Starting phenix.real_space_refine on Fri May 30 00:08:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnk_38505/05_2025/8xnk_38505.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnk_38505/05_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_38505/05_2025/8xnk_38505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnk_38505/05_2025/8xnk_38505.map" model { file = "/net/cci-nas-00/data/ceres_data/8xnk_38505/05_2025/8xnk_38505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnk_38505/05_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 19.75, per 1000 atoms: 0.69 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: 7.67 Conformation dependent library (CDL) restraints added in 3.9 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: 4.31 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: 12.59 Time building geometry restraints manager: 8.88 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: 16.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 1.200 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 77.270 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.410 ------------------------------------------------------------------------------- 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 : 3.105 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: 1.5582 time to fit residues: 661.7021 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 : 3.174 ------------------------------------------------------------------------------- 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 = 0.090030 restraints weight = 114449.900| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.72 r_work: 0.2909 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 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 : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8590 (t0) REVERT: A 332 MET cc_start: 0.2611 (ptm) cc_final: 0.1744 (pp-130) REVERT: A 360 MET cc_start: 0.4217 (tmt) cc_final: 0.3704 (tmt) REVERT: B 1002 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8878 (mm-40) REVERT: C 571 ASP cc_start: 0.9285 (t0) cc_final: 0.9008 (t0) REVERT: C 957 GLN cc_start: 0.8898 (mt0) cc_final: 0.8686 (tt0) REVERT: C 990 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8598 (mm-30) REVERT: C 1010 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8892 (mp10) REVERT: D 133 PHE cc_start: 0.7368 (m-80) cc_final: 0.7122 (m-80) REVERT: D 338 PHE cc_start: 0.8566 (m-10) cc_final: 0.8323 (m-10) REVERT: D 390 LEU cc_start: 0.8933 (mt) cc_final: 0.8731 (mp) REVERT: D 425 LEU cc_start: 0.8902 (mt) cc_final: 0.8522 (tp) REVERT: D 740 MET cc_start: 0.9000 (ttt) cc_final: 0.8633 (ttm) REVERT: D 762 GLN cc_start: 0.9212 (mt0) cc_final: 0.8905 (mm-40) outliers start: 42 outliers final: 17 residues processed: 192 average time/residue: 1.3356 time to fit residues: 304.0149 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 : 3.416 ------------------------------------------------------------------------------- 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: 0.7980 chunk 19 optimal weight: 40.0000 chunk 267 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4307 r_free = 0.4307 target = 0.141507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.091313 restraints weight = 116214.038| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.71 r_work: 0.2975 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29533 Z= 0.126 Angle : 0.569 12.899 40240 Z= 0.287 Chirality : 0.045 0.463 4569 Planarity : 0.004 0.048 5146 Dihedral : 5.583 92.980 4473 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.39 % Allowed : 8.74 % Favored : 89.86 % 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: 1.01 (0.14), residues: 3551 helix: 2.29 (0.16), residues: 1043 sheet: 0.95 (0.19), residues: 676 loop : -0.39 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 436 HIS 0.007 0.001 HIS A 378 PHE 0.027 0.001 PHE D 220 TYR 0.028 0.001 TYR B 453 ARG 0.010 0.000 ARG D 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00690 ( 29) link_NAG-ASN : angle 3.41637 ( 87) hydrogen bonds : bond 0.04057 ( 1244) hydrogen bonds : angle 4.94056 ( 3592) metal coordination : bond 0.00137 ( 2) SS BOND : bond 0.00190 ( 37) SS BOND : angle 0.92602 ( 74) covalent geometry : bond 0.00271 (29465) covalent geometry : angle 0.54561 (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: 44 poor density : 148 time