Starting phenix.real_space_refine on Fri Jun 27 16:01:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ykg_39370/06_2025/8ykg_39370.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ykg_39370/06_2025/8ykg_39370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ykg_39370/06_2025/8ykg_39370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ykg_39370/06_2025/8ykg_39370.map" model { file = "/net/cci-nas-00/data/ceres_data/8ykg_39370/06_2025/8ykg_39370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ykg_39370/06_2025/8ykg_39370.cif" } resolution = 3.28 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= 0.001 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 6588 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 16833 2.51 5 N 4363 2.21 5 O 5118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26426 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 961, 7519 Classifications: {'peptide': 961} Link IDs: {'PTRANS': 51, 'TRANS': 909} Chain breaks: 9 Chain: "B" Number of atoms: 7587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7587 Classifications: {'peptide': 973} Link IDs: {'PTRANS': 52, 'TRANS': 920} Chain breaks: 9 Chain: "C" Number of atoms: 7476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7476 Classifications: {'peptide': 959} Link IDs: {'PTRANS': 52, 'TRANS': 906} Chain breaks: 11 Chain: "D" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1761 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain breaks: 1 Chain: "F" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1761 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 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 Time building chain proxies: 15.86, per 1000 atoms: 0.60 Number of scatterers: 26426 At special positions: 0 Unit cell: (155.283, 133.423, 217.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 5118 8.00 N 4363 7.00 C 16833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 143 " - pdb=" SG CYS D 220 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 143 " - pdb=" SG CYS F 220 " 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=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1134 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1134 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 717 " " NAG C1306 " - " ASN C 801 " " NAG E 1 " - " ASN C 343 " " NAG G 1 " - " ASN B 343 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.24 Conformation dependent library (CDL) restraints added in 3.3 seconds 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6256 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 53 sheets defined 23.1% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.12 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.866A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.242A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.616A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.413A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.098A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.713A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.777A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.927A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.580A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.544A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.350A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.523A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.258A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.576A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.512A pdb=" N ALA C 352 " --> pdb=" O SER C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.389A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.630A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.277A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.534A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 939 removed outlier: 6.893A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.518A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) 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 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.782A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 removed outlier: 4.069A pdb=" N ILE D 192 " --> pdb=" O LYS D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 215 Processing helix chain 'D' and resid 225 through 228 Processing helix chain 'F' and resid 186 through 190 removed outlier: 3.665A pdb=" N LYS F 189 " --> pdb=" O GLY F 186 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N SER F 190 " --> pdb=" O THR F 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 186 through 190' Processing helix chain 'F' and resid 211 through 215 Processing