Starting phenix.real_space_refine on Sat Jun 28 08:12:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnk_38505/06_2025/8xnk_38505.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnk_38505/06_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_38505/06_2025/8xnk_38505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnk_38505/06_2025/8xnk_38505.map" model { file = "/net/cci-nas-00/data/ceres_data/8xnk_38505/06_2025/8xnk_38505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnk_38505/06_2025/8xnk_38505.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 20.03, per 1000 atoms: 0.70 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: 7.77 Conformation dependent library (CDL) restraints added in 5.4 seconds 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: 4.86 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: 19.33 Time building geometry restraints manager: 9.31 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 1139 or resid 1301 through 13 \ 06)) selection = (chain 'C' and (resid 26 through 66 or resid 83 through 142 or resid 167 through \ 244 or resid 260 through 1139 or resid 1301 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 11 \ 39 or resid 1301 through 1306)) } 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: 517.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.020 Extract box with map and model: 1.270 Check model and map are aligned: 0.210 Set scattering table: 0.290 Process input model: 87.320 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.240 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: 0.030 Load rotamer database and sin/cos tables:17.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 626.380 ------------------------------------------------------------------------------- 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 : 7.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (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 TRP 0.032 0.002 TRP C 886 HIS 0.012 0.001 HIS A 378 PHE 0.043 0.002 PHE C 906 TYR 0.027 0.002 TYR D 380 ARG 0.006 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.01185 ( 29) link_NAG-ASN : angle 5.31564 ( 87) hydrogen bonds : bond 0.13652 ( 1244) hydrogen bonds : angle 6.70404 ( 3592) metal coordination : bond 0.20676 ( 2) SS BOND : bond 0.00283 ( 37) SS BOND : angle 1.29388 ( 74) covalent geometry : bond 0.00558 (29465) covalent geometry : angle 0.68124 (40079) *********************** 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 : 3.392 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: A 292 ASP cc_start: 0.4986 (t70) cc_final: 0.4703 (p0) REVERT: A 332 MET cc_start: -0.1457 (ptm) cc_final: -0.1698 (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: 0.9076 (mt) REVERT: D 392 PHE cc_start: 0.8938 (m-80) cc_final: 0.8691 (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: 0.7107 (m-10) outliers start: 6 outliers final: 3 residues processed: 367 average time/residue: 1.5872 time to fit residues: 675.7308 Evaluate side-chains 165 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 162 time to evaluate : 3.708 ------------------------------------------------------------------------------- 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 302 optimal weight: 10.0000 chunk 271 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 92 optimal weight: 0.0060 chunk 183 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 280 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 325 optimal weight: 2.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- 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 61 ASN 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 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4310 r_free = 0.4310 target = 0.141803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.090027 restraints weight = 114449.899| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.73 r_work: 0.2908 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29533 Z= 0.174 Angle : 0.636 16.043 40240 Z= 0.320 Chirality : 0.046 0.488 4569 Planarity : 0.004 0.054 5146 Dihedral : 6.190 100.605 4475 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.33 % Allowed : 7.60 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.14), residues: 3551 helix: 2.11 (0.16), residues: 1047 sheet: 0.99 (0.19), residues: 669 loop : -0.52 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 436 HIS 0.008 0.001 HIS A 228 PHE 0.026 0.001 PHE C 906 TYR 0.022 0.001 TYR C 170 ARG 0.010 0.001 ARG D 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00647 ( 29) link_NAG-ASN : angle 3.59352 ( 87) hydrogen bonds : bond 0.04618 ( 1244) hydrogen bonds : angle 5.25598 ( 3592) metal coordination : bond 0.00534 ( 2) SS BOND : bond 0.00204 ( 37) SS BOND : angle 0.83258 ( 74) covalent geometry : bond 0.00389 (29465) covalent geometry : angle 0.61412 (40079) *********************** 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 208 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 3.