to evaluate : 3.368 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: 0.8700 (OUTLIER) cc_final: 0.8430 (t70) REVERT: A 332 MET cc_start: 0.1269 (ptm) cc_final: 0.0584 (pp-130) REVERT: A 360 MET cc_start: 0.4548 (tmt) cc_final: 0.4086 (tmt) REVERT: A 408 MET cc_start: 0.3933 (mtt) cc_final: 0.3708 (pp-130) REVERT: B 177 MET cc_start: 0.7816 (ppp) cc_final: 0.7498 (ppp) REVERT: B 988 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8863 (mp0) REVERT: B 1002 GLN cc_start: 0.9133 (mm-40) cc_final: 0.8860 (mm-40) REVERT: B 1010 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8959 (mp10) REVERT: C 571 ASP cc_start: 0.9304 (t0) cc_final: 0.9064 (t0) REVERT: C 957 GLN cc_start: 0.8880 (mt0) cc_final: 0.8657 (tt0) REVERT: C 990 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8642 (mm-30) REVERT: C 1010 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8863 (mp10) REVERT: D 133 PHE cc_start: 0.7334 (m-80) cc_final: 0.7091 (m-80) REVERT: D 338 PHE cc_start: 0.8719 (m-10) cc_final: 0.8428 (m-80) REVERT: D 353 TRP cc_start: 0.8791 (p-90) cc_final: 0.8175 (p-90) REVERT: D 389 ASP cc_start: 0.9199 (t0) cc_final: 0.8786 (p0) REVERT: D 390 LEU cc_start: 0.8854 (mt) cc_final: 0.8455 (mt) REVERT: D 425 LEU cc_start: 0.9011 (mt) cc_final: 0.8618 (tp) REVERT: D 762 GLN cc_start: 0.9198 (mt0) cc_final: 0.8945 (mm-40) REVERT: D 912 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8812 (p) REVERT: D 1096 VAL cc_start: 0.9322 (OUTLIER) cc_final: 0.9079 (m) outliers start: 44 outliers final: 14 residues processed: 175 average time/residue: 1.2674 time to fit residues: 265.4392 Evaluate side-chains 154 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 3.077 ------------------------------------------------------------------------------- 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 392 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 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: 0.7980 chunk 55 optimal weight: 0.0970 chunk 5 optimal weight: 9.9990 chunk 330 optimal weight: 0.5980 chunk 262 optimal weight: 4.9990 chunk 293 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 chunk 274 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 B 394 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN D 339 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.135050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.084568 restraints weight = 114352.606| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.71 r_work: 0.2934 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29533 Z= 0.140 Angle : 0.553 14.041 40240 Z= 0.279 Chirality : 0.044 0.488 4569 Planarity : 0.004 0.050 5146 Dihedral : 5.194 86.995 4473 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.68 % Allowed : 9.63 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 3551 helix: 2.36 (0.16), residues: 1034 sheet: 0.96 (0.19), residues: 696 loop : -0.35 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 271 HIS 0.011 0.001 HIS D 339 PHE 0.022 0.001 PHE D 220 TYR 0.019 0.001 TYR A 385 ARG 0.005 0.000 ARG D 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00620 ( 29) link_NAG-ASN : angle 3.24744 ( 87) hydrogen bonds : bond 0.03930 ( 1244) hydrogen bonds : angle 4.84363 ( 3592) metal coordination : bond 0.00042 ( 2) SS BOND : bond 0.00175 ( 37) SS BOND : angle 1.12490 ( 74) covalent geometry : bond 0.00313 (29465) covalent geometry : angle 0.53105 (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 190 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 3.705 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: 0.8639 (OUTLIER) cc_final: 0.8359 (t70) REVERT: A 270 MET cc_start: 0.2194 (ptm) cc_final: 0.1966 (ptp) REVERT: A 332 MET cc_start: 0.1230 (ptm) cc_final: 0.0552 (pp-130) REVERT: A 360 MET cc_start: 0.4881 (tmt) cc_final: 0.4367 (tmt) REVERT: B 101 ILE cc_start: 0.7338 (OUTLIER) cc_final: 0.6486 (pp) REVERT: B 177 MET cc_start: 0.7707 (ppp) cc_final: 0.7093 (ppp) REVERT: B 200 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8406 (t80) REVERT: B 394 ASN cc_start: 0.8981 (OUTLIER) cc_final: 0.8175 (p0) REVERT: B 762 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8404 (mm-40) REVERT: B 988 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8899 (mp0) REVERT: B 1002 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8873 (mm-40) REVERT: C 571 ASP cc_start: 0.9307 (t0) cc_final: 