helix chain 'F' and resid 226 through 228 No H-bonds generated for 'chain 'F' and resid 226 through 228' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.740A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.584A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.109A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.958A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 650 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.600A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.600A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ASN A 394 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 9.347A pdb=" N ALA A 522 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.709A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.605A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.551A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB3, first strand: chain 'A' and resid 717 through 722 removed outlier: 6.495A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 1086 through 1090 removed outlier: 4.644A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.544A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.549A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.852A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 4.167A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.837A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.769A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.155A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.654A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.654A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 removed outlier: 3.505A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD3, first strand: chain 'B' and resid 1086 through 1090 removed outlier: 4.162A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.635A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER C 205 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.760A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.709A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.980A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.636A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.087A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 722 removed outlier: 7.153A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C1047 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 725 through 728 Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.753A pdb=" N ALA D 18 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.336A pdb=" N LEU D 10 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU D 104 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU D 12 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR D 36 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 124 through 128 removed outlier: 3.529A pdb=" N PHE D 203 " --> pdb=" O CYS D 143 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 132 through 133 removed outlier: 3.976A pdb=" N VAL D 133 " --> pdb=" O THR D 241 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 216 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG D 161 " --> pdb=" O TRP D 170 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N TRP D 170 " --> pdb=" O ARG D 161 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER D 163 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LEU D 168 " --> pdb=" O SER D 163 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 132 through 133 removed outlier: 3.976A pdb=" N VAL D 133 " --> pdb=" O THR D 241 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 216 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE D 233 " --> pdb=" O ARG D 222 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 3 through 5 Processing sheet with id=AF4, first strand: chain 'F' and resid 3 through 5 removed outlier: 3.694A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.536A pdb=" N LEU F 10 " --> pdb=" O LYS F 102 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU F 104 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU F 12 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 124 through 128 removed outlier: 3.738A pdb=" N PHE F 203 " --> pdb=" O CYS F 143 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 132 through 133 removed outlier: 3.823A pdb=" N VAL F 133 " --> pdb=" O THR F 241 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA F 221 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N ALA F 155 " --> pdb=" O TYR F 175 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR F 175 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TRP F 157 " --> pdb=" O ARG F 173 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG F 173 " --> pdb=" O TRP F 157 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TRP F 159 " --> pdb=" O LEU F 171 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 132 through 133 removed outlier: 3.823A pdb=" N VAL F 133 " --> pdb=" O THR F 241 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE F 233 " --> pdb=" O ARG F 222 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE F 224 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE F 231 " --> pdb=" O ILE F 224 " (cutoff:3.500A) 1045 hydrogen bonds defined for protein. 