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8587 (t0) REVERT: A 332 MET cc_start: 0.2481 (ptm) cc_final: 0.1621 (pp-130) REVERT: A 360 MET cc_start: 0.4175 (tmt) cc_final: 0.3652 (tmt) REVERT: B 1002 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8865 (mm-40) REVERT: C 571 ASP cc_start: 0.9287 (t0) cc_final: 0.9018 (t0) REVERT: C 957 GLN cc_start: 0.8916 (mt0) cc_final: 0.8706 (tt0) REVERT: C 990 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8596 (mm-30) REVERT: C 1010 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8884 (mp10) REVERT: D 133 PHE cc_start: 0.7350 (m-80) cc_final: 0.7118 (m-80) REVERT: D 338 PHE cc_start: 0.8541 (m-10) cc_final: 0.8305 (m-10) REVERT: D 390 LEU cc_start: 0.8939 (mt) cc_final: 0.8739 (mp) REVERT: D 425 LEU cc_start: 0.8928 (mt) cc_final: 0.8535 (tp) REVERT: D 740 MET cc_start: 0.9001 (ttt) cc_final: 0.8633 (ttm) REVERT: D 762 GLN cc_start: 0.9230 (mt0) cc_final: 0.8926 (mm-40) outliers start: 42 outliers final: 17 residues processed: 192 average time/residue: 1.3483 time to fit residues: 307.6915 Evaluate side-chains 152 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 3.319 ------------------------------------------------------------------------------- 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 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 990 GLU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1107 ARG 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 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 29 optimal weight: 3.9990 chunk 34 optimal weight: 40.0000 chunk 153 optimal weight: 0.6980 chunk 324 optimal weight: 0.5980 chunk 0 optimal weight: 50.0000 chunk 118 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 179 optimal weight: 0.0980 chunk 236 optimal weight: 0.6980 chunk 19 optimal weight: 40.0000 chunk 267 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 599 ASN C 81 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1083 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.141608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.091377 restraints weight = 116327.209| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.78 r_work: 0.2970 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29533 Z= 0.126 Angle : 0.570 12.898 40240 Z= 0.288 Chirality : 0.045 0.462 4569 Planarity : 0.004 0.049 5146 Dihedral : 5.610 94.909 4473 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.43 % Allowed : 8.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.14), residues: 3551 helix: 2.28 (0.16), residues: 1043 sheet: 0.96 (0.19), residues: 681 loop : -0.40 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 436 HIS 0.007 0.001 HIS A 228 PHE 0.025 0.001 PHE D 220 TYR 0.021 0.001 TYR D 170 ARG 0.010 0.000 ARG D 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00697 ( 29) link_NAG-ASN : angle 3.41747 ( 87) hydrogen bonds : bond 0.04075 ( 1244) hydrogen bonds : angle 4.95089 ( 3592) metal coordination : bond 0.00124 ( 2) SS BOND : bond 0.00226 ( 37) SS BOND : angle 0.99003 ( 74) covalent geometry : bond 0.00273 (29465) covalent geometry : angle 0.54634 (40079) *********************** 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 192 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 147 time to evaluate : 3.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8357 (t0) REVERT: A 332 MET cc_start: 0.1267 (ptm) cc_final: 0.0602 (pp-130) REVERT: A 360 MET cc_start: 0.4554 (tmt) cc_final: 0.4102 (tmt) REVERT: B 177 MET cc_start: 0.7823 (ppp) cc_final: 0.7504 (ppp) REVERT: B 515 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.8058 (p90) REVERT: B 1002 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8854 (mm-40) REVERT: B 1010 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8966 (mp10) REVERT: C 571 ASP cc_start: 0.9296 (t0) cc_final: 0.9042 (t0) REVERT: C 957 GLN cc_start: 0.8890 (mt0) cc_final: 0.8669 (tt0) REVERT: C 990 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8651 (mm-30) REVERT: C 1010 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8860 (mp10) REVERT: D 133 PHE cc_start: 0.7361 (m-80) cc_final: 0.7104 (m-80) REVERT: D 338 PHE cc_start: 0.8711 (m-10) cc_final: 0.8425 (m-80) REVERT: D 353 TRP cc_start: 0.8869 (p-90) cc_final: 0.8206 (p-90) REVERT: D 389 ASP cc_start: 0.9194 (t0) cc_final: 0.8783 (p0) REVERT: D 390 LEU cc_start: 0.8853 (mt) cc_final: 0.8463 (mt) REVERT: D 425 LEU cc_start: 0.8999 (mt) cc_final: 0.8593 (tp) REVERT: D 762 GLN cc_start: 0.9188 (mt0) cc_final: 0.8932 (mm-40) REVERT: D 912 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8805 (p) REVERT: D 1096 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.9079 (m) outliers start: 45 outliers final: 14 residues processed: 175 average time/residue: 1.3502 time to fit residues: 283.2603 Evaluate side-chains 153 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 3.304 ------------------------------------------------------------------------------- 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 200 TYR Chi-restraints excluded: chain B residue 515 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 25 THR Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 531 THR 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 327 optimal weight: 0.0570 chunk 55 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 330 optimal weight: 0.8980 chunk 262 optimal weight: 6.9990 chunk 293 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 274 optimal weight: 0.0010 chunk 15 optimal weight: 20.0000 chunk 170 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.3908 ------------------------------------------------------------------------------- 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 ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN D 339 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.134524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.083778 restraints weight = 113697.229| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.79 r_work: 0.2925 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 29533 Z= 0.182 Angle : 0.578 12.962 40240 Z= 0.292 Chirality : 0.045 0.509 4569 Planarity : 0.004 0.090 5146 Dihedral : 5.392 96.317 4473 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.68 % Allowed : 9.76 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.14), residues: 3551 helix: 2.32 (0.16), residues: 1027 sheet: 0.90 (0.19), residues: 696 loop : -0.36 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 436 HIS 0.008 0.001 HIS D 339 PHE 0.025 0.001 PHE D 220 TYR 0.018 0.001 TYR A 385 ARG 0.005 0.000 ARG D 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00604 ( 29) link_NAG-ASN : angle 3.35791 ( 87) hydrogen bonds : bond 0.04146 ( 1244) hydrogen bonds : angle 4.93792 ( 3592) metal coordination : bond 0.00022 ( 2) SS BOND : bond 0.00172 ( 37) SS BOND : angle 1.56781 ( 74) covalent geometry : bond 0.00413 (29465) covalent geometry : angle 0.55395 (40079) *********************** 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 186 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 133 time to evaluate : 3.349 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: A 111 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8409 (t0) REVERT: A 270 MET cc_start: 0.2279 (ptm) cc_final: 0.2016 (ptp) REVERT: A 332 MET cc_start: 0.1561 (ptm) cc_final: 0.0830 (pp-130) REVERT: A 360 MET cc_start: 0.4906 (tmt) cc_final: 0.4378 (tmt) REVERT: B 101 ILE cc_start: 0.7351 (OUTLIER) cc_final: 0.6579 (pp) REVERT: B 200 TYR cc_start: 0.8941 (OUTLIER) cc_final: 0.8409 (t80) REVERT: B 392 PHE cc_start: 0.8904 (m-10) cc_final: 0.8500 (m-10) REVERT: B 394 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8255 (p0) REVERT: B 1002 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8885 (mm-40) REVERT: C 740 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8645 (tpp) REVERT: C 990 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8667 (mm-30) REVERT: C 1010 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8881 (mp10) REVERT: D 133 PHE cc_start: 0.7404 (m-80) cc_final: 0.7173 (m-80) REVERT: D 338 PHE cc_start: 0.8786 (m-10) cc_final: 0.8469 (m-80) REVERT: D 353 TRP cc_start: 0.8574 (p-90) cc_final: 0.7807 (p-90) REVERT: D 389 ASP cc_start: 0.9253 (t0) cc_final: 0.8840 (p0) REVERT: D 390 LEU cc_start: 0.8867 (mt) cc_final: 0.8490 (mt) REVERT: D 425 LEU cc_start: 0.9133 (mt) cc_final: 0.8731 (tp) REVERT: D 740 MET cc_start: 0.8991 (ttt) cc_final: 0.8717 (ttm) REVERT: D 762 GLN cc_start: 0.9225 (mt0) cc_final: 0.8975 (mm-40) REVERT: D 912 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8921 (p) REVERT: D 1096 VAL cc_start: 0.9410 (OUTLIER) cc_final: 0.9169 (m) outliers start: 53 outliers final: 21 residues processed: 166 average time/residue: 1.3441 time to fit residues: 266.5679 Evaluate side-chains 159 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 3.338 ------------------------------------------------------------------------------- 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 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 780 GLU 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 740 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1096 VAL 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 582 LEU Chi-restraints excluded: chain D residue 858 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 314 optimal weight: 5.9990 chunk 355 optimal weight: 0.8980 chunk 277 optimal weight: 4.9990 chunk 301 optimal weight: 6.9990 chunk 318 optimal weight: 0.5980 chunk 271 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 254 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 965 GLN D 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.140831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.090578 restraints weight = 99554.937| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.46 r_work: 0.2944 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29533 Z= 0.131 Angle : 0.538 12.909 40240 Z= 0.272 Chirality : 0.044 0.473 4569 Planarity : 0.004 0.042 5146 Dihedral : 5.092 92.523 4473 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.49 % Allowed : 10.