0.9105 (t0) REVERT: C 740 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8598 (tpp) REVERT: C 762 GLN cc_start: 0.9265 (mt0) cc_final: 0.8919 (mp10) REVERT: C 957 GLN cc_start: 0.8904 (mt0) cc_final: 0.8701 (tt0) REVERT: C 1010 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8868 (mp10) REVERT: D 133 PHE cc_start: 0.7391 (m-80) cc_final: 0.6734 (m-80) REVERT: D 135 PHE cc_start: 0.7400 (m-80) cc_final: 0.6973 (m-80) REVERT: D 338 PHE cc_start: 0.8767 (m-10) cc_final: 0.8482 (m-80) REVERT: D 353 TRP cc_start: 0.8804 (p-90) cc_final: 0.7581 (p-90) REVERT: D 389 ASP cc_start: 0.9232 (t0) cc_final: 0.8830 (p0) REVERT: D 390 LEU cc_start: 0.8871 (mt) cc_final: 0.8490 (mt) REVERT: D 425 LEU cc_start: 0.9132 (mt) cc_final: 0.8714 (tp) REVERT: D 740 MET cc_start: 0.8953 (ttt) cc_final: 0.8693 (ttm) REVERT: D 762 GLN cc_start: 0.9217 (mt0) cc_final: 0.8959 (mm-40) REVERT: D 912 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8847 (p) REVERT: D 1096 VAL cc_start: 0.9358 (OUTLIER) cc_final: 0.9115 (m) outliers start: 53 outliers final: 16 residues processed: 170 average time/residue: 1.2911 time to fit residues: 262.6296 Evaluate side-chains 151 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 3.133 ------------------------------------------------------------------------------- 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 392 PHE Chi-restraints excluded: chain B residue 394 ASN 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 1010 GLN Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 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 1096 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 314 optimal weight: 0.8980 chunk 355 optimal weight: 0.6980 chunk 277 optimal weight: 4.9990 chunk 301 optimal weight: 0.4980 chunk 318 optimal weight: 0.7980 chunk 271 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 254 optimal weight: 0.0670 chunk 143 optimal weight: 0.9980 chunk 243 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.141067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.091591 restraints weight = 99206.278| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.41 r_work: 0.2965 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 29533 Z= 0.115 Angle : 0.528 12.551 40240 Z= 0.267 Chirality : 0.044 0.465 4569 Planarity : 0.004 0.042 5146 Dihedral : 5.070 101.511 4473 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.52 % Allowed : 10.29 % Favored : 88.18 % 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: 1.12 (0.14), residues: 3551 helix: 2.41 (0.16), residues: 1028 sheet: 1.04 (0.19), residues: 697 loop : -0.34 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 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 A 385 ARG 0.004 0.000 ARG D 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00637 ( 29) link_NAG-ASN : angle 3.11967 ( 87) hydrogen bonds : bond 0.03710 ( 1244) hydrogen bonds : angle 4.74796 ( 3592) metal coordination : bond 0.00021 ( 2) SS BOND : bond 0.00243 ( 37) SS BOND : angle 1.17489 ( 74) covalent geometry : bond 0.00252 (29465) covalent geometry : angle 0.50661 (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 179 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 131 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8340 (t0) REVERT: A 249 MET cc_start: 0.3664 (mtt) cc_final: 0.3179 (mmt) REVERT: A 270 MET cc_start: 0.2262 (ptm) cc_final: 0.1928 (ptp) REVERT: A 323 MET cc_start: 0.0209 (tpt) cc_final: -0.0396 (tpt) REVERT: A 332 MET cc_start: 0.1158 (ptm) cc_final: 0.0496 (pp-130) REVERT: A 360 MET cc_start: 0.5293 (tmt) cc_final: 0.4786 (tmt) REVERT: A 383 MET cc_start: 0.6512 (mtt) cc_final: 0.6013 (pp-130) REVERT: B 177 MET cc_start: 0.7658 (ppp) cc_final: 0.6978 (ppp) REVERT: B 200 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.8353 (t80) REVERT: B 394 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8400 (p0) REVERT: B 762 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8379 (mm-40) REVERT: B 1002 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8888 (mm-40) REVERT: C 571 ASP cc_start: 0.9285 (t0) cc_final: 0.9069 (t0) REVERT: C 957 GLN cc_start: 0.8870 (mt0) cc_final: 0.8648 (tt0) REVERT: C 988 GLU cc_start: 0.9186 (mp0) cc_final: 0.8968 (mp0) REVERT: C 1010 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8875 (mp10) REVERT: D 133 PHE cc_start: 0.7435 (m-80) cc_final: 