2823 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: 12.90 Time building geometry restraints manager: 7.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8456 1.35 - 1.47: 6842 1.47 - 1.59: 11576 1.59 - 1.72: 0 1.72 - 1.84: 140 Bond restraints: 27014 Sorted by residual: bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.335 1.367 -0.031 1.36e-02 5.41e+03 5.31e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.97e+00 bond pdb=" CA THR C 114 " pdb=" CB THR C 114 " ideal model delta sigma weight residual 1.526 1.557 -0.030 1.76e-02 3.23e+03 3.00e+00 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.83e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.45e+00 ... (remaining 27009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 36343 2.29 - 4.58: 382 4.58 - 6.87: 26 6.87 - 9.16: 2 9.16 - 11.45: 1 Bond angle restraints: 36754 Sorted by residual: angle pdb=" C THR C 333 " pdb=" CA THR C 333 " pdb=" CB THR C 333 " ideal model delta sigma weight residual 116.34 109.44 6.90 1.40e+00 5.10e-01 2.43e+01 angle pdb=" C VAL C 382 " pdb=" N SER C 383 " pdb=" CA SER C 383 " ideal model delta sigma weight residual 120.49 125.27 -4.78 1.42e+00 4.96e-01 1.13e+01 angle pdb=" CA LEU C 390 " pdb=" CB LEU C 390 " pdb=" CG LEU C 390 " ideal model delta sigma weight residual 116.30 127.75 -11.45 3.50e+00 8.16e-02 1.07e+01 angle pdb=" N THR B 393 " pdb=" CA THR B 393 " pdb=" C THR B 393 " ideal model delta sigma weight residual 110.97 114.36 -3.39 1.09e+00 8.42e-01 9.69e+00 angle pdb=" N THR C 333 " pdb=" CA THR C 333 " pdb=" C THR C 333 " ideal model delta sigma weight residual 108.00 112.51 -4.51 1.48e+00 4.57e-01 9.30e+00 ... (remaining 36749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 15157 17.61 - 35.22: 999 35.22 - 52.84: 180 52.84 - 70.45: 47 70.45 - 88.06: 26 Dihedral angle restraints: 16409 sinusoidal: 6684 harmonic: 9725 Sorted by residual: dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -40.52 -45.48 1 1.00e+01 1.00e-02 2.87e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -42.32 -43.68 1 1.00e+01 1.00e-02 2.66e+01 dihedral pdb=" CA PHE B 392 " pdb=" C PHE B 392 " pdb=" N THR B 393 " pdb=" CA THR B 393 " ideal model delta harmonic sigma weight residual -180.00 -155.43 -24.57 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 16406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3854 0.084 - 0.168: 391 0.168 - 0.253: 2 0.253 - 0.337: 2 0.337 - 0.421: 1 Chirality restraints: 4250 Sorted by residual: chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 717 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 4247 not shown) Planarity restraints: 4734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.044 5.00e-02 4.00e+02 6.62e-02 7.02e+00 pdb=" N PRO A 986 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 79 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO D 80 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 80 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 80 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO A 987 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.028 5.00e-02 4.00e+02 ... (remaining 4731 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1463 2.73 - 3.27: 25890 3.27 - 3.81: 41159 3.81 - 4.36: 47634 4.36 - 4.90: 84651 Nonbonded interactions: 200797 Sorted by model distance: nonbonded pdb=" OG SER A 758 " pdb=" OG1 THR A 761 " model vdw 2.183 3.040 nonbonded pdb=" O ASP B 290 " pdb=" OG SER B 297 " model vdw 2.186 3.040 nonbonded pdb=" O ASP C 290 " pdb=" OG SER C 297 " model vdw 2.198 3.040 nonbonded pdb=" NE2 GLN A 804 " pdb=" OE1 GLN A 935 " model vdw 2.207 3.120 nonbonded pdb=" OG1 THR C 912 " pdb=" OD1 ASN C 914 " model vdw 2.208 3.040 ... (remaining 200792 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 'A' and (resid 27 through 65 or resid 81 through 95 or resid 103 through \ 120 or resid 127 through 131 or resid 166 through 209 or resid 217 through 1144 \ or resid 1301 through 1306)) selection = (chain 'B' and (resid 27 through 65 or resid 81 through 95 or resid 103 through \ 131 or resid 166 through 209 or resid 217 through 241 or resid 264 through 473 o \ r resid 490 