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.14), residues: 3551 helix: 2.35 (0.16), residues: 1033 sheet: 0.95 (0.19), residues: 690 loop : -0.31 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 436 HIS 0.006 0.001 HIS A 228 PHE 0.020 0.001 PHE D 220 TYR 0.017 0.001 TYR D1067 ARG 0.005 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00627 ( 29) link_NAG-ASN : angle 3.17186 ( 87) hydrogen bonds : bond 0.03791 ( 1244) hydrogen bonds : angle 4.80510 ( 3592) metal coordination : bond 0.00025 ( 2) SS BOND : bond 0.00218 ( 37) SS BOND : angle 1.25299 ( 74) covalent geometry : bond 0.00289 (29465) covalent geometry : angle 0.51568 (40079) *********************** 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 177 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8362 (t0) REVERT: A 249 MET cc_start: 0.3702 (mtt) cc_final: 0.3263 (mmt) REVERT: A 270 MET cc_start: 0.2297 (ptm) cc_final: 0.1927 (ptp) REVERT: A 323 MET cc_start: 0.0110 (tpt) cc_final: -0.0362 (tpt) REVERT: A 332 MET cc_start: 0.1281 (ptm) cc_final: 0.0576 (pp-130) REVERT: A 360 MET cc_start: 0.5269 (tmt) cc_final: 0.4754 (tmt) REVERT: A 383 MET cc_start: 0.6710 (mtt) cc_final: 0.6268 (pp-130) REVERT: B 104 TRP cc_start: 0.7729 (OUTLIER) cc_final: 0.7492 (m100) REVERT: B 200 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8389 (t80) REVERT: B 392 PHE cc_start: 0.8725 (m-10) cc_final: 0.8330 (m-10) REVERT: B 1002 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8897 (mm-40) REVERT: C 1010 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8866 (mp10) REVERT: C 1092 GLU cc_start: 0.8716 (tp30) cc_final: 0.8494 (tp30) REVERT: D 133 PHE cc_start: 0.7435 (m-80) cc_final: 0.7200 (m-80) REVERT: D 338 PHE cc_start: 0.8856 (m-10) cc_final: 0.8582 (m-80) REVERT: D 353 TRP cc_start: 0.8102 (p-90) cc_final: 0.7900 (p-90) REVERT: D 389 ASP cc_start: 0.9214 (t0) cc_final: 0.8824 (p0) REVERT: D 390 LEU cc_start: 0.8854 (mt) cc_final: 0.8494 (mt) REVERT: D 425 LEU cc_start: 0.9121 (mt) cc_final: 0.8727 (tp) REVERT: D 740 MET cc_start: 0.8960 (ttt) cc_final: 0.8682 (ttm) REVERT: D 762 GLN cc_start: 0.9198 (mt0) cc_final: 0.8934 (mm-40) REVERT: D 904 TYR cc_start: 0.8620 (m-10) cc_final: 0.8408 (m-10) REVERT: D 912 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8856 (p) REVERT: D 1096 VAL cc_start: 0.9352 (OUTLIER) cc_final: 0.9068 (p) outliers start: 47 outliers final: 19 residues processed: 161 average time/residue: 1.3229 time to fit residues: 256.4847 Evaluate side-chains 152 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 3.200 ------------------------------------------------------------------------------- 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 104 TRP 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 582 LEU 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 114 THR Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 697 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 524 VAL Chi-restraints excluded: chain D residue 531 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 21 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 256 optimal weight: 0.9980 chunk 336 optimal weight: 1.9990 chunk 246 optimal weight: 0.7980 chunk 309 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 49 optimal weight: 40.0000 chunk 290 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ** C 544 ASN ** 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 = 0.4294 r_free = 0.4294 target = 0.140438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.089942 restraints weight = 110288.728| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.59 r_work: 0.2926 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29533 Z= 0.143 Angle : 0.540 12.650 40240 Z= 0.272 Chirality : 0.044 0.484 4569 Planarity : 0.004 0.043 5146 Dihedral : 4.930 93.257 4473 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.18 % Rotamer: Outliers : 1.33 % Allowed : 10.64 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.14), residues: 3551 helix: 2.37 (0.16), residues: 1018 sheet: 0.95 (0.19), residues: 690 loop : -0.31 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 436 HIS 0.007 0.001 HIS A 374 PHE 0.019 0.001 PHE D 759 TYR 0.019 0.001 TYR B 904 ARG 0.009 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 29) link_NAG-ASN : angle 3.09640 ( 87) hydrogen bonds : bond 0.03780 ( 1244) hydrogen bonds : angle 4.78647 ( 3592) metal coordination : bond 0.00783 ( 2) SS BOND : bond 0.00286 ( 37) SS BOND : angle 1.25511 ( 74) covalent geometry : bond 0.00319 (29465) covalent geometry : angle 0.51910 (40079) *********************** 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 173 