0.7207 (m-80) REVERT: D 338 PHE cc_start: 0.8827 (m-10) cc_final: 0.8544 (m-80) REVERT: D 353 TRP cc_start: 0.8552 (p-90) cc_final: 0.8256 (p-90) REVERT: D 389 ASP cc_start: 0.9213 (t0) cc_final: 0.8839 (p0) REVERT: D 390 LEU cc_start: 0.8873 (mt) cc_final: 0.8482 (mt) REVERT: D 425 LEU cc_start: 0.9135 (mt) cc_final: 0.8729 (tp) REVERT: D 740 MET cc_start: 0.8947 (ttt) cc_final: 0.8683 (ttm) REVERT: D 762 GLN cc_start: 0.9182 (mt0) cc_final: 0.8932 (mm-40) REVERT: D 895 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7944 (pt0) REVERT: D 912 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8900 (p) REVERT: D 1096 VAL cc_start: 0.9344 (OUTLIER) cc_final: 0.9064 (p) outliers start: 48 outliers final: 23 residues processed: 162 average time/residue: 1.2722 time to fit residues: 247.5366 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 : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 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 392 PHE Chi-restraints excluded: chain B residue 394 ASN 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 D residue 47 VAL Chi-restraints excluded: chain D residue 342 PHE 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 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: 7.9990 chunk 137 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 256 optimal weight: 0.6980 chunk 336 optimal weight: 1.9990 chunk 246 optimal weight: 0.6980 chunk 309 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 290 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 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 = 0.4289 r_free = 0.4289 target = 0.140546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.089401 restraints weight = 109885.308| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 4.12 r_work: 0.2916 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29533 Z= 0.169 Angle : 0.545 12.776 40240 Z= 0.274 Chirality : 0.044 0.491 4569 Planarity : 0.004 0.043 5146 Dihedral : 4.743 55.462 4471 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.82 % Favored : 97.15 % Rotamer: Outliers : 1.62 % Allowed : 10.52 % Favored : 87.87 % 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: 2.37 (0.16), residues: 1020 sheet: 1.00 (0.19), residues: 697 loop : -0.32 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 436 HIS 0.006 0.001 HIS A 228 PHE 0.019 0.001 PHE D 220 TYR 0.017 0.001 TYR A 385 ARG 0.005 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 29) link_NAG-ASN : angle 3.12095 ( 87) hydrogen bonds : bond 0.03817 ( 1244) hydrogen bonds : angle 4.78789 ( 3592) metal coordination : bond 0.01489 ( 2) SS BOND : bond 0.00288 ( 37) SS BOND : angle 1.24309 ( 74) covalent geometry : bond 0.00384 (29465) covalent geometry : angle 0.52387 (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 178 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 127 time to evaluate : 3.599 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: 0.8667 (OUTLIER) cc_final: 0.8391 (t0) REVERT: A 249 MET cc_start: 0.3951 (mtt) cc_final: 0.3478 (mmt) REVERT: A 270 MET cc_start: 0.2307 (ptm) cc_final: 0.1960 (ptp) REVERT: A 323 MET cc_start: 0.0326 (tpt) cc_final: -0.0332 (tpt) REVERT: A 332 MET cc_start: 0.1587 (ptm) cc_final: 0.0880 (pp-130) REVERT: A 360 MET cc_start: 0.5599 (tmt) cc_final: 0.5100 (tmt) REVERT: A 383 MET cc_start: 0.6448 (mtt) cc_final: 0.5984 (pp-130) REVERT: B 177 MET cc_start: 0.7768 (ppp) cc_final: 0.7076 (ppp) REVERT: B 200 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.8406 (t80) REVERT: B 762 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8478 (mm-40) REVERT: B 1002 GLN cc_start: 0.9252 (mm-40) cc_final: 0.8927 (mm-40) REVERT: C 762 GLN cc_start: 0.8984 (mm110) cc_final: 0.8691 (mm-40) REVERT: C 957 GLN cc_start: 0.8901 (mt0) cc_final: 0.8684 (tt0) REVERT: C 988 GLU cc_start: 0.9201 (mp0) cc_final: 0.8992 (mp0) REVERT: C 1010 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.8930 (mp10) REVERT: D 338 PHE cc_start: 0.8874 (m-10) cc_final: 0.8615 (m-80) REVERT: D 353 TRP cc_start: 0.8522 (p-90) cc_final: 0.8273 (p-90) REVERT: D 389 ASP cc_start: 0.9223 (t0) cc_final: 0.8848 (p0) REVERT: D 390 LEU cc_start: 0.8887 (mt) cc_final: 0.8507 (mt) REVERT: D 425 LEU cc_start: 0.9191 (mt) cc_final: 0.8798 (tp) REVERT: D 740 MET cc_start: 0.9005 (ttt) cc_final: 0.8727 (ttm) REVERT: D 762 GLN cc_start: 0.9227 (mt0) cc_final: 