (tm-30) REVERT: D 338 PHE cc_start: 0.8955 (m-10) cc_final: 0.8690 (m-80) REVERT: D 353 TRP cc_start: 0.8855 (p-90) cc_final: 0.6894 (p-90) REVERT: D 425 LEU cc_start: 0.9216 (mt) cc_final: 0.8838 (tp) REVERT: D 740 MET cc_start: 0.8988 (ttt) cc_final: 0.8694 (ttm) REVERT: D 1019 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8428 (ttt-90) REVERT: D 1096 VAL cc_start: 0.9390 (OUTLIER) cc_final: 0.9117 (p) outliers start: 43 outliers final: 26 residues processed: 155 average time/residue: 0.5923 time to fit residues: 109.6599 Evaluate side-chains 150 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1019 ARG Chi-restraints excluded: chain D residue 1043 CYS Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 86 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 338 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 322 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 286 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 263 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.139433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.088388 restraints weight = 98303.571| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.50 r_work: 0.2903 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29533 Z= 0.168 Angle : 0.566 12.765 40240 Z= 0.283 Chirality : 0.044 0.495 4569 Planarity : 0.004 0.043 5146 Dihedral : 4.604 54.966 4469 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 1.30 % Allowed : 11.72 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.14), residues: 3551 helix: 2.33 (0.16), residues: 1031 sheet: 0.79 (0.19), residues: 704 loop : -0.31 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 983 TYR 0.019 0.001 TYR D 904 PHE 0.057 0.001 PHE B 392 TRP 0.044 0.001 TRP B 104 HIS 0.008 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00382 (29465) covalent geometry : angle 0.54718 (40079) SS BOND : bond 0.00250 ( 37) SS BOND : angle 1.14484 ( 74) hydrogen bonds : bond 0.03825 ( 1244) hydrogen bonds : angle 4.79131 ( 3592) metal coordination : bond 0.00005 ( 2) link_NAG-ASN : bond 0.00597 ( 29) link_NAG-ASN : angle 3.05287 ( 87) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.0267 (tmt) cc_final: -0.0144 (ppp) REVERT: A 249 MET cc_start: 0.3792 (mtt) cc_final: 0.3365 (mmt) REVERT: A 270 MET cc_start: 0.3140 (ptp) cc_final: 0.2897 (ptp) REVERT: A 323 MET cc_start: -0.0017 (tpt) cc_final: -0.1138 (tpt) REVERT: A 332 MET cc_start: 0.1972 (ptm) cc_final: 0.1421 (pp-130) REVERT: A 383 MET cc_start: 0.6001 (mtt) cc_final: 0.5578 (pp-130) REVERT: B 177 MET cc_start: 0.7862 (ppp) cc_final: 0.7168 (ppp) REVERT: B 200 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.8528 (t80) REVERT: B 762 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8493 (mm-40) REVERT: B 904 TYR cc_start: 0.7438 (m-80) cc_final: 0.7075 (m-10) REVERT: B 1002 GLN cc_start: 0.9289 (mm-40) cc_final: 0.8922 (mm-40) REVERT: C 762 GLN cc_start: 0.8896 (mm110) cc_final: 0.8625 (mm-40) REVERT: C 957 GLN cc_start: 0.8870 (tt0) cc_final: 0.8663 (tt0) REVERT: C 1010 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.8825 (mp10) REVERT: D 133 PHE cc_start: 0.7507 (m-80) cc_final: 0.6727 (t80) REVERT: D 314 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8686 (tm-30) REVERT: D 338 PHE cc_start: 0.8945 (m-10) cc_final: 0.8685 (m-80) REVERT: D 394 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8412 (p0) REVERT: D 425 LEU cc_start: 0.9212 (mt) cc_final: 0.8861 (tp) REVERT: D 740 MET cc_start: 0.8971 (ttt) cc_final: 0.8765 (ttm) REVERT: D 1019 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8410 (ttt-90) REVERT: D 1096 VAL cc_start: 0.9431 (OUTLIER) cc_final: 0.9173 (p) outliers start: 41 outliers final: 24 residues processed: 150 average time/residue: 0.5988 time to fit residues: 108.0122 Evaluate side-chains 145 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 1019 ARG Chi-restraints excluded: chain D residue 1043 CYS Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 33 optimal weight: 40.0000 chunk 68 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 chunk 216 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 346 optimal weight: 0.9990 chunk 167 optimal weight: 0.3980 chunk 116 optimal weight: 9.9990 chunk 294 optimal weight: 0.0000 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.139974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.088808 