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 3.350 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 111 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8327 (t0) REVERT: A 249 MET cc_start: 0.3725 (mtt) cc_final: 0.3290 (mmt) REVERT: A 270 MET cc_start: 0.2243 (ptm) cc_final: 0.1519 (ptp) REVERT: A 323 MET cc_start: 0.0214 (tpt) cc_final: -0.0352 (tpt) REVERT: A 332 MET cc_start: 0.1429 (ptm) cc_final: 0.0745 (pp-130) REVERT: A 360 MET cc_start: 0.5544 (tmt) cc_final: 0.5060 (tmt) REVERT: A 383 MET cc_start: 0.6491 (mtt) cc_final: 0.6033 (pp-130) REVERT: B 177 MET cc_start: 0.7746 (ppp) cc_final: 0.7061 (ppp) REVERT: B 200 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8417 (t80) REVERT: B 392 PHE cc_start: 0.8740 (m-10) cc_final: 0.8357 (m-10) REVERT: B 1002 GLN cc_start: 0.9242 (mm-40) cc_final: 0.8898 (mm-40) REVERT: C 1010 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.8903 (mp10) REVERT: D 338 PHE cc_start: 0.8873 (m-10) cc_final: 0.8591 (m-80) REVERT: D 353 TRP cc_start: 0.8129 (p-90) cc_final: 0.7926 (p-90) REVERT: D 389 ASP cc_start: 0.9240 (t0) cc_final: 0.8829 (p0) REVERT: D 390 LEU cc_start: 0.8833 (mt) cc_final: 0.8454 (mt) REVERT: D 425 LEU cc_start: 0.9177 (mt) cc_final: 0.8771 (tp) REVERT: D 740 MET cc_start: 0.8948 (ttt) cc_final: 0.8677 (ttm) REVERT: D 762 GLN cc_start: 0.9209 (mt0) cc_final: 0.8955 (mm-40) REVERT: D 912 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8883 (p) REVERT: D 1096 VAL cc_start: 0.9385 (OUTLIER) cc_final: 0.9109 (p) outliers start: 42 outliers final: 23 residues processed: 156 average time/residue: 1.2828 time to fit residues: 242.2838 Evaluate side-chains 153 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 3.401 ------------------------------------------------------------------------------- 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 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 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 160 TYR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 47 VAL 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 518 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 1043 CYS Chi-restraints excluded: chain D residue 1096 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 349 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 318 optimal weight: 0.5980 chunk 323 optimal weight: 0.7980 chunk 195 optimal weight: 0.9990 chunk 329 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** A 524 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS D 703 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.140316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.088489 restraints weight = 137458.724| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.46 r_work: 0.2888 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29533 Z= 0.146 Angle : 0.543 12.677 40240 Z= 0.273 Chirality : 0.044 0.484 4569 Planarity : 0.004 0.055 5146 Dihedral : 4.880 100.636 4473 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Rotamer: Outliers : 1.36 % Allowed : 11.05 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.14), residues: 3551 helix: 2.40 (0.16), residues: 1024 sheet: 0.95 (0.19), residues: 689 loop : -0.31 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 436 HIS 0.007 0.001 HIS A 378 PHE 0.024 0.001 PHE D 220 TYR 0.018 0.001 TYR A 385 ARG 0.009 0.000 ARG B 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 29) link_NAG-ASN : angle 3.06899 ( 87) hydrogen bonds : bond 0.03765 ( 1244) hydrogen bonds : angle 4.77350 ( 3592) metal coordination : bond 0.00064 ( 2) SS BOND : bond 0.00242 ( 37) SS BOND : angle 1.14669 ( 74) covalent geometry : bond 0.00329 (29465) covalent geometry : angle 0.52273 (40079) *********************** 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 168 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 3.279 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 111 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8306 (t0) REVERT: A 249 MET cc_start: 0.3696 (mtt) cc_final: 0.3281 (mmt) REVERT: A 323 MET cc_start: 0.0104 (tpt) cc_final: -0.0288 (tpt) REVERT: A 332 MET cc_start: 0.1666 (ptm) cc_final: 0.1041 (pp-130) REVERT: A 360 MET cc_start: 0.5545 (tmt) cc_final: 0.5095 (tmt) REVERT: A 383 MET cc_start: 0.6465 (mtt) cc_final: 0.6013 (pp-130) REVERT: B 104 TRP cc_start: 0.7541 (OUTLIER) cc_final: 0.7318 (m100) REVERT: B 177 MET cc_start: 0.7893 (ppp) cc_final: 0.7194 (ppp) REVERT: B 200 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.8474 (t80) REVERT: B 1002 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8949 (mm-40) REVERT: C 762 GLN cc_start: 0.9082 (mm110) cc_final: 0.8770 (mm-40) REVERT: C 1010 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.8921 (mp10) REVERT: D 133 PHE cc_start: 0.6382 (m-80) cc_final: 0.6118 (t80) REVERT: D 338 PHE cc_start: 0.8861 (m-10) cc_final: 0.8604 (m-80) REVERT: D 353 TRP cc_start: 0.8114 (p-90) cc_final: 0.7882 (p-90) REVERT: D 389 