0.8982 (mm-40) REVERT: D 912 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8948 (p) REVERT: D 1096 VAL cc_start: 0.9408 (OUTLIER) cc_final: 0.9130 (p) outliers start: 51 outliers final: 29 residues processed: 161 average time/residue: 1.2990 time to fit residues: 252.4800 Evaluate side-chains 158 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 3.129 ------------------------------------------------------------------------------- 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 392 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 565 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 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 36 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 67 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 81 optimal weight: 0.0670 chunk 349 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 318 optimal weight: 0.8980 chunk 323 optimal weight: 0.6980 chunk 195 optimal weight: 0.0980 chunk 329 optimal weight: 0.2980 chunk 210 optimal weight: 0.6980 overall best weight: 0.3718 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.140873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.090090 restraints weight = 135008.633| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 4.04 r_work: 0.2932 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29533 Z= 0.104 Angle : 0.529 12.313 40240 Z= 0.267 Chirality : 0.044 0.457 4569 Planarity : 0.004 0.041 5146 Dihedral : 4.572 55.271 4471 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.76 % Favored : 97.21 % Rotamer: Outliers : 1.24 % Allowed : 11.21 % Favored : 87.55 % 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: 1.19 (0.14), residues: 3551 helix: 2.46 (0.16), residues: 1020 sheet: 1.05 (0.19), residues: 695 loop : -0.28 (0.14), residues: 1836 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 0.018 0.001 PHE B 759 TYR 0.018 0.001 TYR A 385 ARG 0.005 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00645 ( 29) link_NAG-ASN : angle 2.99746 ( 87) hydrogen bonds : bond 0.03599 ( 1244) hydrogen bonds : angle 4.67854 ( 3592) metal coordination : bond 0.00104 ( 2) SS BOND : bond 0.00247 ( 37) SS BOND : angle 1.11117 ( 74) covalent geometry : bond 0.00222 (29465) covalent geometry : angle 0.50934 (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: 39 poor density : 129 time to evaluate : 3.186 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: 0.8590 (OUTLIER) cc_final: 0.8306 (t0) REVERT: A 249 MET cc_start: 0.3745 (mtt) cc_final: 0.3283 (mmt) REVERT: A 270 MET cc_start: 0.2508 (ptm) cc_final: 0.1880 (ptp) REVERT: A 323 MET cc_start: 0.0102 (tpt) cc_final: -0.0421 (tpt) REVERT: A 332 MET cc_start: 0.1809 (ptm) cc_final: 0.1142 (pp-130) REVERT: A 360 MET cc_start: 0.5581 (tmt) cc_final: 0.5104 (tmt) REVERT: A 383 MET cc_start: 0.6450 (mtt) cc_final: 0.6013 (pp-130) REVERT: B 177 MET cc_start: 0.7783 (ppp) cc_final: 0.7044 (ppp) REVERT: B 200 TYR cc_start: 0.8910 (OUTLIER) cc_final: 0.8406 (t80) REVERT: B 762 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8458 (mm-40) REVERT: B 780 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8699 (mp0) REVERT: B 1002 GLN cc_start: 0.9234 (mm-40) cc_final: 0.8928 (mm-40) REVERT: C 762 GLN cc_start: 0.8923 (mm110) cc_final: 0.8674 (mm-40) REVERT: C 957 GLN cc_start: 0.8901 (mt0) cc_final: 0.8675 (tt0) REVERT: C 1010 GLN cc_start: 0.9268 (OUTLIER) cc_final: 0.8916 (mp10) REVERT: D 338 PHE cc_start: 0.8819 (m-10) cc_final: 0.8567 (m-80) REVERT: D 353 TRP cc_start: 0.8435 (p-90) cc_final: 0.8169 (p-90) REVERT: D 389 ASP cc_start: 0.9255 (t0) cc_final: 0.8850 (p0) REVERT: D 390 LEU cc_start: 0.8824 (mt) cc_final: 0.8416 (mt) REVERT: D 425 LEU cc_start: 0.9160 (mt) cc_final: 0.8745 (tp) REVERT: D 740 MET cc_start: 0.8967 (ttt) cc_final: 0.8699 (ttm) REVERT: D 762 GLN cc_start: 0.9209 (mt0) cc_final: 0.8953 (mm-40) REVERT: D 895 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7981 (pt0) REVERT: D 912 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8920 (p) REVERT: D 1096 VAL cc_start: 0.9360 (OUTLIER) cc_final: 0.9090 (p) outliers start: 39 outliers final: 23 residues processed: 155 average time/residue: 1.2389 time to fit residues: 230.9634 Evaluate side-chains 154 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 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 515 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 