through 517 or resid 521 through 1144 or resid 1301 through 1306)) selection = (chain 'C' and (resid 27 through 65 or resid 81 through 131 or resid 166 through \ 241 or resid 264 through 473 or resid 490 through 517 or resid 521 through 1144 \ or resid 1301 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.020 Extract box with map and model: 1.210 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 64.100 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.120 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 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 : 0.004 0.040 27080 Z= 0.180 Angle : 0.609 20.593 36907 Z= 0.320 Chirality : 0.045 0.421 4250 Planarity : 0.004 0.066 4713 Dihedral : 12.367 88.061 10027 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -0.56 (0.15), residues: 3281 helix: 2.15 (0.21), residues: 643 sheet: -0.30 (0.18), residues: 830 loop : -1.39 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 886 HIS 0.003 0.001 HIS B1058 PHE 0.025 0.001 PHE A 559 TYR 0.019 0.001 TYR B 265 ARG 0.003 0.000 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00720 ( 21) link_NAG-ASN : angle 4.34513 ( 63) link_BETA1-4 : bond 0.00123 ( 2) link_BETA1-4 : angle 1.59595 ( 6) hydrogen bonds : bond 0.21092 ( 1019) hydrogen bonds : angle 7.85469 ( 2823) SS BOND : bond 0.00451 ( 42) SS BOND : angle 1.03783 ( 84) covalent geometry : bond 0.00384 (27014) covalent geometry : angle 0.58096 (36754) Misc. bond : bond 0.00233 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 2.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1133 VAL cc_start: 0.8493 (t) cc_final: 0.8206 (m) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.4345 time to fit residues: 138.9924 Evaluate side-chains 96 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 282 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 261 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 chunk 159 optimal weight: 0.8980 chunk 194 optimal weight: 8.9990 chunk 303 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 953 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.101474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.068987 restraints weight = 105438.426| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.71 r_work: 0.3000 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27080 Z= 0.161 Angle : 0.609 20.190 36907 Z= 0.311 Chirality : 0.047 0.283 4250 Planarity : 0.005 0.057 4713 Dihedral : 6.732 59.834 4068 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.44 % Allowed : 5.23 % Favored : 94.33 % 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: -0.41 (0.15), residues: 3281 helix: 2.09 (0.21), residues: 648 sheet: -0.09 (0.18), residues: 845 loop : -1.30 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 35 HIS 0.004 0.001 HIS A1048 PHE 0.019 0.001 PHE B 220 TYR 0.023 0.001 TYR B 904 ARG 0.005 0.001 ARG D 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00643 ( 21) link_NAG-ASN : angle 4.05265 ( 63) link_BETA1-4 : bond 0.01230 ( 2) link_BETA1-4 : angle 1.11818 ( 6) hydrogen bonds : bond 0.06117 ( 1019) hydrogen bonds : angle 6.01327 ( 2823) SS BOND : bond 0.00491 ( 42) SS BOND : angle 1.16218 ( 84) covalent geometry : bond 0.00366 (27014) covalent geometry : angle 0.58351 (36754) Misc. bond : bond 0.00268 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 ASN cc_start: 0.8338 (m-40) cc_final: 0.8066 (t0) REVERT: C 493 GLN cc_start: 0.6272 (mm-40) cc_final: 0.5815 (mp10) REVERT: C 902 MET cc_start: 0.8897 (tpt) cc_final: 0.8636 (tpt) REVERT: C 1138 TYR cc_start: 0.8336 (t80) cc_final: 0.7818 (t80) REVERT: D 35 TRP cc_start: 0.5548 (t-100) cc_final: 0.4966 (t-100) REVERT: D 70 ASP cc_start: 0.7091 (p0) cc_final: 0.6686 (p0) REVERT: D 157 TRP cc_start: 0.6788 (m-90) cc_final: 0.6352 (m-90) REVERT: F 159 TRP cc_start: 0.5209 (m100) cc_final: 0.4939 (m100) outliers start: 13 outliers final: 3 residues processed: 113 average time/residue: 0.3849 time to fit residues: 71.3259 Evaluate side-chains 90 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain F residue 190 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 44 optimal weight: 9.9990 chunk 300 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 132 optimal weight: 30.0000 chunk 315 optimal weight: 50.0000 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 143 optimal weight: 10.0000 chunk 310 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 258 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS D 37 GLN D 195 ASN ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.095539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.061799 restraints weight = 83357.962| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.78 