ASP cc_start: 0.9263 (t0) cc_final: 0.8840 (p0) REVERT: D 390 LEU cc_start: 0.8798 (mt) cc_final: 0.8407 (mt) REVERT: D 425 LEU cc_start: 0.9238 (mt) cc_final: 0.8825 (tp) REVERT: D 740 MET cc_start: 0.8988 (ttt) cc_final: 0.8706 (ttm) REVERT: D 762 GLN cc_start: 0.9218 (mt0) cc_final: 0.8948 (mm-40) REVERT: D 912 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8899 (p) REVERT: D 1096 VAL cc_start: 0.9410 (OUTLIER) cc_final: 0.9133 (p) outliers start: 43 outliers final: 30 residues processed: 155 average time/residue: 1.5408 time to fit residues: 286.9383 Evaluate side-chains 157 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 3.205 ------------------------------------------------------------------------------- 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 104 TRP 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 394 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 884 SER 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 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 C residue 1096 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 160 TYR 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 518 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 858 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 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 328 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 129 optimal weight: 2.9990 chunk 229 optimal weight: 0.9990 chunk 216 optimal weight: 0.1980 chunk 261 optimal weight: 5.9990 chunk 43 optimal weight: 30.0000 chunk 147 optimal weight: 0.8980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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** ** C 544 ASN ** 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 = 0.4295 r_free = 0.4295 target = 0.140757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.090124 restraints weight = 108389.878| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 4.02 r_work: 0.2934 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3189 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= 0.115 Angle : 0.527 12.317 40240 Z= 0.265 Chirality : 0.044 0.462 4569 Planarity : 0.004 0.042 5146 Dihedral : 4.733 97.860 4473 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.76 % Favored : 97.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.14), residues: 3551 helix: 2.44 (0.16), residues: 1026 sheet: 0.96 (0.19), residues: 689 loop : -0.27 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 436 HIS 0.007 0.001 HIS A 378 PHE 0.035 0.001 PHE B 392 TYR 0.018 0.001 TYR A 385 ARG 0.007 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 29) link_NAG-ASN : angle 2.97442 ( 87) hydrogen bonds : bond 0.03596 ( 1244) hydrogen bonds : angle 4.70102 ( 3592) metal coordination : bond 0.00058 ( 2) SS BOND : bond 0.00245 ( 37) SS BOND : angle 1.11819 ( 74) covalent geometry : bond 0.00252 (29465) covalent geometry : angle 0.50704 (40079) *********************** 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 168 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 3.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.8584 (p0) cc_final: 0.8293 (t0) REVERT: A 152 MET cc_start: -0.0923 (OUTLIER) cc_final: -0.1399 (ppp) REVERT: A 249 MET cc_start: 0.3927 (mtt) cc_final: 0.3426 (mmt) REVERT: A 332 MET cc_start: 0.1776 (ptm) cc_final: 0.1250 (pp-130) REVERT: A 360 MET cc_start: 0.5677 (tmt) cc_final: 0.5310 (tmt) REVERT: B 177 MET cc_start: 0.7879 (ppp) cc_final: 0.7164 (ppp) REVERT: B 200 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.8481 (t80) REVERT: B 394 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8455 (p0) REVERT: B 740 MET cc_start: 0.8925 (ttt) cc_final: 0.8719 (ttm) REVERT: B 1002 GLN cc_start: 0.9268 (mm-40) cc_final: 0.8917 (mm-40) REVERT: C 957 GLN cc_start: 0.8821 (tt0) cc_final: 0.8251 (tm-30) REVERT: C 1010 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.8844 (mp10) REVERT: D 133 PHE cc_start: 0.6319 (m-80) cc_final: 0.6054 (t80) REVERT: D 338 PHE cc_start: 0.8831 (m-10) cc_final: 0.8613 (m-80) REVERT: D 353 TRP cc_start: 0.8171 (p-90) cc_final: 0.7954 (p-90) REVERT: D 389 ASP cc_start: 0.9259 (t0) cc_final: 0.8851 (p0) REVERT: D 390 LEU cc_start: 0.8772 (mt) cc_final: 0.8373 (mt) REVERT: D 425 LEU cc_start: 0.9215 (mt) cc_final: 0.8812 (tp) REVERT: D 740 MET cc_start: 0.8933 (ttt) cc_final: 0.8648 (ttm) REVERT: D 912 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8958 (p) REVERT: D 1096 VAL cc_start: 0.9372 (OUTLIER) cc_final: 0.9111 (p) outliers start: 43 outliers final: 23 residues processed: 154 average time/residue: 1.2632 time to fit residues: 237.0097 Evaluate side-chains 147 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET 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 576 VAL 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 160 TYR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 160 TYR 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 518 