780 GLU 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 36 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 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: 1.9990 chunk 77 optimal weight: 0.0040 chunk 143 optimal weight: 0.5980 chunk 27 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 129 optimal weight: 2.9990 chunk 229 optimal weight: 0.4980 chunk 216 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 43 optimal weight: 30.0000 chunk 147 optimal weight: 0.9980 overall best weight: 0.8194 ------------------------------------------------------------------------------- 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** D 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.140510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.089607 restraints weight = 107628.883| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.83 r_work: 0.2926 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- 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 = 0.26 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 = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29533 Z= 0.129 Angle : 0.528 12.247 40240 Z= 0.265 Chirality : 0.044 0.474 4569 Planarity : 0.004 0.042 5146 Dihedral : 4.465 55.249 4471 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.27 % Rotamer: Outliers : 1.14 % Allowed : 11.59 % Favored : 87.27 % 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: 1.20 (0.14), residues: 3551 helix: 2.48 (0.16), residues: 1025 sheet: 1.05 (0.19), residues: 695 loop : -0.28 (0.15), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 104 HIS 0.008 0.001 HIS A 378 PHE 0.019 0.001 PHE D 759 TYR 0.018 0.001 TYR A 385 ARG 0.005 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 29) link_NAG-ASN : angle 2.96417 ( 87) hydrogen bonds : bond 0.03618 ( 1244) hydrogen bonds : angle 4.68227 ( 3592) metal coordination : bond 0.00035 ( 2) SS BOND : bond 0.00207 ( 37) SS BOND : angle 1.03460 ( 74) covalent geometry : bond 0.00287 (29465) covalent geometry : angle 0.50920 (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 157 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 3.272 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: 0.8627 (p0) cc_final: 0.8341 (t0) REVERT: A 249 MET cc_start: 0.3943 (mtt) cc_final: 0.3447 (mmt) REVERT: A 332 MET cc_start: 0.1892 (ptm) cc_final: 0.1372 (pp-130) REVERT: A 360 MET cc_start: 0.5663 (tmt) cc_final: 0.5260 (tmt) REVERT: B 177 MET cc_start: 0.7866 (ppp) cc_final: 0.7141 (ppp) REVERT: B 200 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8442 (t80) REVERT: B 571 ASP cc_start: 0.9127 (m-30) cc_final: 0.8765 (t0) REVERT: B 762 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8445 (mm-40) REVERT: B 1002 GLN cc_start: 0.9251 (mm-40) cc_final: 0.8922 (mm-40) REVERT: C 762 GLN cc_start: 0.8833 (mm110) cc_final: 0.8565 (mm-40) REVERT: C 957 GLN cc_start: 0.8878 (mt0) cc_final: 0.8657 (tt0) REVERT: C 1010 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.8840 (mp10) REVERT: D 338 PHE cc_start: 0.8788 (m-10) cc_final: 0.8560 (m-80) REVERT: D 353 TRP cc_start: 0.8414 (p-90) cc_final: 0.7360 (p-90) REVERT: D 389 ASP cc_start: 0.9249 (t0) cc_final: 0.8839 (p0) REVERT: D 390 LEU cc_start: 0.8759 (mt) cc_final: 0.8331 (mt) REVERT: D 425 LEU cc_start: 0.9217 (mt) cc_final: 0.8807 (tp) REVERT: D 740 MET cc_start: 0.8937 (ttt) cc_final: 0.8665 (ttm) REVERT: D 912 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8900 (p) REVERT: D 1096 VAL cc_start: 0.9365 (OUTLIER) cc_final: 0.9083 (p) outliers start: 36 outliers final: 24 residues processed: 148 average time/residue: 1.2335 time to fit residues: 221.8100 Evaluate side-chains 148 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 515 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 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 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 1096 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 112 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 312 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 7 optimal weight: 40.0000 chunk 49 optimal weight: 30.0000 chunk 327 optimal weight: 0.0370 overall best weight: 1.2064 ------------------------------------------------------------------------------- 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 D 703 