r_work: 0.2989 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27080 Z= 0.150 Angle : 0.574 20.085 36907 Z= 0.293 Chirality : 0.046 0.289 4250 Planarity : 0.004 0.066 4713 Dihedral : 6.441 59.857 4068 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.68 % Allowed : 8.03 % Favored : 91.29 % 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: -0.30 (0.15), residues: 3281 helix: 2.07 (0.21), residues: 647 sheet: 0.09 (0.18), residues: 852 loop : -1.24 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 886 HIS 0.004 0.001 HIS B1058 PHE 0.024 0.001 PHE D 219 TYR 0.023 0.001 TYR B 904 ARG 0.006 0.000 ARG F 222 Details of bonding type rmsd link_NAG-ASN : bond 0.00631 ( 21) link_NAG-ASN : angle 3.90124 ( 63) link_BETA1-4 : bond 0.00391 ( 2) link_BETA1-4 : angle 1.40980 ( 6) hydrogen bonds : bond 0.06038 ( 1019) hydrogen bonds : angle 5.56476 ( 2823) SS BOND : bond 0.00443 ( 42) SS BOND : angle 1.36957 ( 84) covalent geometry : bond 0.00344 (27014) covalent geometry : angle 0.54789 (36754) Misc. bond : bond 0.00267 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 3.183 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 906 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8378 (t80) REVERT: B 392 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.6522 (p90) REVERT: C 902 MET cc_start: 0.8958 (tpt) cc_final: 0.8609 (tpt) REVERT: C 1138 TYR cc_start: 0.8371 (t80) cc_final: 0.7969 (t80) REVERT: D 35 TRP cc_start: 0.5229 (t-100) cc_final: 0.4676 (t-100) REVERT: D 157 TRP cc_start: 0.7034 (m-90) cc_final: 0.6731 (m-90) REVERT: F 169 GLU cc_start: 0.8577 (tp30) cc_final: 0.8343 (tm-30) outliers start: 20 outliers final: 4 residues processed: 107 average time/residue: 0.3601 time to fit residues: 65.8744 Evaluate side-chains 92 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain F residue 190 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 61 optimal weight: 1.9990 chunk 333 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 310 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 263 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.091899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.058828 restraints weight = 94100.740| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.54 r_work: 0.2965 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27080 Z= 0.171 Angle : 0.592 19.876 36907 Z= 0.300 Chirality : 0.046 0.286 4250 Planarity : 0.004 0.066 4713 Dihedral : 6.308 58.405 4068 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.03 % Allowed : 9.30 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 3281 helix: 2.01 (0.21), residues: 649 sheet: 0.13 (0.18), residues: 821 loop : -1.21 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 886 HIS 0.005 0.001 HIS B1058 PHE 0.019 0.001 PHE A 906 TYR 0.021 0.001 TYR A1067 ARG 0.006 0.001 ARG D 173 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 21) link_NAG-ASN : angle 3.86244 ( 63) link_BETA1-4 : bond 0.00317 ( 2) link_BETA1-4 : angle 1.55622 ( 6) hydrogen bonds : bond 0.06198 ( 1019) hydrogen bonds : angle 5.43773 ( 2823) SS BOND : bond 0.00431 ( 42) SS BOND : angle 1.33352 ( 84) covalent geometry : bond 0.00402 (27014) covalent geometry : angle 0.56753 (36754) Misc. bond : bond 0.00333 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 ASN cc_start: 0.8363 (t0) cc_final: 0.8136 (t0) REVERT: A 906 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8395 (t80) REVERT: B 392 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.6043 (p90) REVERT: C 902 MET cc_start: 0.9046 (tpt) cc_final: 0.8595 (tpt) REVERT: D 28 VAL cc_start: -0.0012 (OUTLIER) cc_final: -0.0228 (p) REVERT: D 35 TRP cc_start: 0.5164 (t-100) cc_final: 0.4613 (t-100) REVERT: D 157 TRP cc_start: 0.7263 (m-90) cc_final: 0.7038 (m-90) outliers start: 30 outliers final: 14 residues processed: 118 average time/residue: 0.3599 time to fit residues: 72.0508 Evaluate side-chains 97 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 83 PHE Chi-restraints excluded: chain F residue 190 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 252 optimal weight: 0.0770 chunk 75 optimal weight: 3.9990 chunk 33 optimal weight: 30.0000 chunk 146 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 256 optimal weight: 0.0050 chunk 21 optimal weight: 7.9990 chunk 258 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 chunk 282 optimal weight: 1.9990 overall best weight: 1.2158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.089977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.057633 restraints weight = 108250.202| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.62 r_work: 0.2995 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27080 