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 973 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 112 optimal weight: 0.9980 chunk 179 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 chunk 312 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 93 optimal weight: 0.0970 chunk 13 optimal weight: 30.0000 chunk 97 optimal weight: 9.9990 chunk 7 optimal weight: 40.0000 chunk 49 optimal weight: 2.9990 chunk 327 optimal weight: 0.4980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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** C 544 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.140636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.089423 restraints weight = 137326.637| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 4.20 r_work: 0.2916 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29533 Z= 0.116 Angle : 0.533 12.200 40240 Z= 0.267 Chirality : 0.043 0.460 4569 Planarity : 0.004 0.042 5146 Dihedral : 4.632 99.925 4471 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.24 % Rotamer: Outliers : 1.11 % Allowed : 11.94 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.14), residues: 3551 helix: 2.44 (0.16), residues: 1027 sheet: 0.96 (0.20), residues: 687 loop : -0.26 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 436 HIS 0.008 0.001 HIS A 378 PHE 0.023 0.001 PHE B 392 TYR 0.017 0.001 TYR D1067 ARG 0.006 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00624 ( 29) link_NAG-ASN : angle 2.91552 ( 87) hydrogen bonds : bond 0.03546 ( 1244) hydrogen bonds : angle 4.67288 ( 3592) metal coordination : bond 0.00010 ( 2) SS BOND : bond 0.00220 ( 37) SS BOND : angle 0.99942 ( 74) covalent geometry : bond 0.00256 (29465) covalent geometry : angle 0.51482 (40079) *********************** 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 158 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 3.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.8614 (p0) cc_final: 0.8330 (t0) REVERT: A 249 MET cc_start: 0.3885 (mtt) cc_final: 0.3404 (mmt) REVERT: A 323 MET cc_start: 0.0144 (tpt) cc_final: -0.0667 (tpt) REVERT: A 332 MET cc_start: 0.1802 (ptm) cc_final: 0.1334 (pp-130) REVERT: A 360 MET cc_start: 0.5650 (tmt) cc_final: 0.5290 (tmt) REVERT: A 383 MET cc_start: 0.5648 (mtt) cc_final: 0.5210 (pp-130) REVERT: B 177 MET cc_start: 0.7891 (ppp) cc_final: 0.7170 (ppp) REVERT: B 200 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8473 (t80) REVERT: B 571 ASP cc_start: 0.9129 (m-30) cc_final: 0.8766 (t0) REVERT: B 740 MET cc_start: 0.8907 (ttt) cc_final: 0.8657 (ttm) REVERT: B 1002 GLN cc_start: 0.9281 (mm-40) cc_final: 0.8923 (mm-40) REVERT: C 762 GLN cc_start: 0.8953 (mm-40) cc_final: 0.8669 (mm-40) REVERT: C 957 GLN cc_start: 0.8832 (tt0) cc_final: 0.8276 (tm-30) REVERT: C 1010 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.8852 (mp10) REVERT: D 133 PHE cc_start: 0.6325 (m-80) cc_final: 0.6100 (t80) REVERT: D 338 PHE cc_start: 0.8795 (m-10) cc_final: 0.8571 (m-80) REVERT: D 353 TRP cc_start: 0.8136 (p-90) cc_final: 0.7837 (p-90) REVERT: D 386 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8154 (mtmt) REVERT: D 389 ASP cc_start: 0.9239 (t0) cc_final: 0.8862 (p0) REVERT: D 390 LEU cc_start: 0.8766 (mt) cc_final: 0.8325 (mt) REVERT: D 425 LEU cc_start: 0.9217 (mt) cc_final: 0.8828 (tp) REVERT: D 740 MET cc_start: 0.8965 (ttt) cc_final: 0.8684 (ttm) REVERT: D 912 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8935 (p) REVERT: D 1096 VAL cc_start: 0.9377 (OUTLIER) cc_final: 0.9109 (p) outliers start: 35 outliers final: 23 residues processed: 147 average time/residue: 1.2696 time to fit residues: 225.5790 Evaluate side-chains 146 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 3.475 ------------------------------------------------------------------------------- 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 244 LEU Chi-restraints excluded: chain B residue 576 VAL 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 160 TYR Chi-restraints excluded: chain C residue 697 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 160 TYR Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 386 LYS 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 858 LEU Chi-restraints excluded: chain D residue 895 GLN Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 1043 CYS Chi-restraints excluded: chain D residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 278 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 6 optimal weight: 0.0060 chunk 249 optimal weight: 2.9990 chunk 229 optimal weight: 0.0770 chunk 99 optimal weight: 6.9990 chunk 144 optimal weight: 0.6980 chunk 38 optimal weight: 30.0000 chunk 191 optimal weight: 30.0000 chunk 299 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 overall best weight: 0.9356 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.140110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.088342 restraints weight = 