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.140055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.090145 restraints weight = 137956.470| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 5.15 r_work: 0.2836 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29533 Z= 0.161 Angle : 0.544 12.461 40240 Z= 0.273 Chirality : 0.044 0.487 4569 Planarity : 0.004 0.042 5146 Dihedral : 4.416 55.109 4469 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Rotamer: Outliers : 1.14 % Allowed : 11.75 % 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: 1.13 (0.14), residues: 3551 helix: 2.40 (0.16), residues: 1025 sheet: 0.94 (0.19), residues: 706 loop : -0.28 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 104 HIS 0.008 0.001 HIS A 378 PHE 0.037 0.001 PHE B 371 TYR 0.023 0.001 TYR D 380 ARG 0.005 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 29) link_NAG-ASN : angle 2.97503 ( 87) hydrogen bonds : bond 0.03724 ( 1244) hydrogen bonds : angle 4.74662 ( 3592) metal coordination : bond 0.00036 ( 2) SS BOND : bond 0.00216 ( 37) SS BOND : angle 1.04318 ( 74) covalent geometry : bond 0.00366 (29465) covalent geometry : angle 0.52552 (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 164 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.8644 (p0) cc_final: 0.8372 (t0) REVERT: A 249 MET cc_start: 0.4015 (mtt) cc_final: 0.3518 (mmt) REVERT: A 323 MET cc_start: -0.0005 (tpt) cc_final: -0.0790 (tpt) REVERT: A 332 MET cc_start: 0.2167 (ptm) cc_final: 0.1558 (pp-130) REVERT: A 360 MET cc_start: 0.5651 (tmt) cc_final: 0.5268 (tmt) REVERT: A 383 MET cc_start: 0.5776 (mtt) cc_final: 0.5371 (pp-130) REVERT: B 177 MET cc_start: 0.7856 (ppp) cc_final: 0.7147 (ppp) REVERT: B 200 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8455 (t80) REVERT: B 571 ASP cc_start: 0.9165 (m-30) cc_final: 0.8820 (t0) REVERT: B 762 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8514 (mm-40) REVERT: B 1002 GLN cc_start: 0.9320 (mm-40) cc_final: 0.8974 (mm-40) REVERT: C 762 GLN cc_start: 0.8852 (mm110) cc_final: 0.8578 (mm-40) REVERT: C 957 GLN cc_start: 0.8936 (mt0) cc_final: 0.8727 (tt0) REVERT: C 1010 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.8901 (mp10) REVERT: D 338 PHE cc_start: 0.8759 (m-10) cc_final: 0.8553 (m-80) REVERT: D 353 TRP cc_start: 0.8427 (p-90) cc_final: 0.7351 (p-90) REVERT: D 389 ASP cc_start: 0.9291 (t0) cc_final: 0.8853 (p0) REVERT: D 390 LEU cc_start: 0.8733 (mt) cc_final: 0.8319 (mt) REVERT: D 425 LEU cc_start: 0.9230 (mt) cc_final: 0.8852 (tp) REVERT: D 740 MET cc_start: 0.8981 (ttt) cc_final: 0.8701 (ttm) REVERT: D 912 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8873 (p) REVERT: D 1096 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9157 (p) outliers start: 36 outliers final: 24 residues processed: 153 average time/residue: 1.2515 time to fit residues: 230.6195 Evaluate side-chains 151 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 3.207 ------------------------------------------------------------------------------- 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 515 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 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 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 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 278 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 chunk 249 optimal weight: 0.6980 chunk 229 optimal weight: 0.0020 chunk 99 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 38 optimal weight: 20.0000 chunk 191 optimal weight: 20.0000 chunk 299 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.5148 ------------------------------------------------------------------------------- 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** C 544 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.140475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.088654 restraints weight = 115929.910| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 4.65 r_work: 0.2948 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 29533 Z= 0.107 Angle : 0.529 13.204 40240 Z= 0.264 Chirality : 0.043 0.449 4569 Planarity : 0.004 0.042 5146 Dihedral : 4.296 54.938 4469 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.24 % Rotamer: Outliers : 0.89 % Allowed : 12.20 % 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: 1.17 (0.14), residues: 3551 helix: 2.41 (0.16), residues: 1025 sheet: 