Z= 0.105 Angle : 0.570 22.826 36907 Z= 0.284 Chirality : 0.045 0.323 4250 Planarity : 0.004 0.046 4713 Dihedral : 5.940 58.628 4068 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.92 % Allowed : 10.53 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.07 (0.15), residues: 3281 helix: 2.33 (0.21), residues: 645 sheet: 0.18 (0.18), residues: 845 loop : -1.09 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.002 0.000 HIS B1058 PHE 0.019 0.001 PHE C 392 TYR 0.021 0.001 TYR B 170 ARG 0.003 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00668 ( 21) link_NAG-ASN : angle 3.81114 ( 63) link_BETA1-4 : bond 0.00319 ( 2) link_BETA1-4 : angle 1.44658 ( 6) hydrogen bonds : bond 0.05158 ( 1019) hydrogen bonds : angle 5.14447 ( 2823) SS BOND : bond 0.00379 ( 42) SS BOND : angle 2.06748 ( 84) covalent geometry : bond 0.00221 (27014) covalent geometry : angle 0.53928 (36754) Misc. bond : bond 0.00189 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 2.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 ASN cc_start: 0.8337 (t0) cc_final: 0.8098 (t0) REVERT: A 858 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8856 (pp) REVERT: B 204 TYR cc_start: 0.8577 (m-80) cc_final: 0.8369 (m-80) REVERT: B 392 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.5802 (p90) REVERT: C 902 MET cc_start: 0.9057 (tpt) cc_final: 0.8630 (tpt) REVERT: C 1100 THR cc_start: 0.7166 (t) cc_final: 0.6920 (m) REVERT: D 28 VAL cc_start: 0.0733 (OUTLIER) cc_final: 0.0512 (p) REVERT: D 35 TRP cc_start: 0.5331 (t-100) cc_final: 0.4797 (t-100) REVERT: D 157 TRP cc_start: 0.7163 (m-90) cc_final: 0.6933 (m-90) outliers start: 27 outliers final: 11 residues processed: 112 average time/residue: 0.3518 time to fit residues: 67.0195 Evaluate side-chains 99 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 83 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 177 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 212 optimal weight: 20.0000 chunk 232 optimal weight: 9.9990 chunk 150 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 36 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 311 optimal weight: 40.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.098880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.070041 restraints weight = 105074.956| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 4.00 r_work: 0.2943 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27080 Z= 0.154 Angle : 0.578 19.714 36907 Z= 0.290 Chirality : 0.045 0.284 4250 Planarity : 0.004 0.045 4713 Dihedral : 5.979 59.646 4068 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.09 % Allowed : 11.07 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.10 (0.15), residues: 3281 helix: 2.12 (0.21), residues: 656 sheet: 0.26 (0.19), residues: 828 loop : -1.10 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 886 HIS 0.006 0.001 HIS B1058 PHE 0.017 0.001 PHE A 906 TYR 0.022 0.001 TYR C 351 ARG 0.006 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 21) link_NAG-ASN : angle 3.78867 ( 63) link_BETA1-4 : bond 0.00319 ( 2) link_BETA1-4 : angle 1.55172 ( 6) hydrogen bonds : bond 0.05836 ( 1019) hydrogen bonds : angle 5.18365 ( 2823) SS BOND : bond 0.00450 ( 42) SS BOND : angle 1.65818 ( 84) covalent geometry : bond 0.00359 (27014) covalent geometry : angle 0.55170 (36754) Misc. bond : bond 0.00323 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 3.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 ASN cc_start: 0.8291 (t0) cc_final: 0.8080 (t0) REVERT: A 858 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8898 (pp) REVERT: A 906 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8426 (t80) REVERT: B 392 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.5764 (p90) REVERT: C 347 PHE cc_start: 0.6057 (m-10) cc_final: 0.5527 (m-80) REVERT: C 902 MET cc_start: 0.9157 (tpt) cc_final: 0.8683 (tpt) REVERT: C 1100 THR cc_start: 0.7201 (t) cc_final: 0.6942 (m) REVERT: D 35 TRP cc_start: 0.5136 (t-100) cc_final: 0.4656 (t-100) REVERT: D 88 CYS cc_start: 0.5328 (OUTLIER) cc_final: 0.5024 (p) REVERT: D 157 TRP cc_start: 0.7208 (m-90) cc_final: 0.6985 (m-90) outliers start: 32 outliers final: 20 residues processed: 112 average time/residue: 0.4477 time to fit residues: 87.8616 Evaluate side-chains 103 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 83 PHE Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 242 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 310 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 168 optimal weight: 0.0070 chunk 102 optimal weight: 10.0000 chunk 242 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 251 optimal weight: 7.