115542.242| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 4.51 r_work: 0.2889 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29533 Z= 0.137 Angle : 0.541 13.353 40240 Z= 0.270 Chirality : 0.044 0.473 4569 Planarity : 0.004 0.042 5146 Dihedral : 4.563 88.451 4471 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.01 % Rotamer: Outliers : 0.98 % Allowed : 12.10 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.14), residues: 3551 helix: 2.41 (0.16), residues: 1024 sheet: 0.97 (0.19), residues: 684 loop : -0.27 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 104 HIS 0.017 0.001 HIS A 228 PHE 0.018 0.001 PHE D 220 TYR 0.019 0.001 TYR C 170 ARG 0.007 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 29) link_NAG-ASN : angle 2.90331 ( 87) hydrogen bonds : bond 0.03627 ( 1244) hydrogen bonds : angle 4.70422 ( 3592) metal coordination : bond 0.00037 ( 2) SS BOND : bond 0.00225 ( 37) SS BOND : angle 0.97722 ( 74) covalent geometry : bond 0.00307 (29465) covalent geometry : angle 0.52322 (40079) ********************** 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 152 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.8688 (p0) cc_final: 0.8448 (t0) REVERT: A 249 MET cc_start: 0.5084 (mtt) cc_final: 0.4612 (mmt) REVERT: A 323 MET cc_start: 0.1879 (tpt) cc_final: 0.0428 (tpt) REVERT: A 332 MET cc_start: 0.3132 (ptm) cc_final: 0.2429 (pp-130) REVERT: A 360 MET cc_start: 0.6000 (tmt) cc_final: 0.5577 (tmt) REVERT: B 177 MET cc_start: 0.7839 (ppp) cc_final: 0.7111 (ppp) REVERT: B 200 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.8469 (t80) REVERT: B 571 ASP cc_start: 0.9117 (m-30) cc_final: 0.8773 (t0) REVERT: B 1002 GLN cc_start: 0.9310 (mm-40) cc_final: 0.8946 (mm-40) REVERT: C 532 ASN cc_start: 0.9320 (m-40) cc_final: 0.8784 (t0) REVERT: C 762 GLN cc_start: 0.8925 (mm110) cc_final: 0.8670 (mm-40) REVERT: C 957 GLN cc_start: 0.8799 (tt0) cc_final: 0.8241 (tm-30) REVERT: C 1010 GLN cc_start: 0.9294 (OUTLIER) cc_final: 0.8877 (mp10) REVERT: D 133 PHE cc_start: 0.6478 (m-80) cc_final: 0.6181 (t80) REVERT: D 338 PHE cc_start: 0.8792 (m-10) cc_final: 0.8582 (m-80) REVERT: D 386 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8032 (mtpt) REVERT: D 389 ASP cc_start: 0.9282 (t0) cc_final: 0.8871 (p0) REVERT: D 390 LEU cc_start: 0.8633 (mt) cc_final: 0.8168 (mt) REVERT: D 421 TYR cc_start: 0.7841 (m-10) cc_final: 0.7557 (m-10) REVERT: D 425 LEU cc_start: 0.9063 (mt) cc_final: 0.8719 (tp) REVERT: D 740 MET cc_start: 0.8929 (ttt) cc_final: 0.8664 (ttm) REVERT: D 912 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8949 (p) REVERT: D 1096 VAL cc_start: 0.9403 (OUTLIER) cc_final: 0.9131 (p) outliers start: 31 outliers final: 20 residues processed: 143 average time/residue: 1.2596 time to fit residues: 218.9813 Evaluate side-chains 144 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 4.049 ------------------------------------------------------------------------------- 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 576 VAL 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 160 TYR Chi-restraints excluded: chain C residue 697 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 342 PHE Chi-restraints excluded: chain D residue 386 LYS 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 858 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 1043 CYS Chi-restraints excluded: chain D residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 354 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 chunk 13 optimal weight: 40.0000 chunk 80 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 41 optimal weight: 30.0000 chunk 236 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 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 = 0.139902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.088635 restraints weight = 103793.134| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.56 r_work: 0.2941 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29533 Z= 0.151 Angle : 0.554 14.469 40240 Z= 0.277 Chirality : 0.044 0.477 4569 Planarity : 0.004 0.043 5146 Dihedral : 4.359 54.947 4469 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 0.92 % Allowed : 12.13 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.14), residues: 3551 helix: 2.32 (0.16), residues: 1024 sheet: 0.94 (0.19), residues: 684 loop : -0.26 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 104 HIS 0.015 0.001 HIS A 228 PHE 0.017 0.001 PHE D 220 TYR 0.018 0.001 TYR A 385 ARG 0.007 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 29) link_NAG-ASN : angle 2.90479 ( 87) hydrogen bonds : bond 0.03681 ( 1244) hydrogen bonds : angle 4.74714 ( 3592) metal coordination : bond 0.00092 ( 2) SS BOND : bond 0.00234 ( 37) SS BOND : angle 1.01626 ( 74) covalent geometry : bond 0.00342 (29465) covalent geometry : angle 0.53681 (40079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30317.78 seconds wall clock time: 521 minutes 42.32 seconds (31302.32 seconds total)