1.03 (0.19), residues: 690 loop : -0.25 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 104 HIS 0.016 0.001 HIS A 228 PHE 0.023 0.001 PHE B 392 TYR 0.023 0.001 TYR D 380 ARG 0.009 0.000 ARG D 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00626 ( 29) link_NAG-ASN : angle 2.86343 ( 87) hydrogen bonds : bond 0.03500 ( 1244) hydrogen bonds : angle 4.65680 ( 3592) metal coordination : bond 0.00010 ( 2) SS BOND : bond 0.00217 ( 37) SS BOND : angle 0.95331 ( 74) covalent geometry : bond 0.00235 (29465) covalent geometry : angle 0.51104 (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 151 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 3.157 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: 0.8522 (p0) cc_final: 0.8201 (t0) REVERT: A 249 MET cc_start: 0.3245 (mtt) cc_final: 0.2870 (mmt) REVERT: A 323 MET cc_start: -0.0125 (tpt) cc_final: -0.0730 (tpt) REVERT: A 332 MET cc_start: 0.1078 (ptm) cc_final: 0.0708 (pp-130) REVERT: A 383 MET cc_start: 0.5652 (mtt) cc_final: 0.5094 (pp-130) REVERT: B 177 MET cc_start: 0.7773 (ppp) cc_final: 0.7041 (ppp) REVERT: B 200 TYR cc_start: 0.8907 (OUTLIER) cc_final: 0.8451 (t80) REVERT: B 571 ASP cc_start: 0.9152 (m-30) cc_final: 0.8796 (t0) REVERT: B 762 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8499 (mm-40) REVERT: B 1002 GLN cc_start: 0.9261 (mm-40) cc_final: 0.8919 (mm-40) REVERT: B 1017 GLU cc_start: 0.9155 (tp30) cc_final: 0.8941 (tp30) REVERT: C 762 GLN cc_start: 0.8810 (mm110) cc_final: 0.8558 (mm-40) REVERT: C 1010 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.8846 (mp10) REVERT: D 353 TRP cc_start: 0.8287 (p-90) cc_final: 0.7232 (p-90) REVERT: D 389 ASP cc_start: 0.9288 (t0) cc_final: 0.8880 (p0) REVERT: D 390 LEU cc_start: 0.8713 (mt) cc_final: 0.8264 (mt) REVERT: D 421 TYR cc_start: 0.7975 (m-10) cc_final: 0.7573 (m-10) REVERT: D 425 LEU cc_start: 0.9156 (mt) cc_final: 0.8742 (tp) REVERT: D 740 MET cc_start: 0.8999 (ttt) cc_final: 0.8725 (ttm) REVERT: D 912 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8978 (p) REVERT: D 1096 VAL cc_start: 0.9379 (OUTLIER) cc_final: 0.9127 (p) outliers start: 28 outliers final: 17 residues processed: 142 average time/residue: 1.3402 time to fit residues: 229.1725 Evaluate side-chains 140 residues out of total 3155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 3.208 ------------------------------------------------------------------------------- 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 515 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 1010 GLN Chi-restraints excluded: chain D residue 47 VAL 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 524 VAL 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: 50.0000 chunk 132 optimal weight: 1.9990 chunk 65 optimal weight: 0.0020 chunk 135 optimal weight: 0.0170 chunk 13 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 41 optimal weight: 40.0000 chunk 236 optimal weight: 1.9990 overall best weight: 0.9430 ------------------------------------------------------------------------------- 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 = 0.4287 r_free = 0.4287 target = 0.140041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.088894 restraints weight = 103755.846| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.70 r_work: 0.2932 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29533 Z= 0.139 Angle : 0.545 13.648 40240 Z= 0.272 Chirality : 0.044 0.469 4569 Planarity : 0.004 0.042 5146 Dihedral : 4.288 55.106 4469 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.85 % Favored : 97.13 % Rotamer: Outliers : 0.82 % Allowed : 12.13 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.37 (0.16), residues: 1025 sheet: 0.98 (0.19), residues: 689 loop : -0.24 (0.15), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 104 HIS 0.015 0.001 HIS A 228 PHE 0.018 0.001 PHE D 220 TYR 0.028 0.001 TYR B 904 ARG 0.008 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 29) link_NAG-ASN : angle 2.87339 ( 87) hydrogen bonds : bond 0.03600 ( 1244) hydrogen bonds : angle 4.70271 ( 3592) metal coordination : bond 0.00016 ( 2) SS BOND : bond 0.00224 ( 37) SS BOND : angle 0.99210 ( 74) covalent geometry : bond 0.00315 (29465) covalent geometry : angle 0.52752 (40079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28834.71 seconds wall clock time: 495 minutes 38.99 seconds (29738.99 seconds total)