restraints weight = 92755.978| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.42 r_work: 0.2939 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29533 Z= 0.120 Angle : 0.557 13.399 40240 Z= 0.278 Chirality : 0.044 0.467 4569 Planarity : 0.004 0.042 5146 Dihedral : 4.535 54.907 4469 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.04 % Rotamer: Outliers : 1.08 % Allowed : 11.94 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.14), residues: 3551 helix: 2.34 (0.16), residues: 1025 sheet: 0.85 (0.20), residues: 674 loop : -0.27 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 983 TYR 0.018 0.001 TYR A 385 PHE 0.020 0.001 PHE D 515 TRP 0.045 0.001 TRP B 104 HIS 0.008 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00266 (29465) covalent geometry : angle 0.53854 (40079) SS BOND : bond 0.00222 ( 37) SS BOND : angle 1.02438 ( 74) hydrogen bonds : bond 0.03638 ( 1244) hydrogen bonds : angle 4.73262 ( 3592) metal coordination : bond 0.00003 ( 2) link_NAG-ASN : bond 0.00622 ( 29) link_NAG-ASN : angle 2.97324 ( 87) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.0111 (tmt) cc_final: -0.0235 (ppp) REVERT: A 249 MET cc_start: 0.3684 (mtt) cc_final: 0.3285 (mmt) REVERT: A 323 MET cc_start: -0.0456 (tpt) cc_final: -0.1333 (tpt) REVERT: A 332 MET cc_start: 0.1614 (ptm) cc_final: 0.1112 (pp-130) REVERT: A 383 MET cc_start: 0.6016 (mtt) cc_final: 0.5526 (pp-130) REVERT: B 177 MET cc_start: 0.7824 (ppp) cc_final: 0.7139 (ppp) REVERT: B 200 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.8497 (t80) REVERT: B 740 MET cc_start: 0.8884 (ttt) cc_final: 0.8682 (ttm) REVERT: B 762 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8492 (mm-40) REVERT: B 1002 GLN cc_start: 0.9249 (mm-40) cc_final: 0.8882 (mm-40) REVERT: C 762 GLN cc_start: 0.8900 (mm110) cc_final: 0.8623 (mm-40) REVERT: C 957 GLN cc_start: 0.8851 (tt0) cc_final: 0.8642 (tt0) REVERT: C 1010 GLN cc_start: 0.9240 (OUTLIER) cc_final: 0.8832 (mp10) REVERT: D 133 PHE cc_start: 0.7462 (m-80) cc_final: 0.6669 (t80) REVERT: D 314 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8679 (tm-30) REVERT: D 338 PHE cc_start: 0.8934 (m-10) cc_final: 0.8700 (m-80) REVERT: D 425 LEU cc_start: 0.9196 (mt) cc_final: 0.8838 (tp) REVERT: D 740 MET cc_start: 0.8970 (ttt) cc_final: 0.8668 (ttm) REVERT: D 1019 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8370 (ttt-90) REVERT: D 1096 VAL cc_start: 0.9380 (OUTLIER) cc_final: 0.9120 (p) outliers start: 34 outliers final: 22 residues processed: 146 average time/residue: 0.6115 time to fit residues: 108.3731 Evaluate side-chains 144 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 1019 ARG Chi-restraints excluded: chain D residue 1043 CYS Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 295 optimal weight: 5.9990 chunk 266 optimal weight: 5.9990 chunk 292 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 257 optimal weight: 5.9990 chunk 345 optimal weight: 0.8980 chunk 25 optimal weight: 20.0000 chunk 256 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN ** D 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.138603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.085997 restraints weight = 116199.252| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 4.52 r_work: 0.2833 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 29533 Z= 0.238 Angle : 0.608 13.157 40240 Z= 0.305 Chirality : 0.046 0.540 4569 Planarity : 0.004 0.043 5146 Dihedral : 4.742 54.814 4469 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.30 % Favored : 96.67 % Rotamer: Outliers : 1.11 % Allowed : 12.01 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.14), residues: 3551 helix: 2.24 (0.16), residues: 1025 sheet: 0.69 (0.19), residues: 691 loop : -0.36 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 983 TYR 0.024 0.001 TYR D 904 PHE 0.021 0.001 PHE B 392 TRP 0.048 0.002 TRP D 353 HIS 0.015 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00547 (29465) covalent geometry : angle 0.58898 (40079) SS BOND : bond 0.00251 ( 37) SS BOND : angle 1.15757 ( 74) hydrogen bonds : bond 0.04158 ( 1244) hydrogen bonds : angle 4.96666 ( 3592) metal coordination : bond 0.00011 ( 2) link_NAG-ASN : bond 0.00609 ( 29) link_NAG-ASN : angle 3.15463 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14614.07 seconds wall clock time: 248 minutes 42.25 seconds (14922.25 seconds total)