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 GLN ** 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 = 0.3931 r_free = 0.3931 target = 0.088493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.055654 restraints weight = 107868.814| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.94 r_work: 0.2949 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 27080 Z= 0.195 Angle : 0.598 19.809 36907 Z= 0.302 Chirality : 0.046 0.289 4250 Planarity : 0.004 0.046 4713 Dihedral : 6.186 59.916 4068 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.37 % Allowed : 11.14 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.20 (0.15), residues: 3281 helix: 2.01 (0.21), residues: 656 sheet: 0.23 (0.18), residues: 839 loop : -1.17 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.005 0.001 HIS B1058 PHE 0.022 0.001 PHE A 906 TYR 0.022 0.001 TYR A1067 ARG 0.004 0.000 ARG D 173 Details of bonding type rmsd link_NAG-ASN : bond 0.00613 ( 21) link_NAG-ASN : angle 3.83696 ( 63) link_BETA1-4 : bond 0.00344 ( 2) link_BETA1-4 : angle 1.71725 ( 6) hydrogen bonds : bond 0.06461 ( 1019) hydrogen bonds : angle 5.30042 ( 2823) SS BOND : bond 0.00516 ( 42) SS BOND : angle 1.29951 ( 84) covalent geometry : bond 0.00463 (27014) covalent geometry : angle 0.57374 (36754) Misc. bond : bond 0.00398 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 83 time to evaluate : 3.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 ASN cc_start: 0.8335 (t0) cc_final: 0.8124 (t0) REVERT: A 858 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8898 (pp) REVERT: A 906 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8389 (t80) REVERT: B 392 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.6004 (p90) REVERT: C 493 GLN cc_start: 0.6864 (mm-40) cc_final: 0.6619 (mm110) REVERT: C 902 MET cc_start: 0.9107 (tpt) cc_final: 0.8671 (tpt) REVERT: C 1100 THR cc_start: 0.7240 (t) cc_final: 0.6969 (m) REVERT: D 35 TRP cc_start: 0.5128 (t-100) cc_final: 0.4715 (t-100) outliers start: 40 outliers final: 26 residues processed: 117 average time/residue: 0.3404 time to fit residues: 69.5768 Evaluate side-chains 105 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 83 PHE Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 242 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 256 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 chunk 30 optimal weight: 0.0670 chunk 22 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 294 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.100551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.068916 restraints weight = 104984.752| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.53 r_work: 0.2998 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27080 Z= 0.102 Angle : 0.538 19.708 36907 Z= 0.269 Chirality : 0.045 0.397 4250 Planarity : 0.004 0.046 4713 Dihedral : 5.808 59.016 4068 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.96 % Allowed : 11.86 % Favored : 87.18 % 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: 0.03 (0.15), residues: 3281 helix: 2.33 (0.21), residues: 647 sheet: 0.35 (0.18), residues: 829 loop : -1.04 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 157 HIS 0.002 0.000 HIS C1048 PHE 0.010 0.001 PHE A 782 TYR 0.016 0.001 TYR C 351 ARG 0.009 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00674 ( 21) link_NAG-ASN : angle 3.78409 ( 63) link_BETA1-4 : bond 0.00358 ( 2) link_BETA1-4 : angle 1.44463 ( 6) hydrogen bonds : bond 0.05094 ( 1019) hydrogen bonds : angle 4.98561 ( 2823) SS BOND : bond 0.00403 ( 42) SS BOND : angle 0.99008 ( 84) covalent geometry : bond 0.00217 (27014) covalent geometry : angle 0.51308 (36754) Misc. bond : bond 0.00188 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 2.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 858 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8882 (pp) REVERT: B 392 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.6081 (p90) REVERT: C 1100 THR cc_start: 0.7114 (t) cc_final: 0.6854 (m) REVERT: D 35 TRP cc_start: 0.4827 (t-100) cc_final: 0.4398 (t-100) REVERT: D 231 PHE cc_start: 0.5618 (m-80) cc_final: 0.5294 (m-80) outliers start: 28 outliers final: 18 residues processed: 102 average time/residue: 0.3408 time to fit residues: 60.4025 Evaluate side-chains 96 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 83 PHE Chi-restraints excluded: chain F residue 242 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 47 optimal weight: 3.9990 chunk 330 optimal weight: 50.0000 chunk 139 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 147 optimal weight: 0.7980 chunk 258 optimal weight: 0.9990 chunk 255 optimal weight: 5.9990 chunk 247 optimal weight: 10.0000 chunk 149 optimal weight: 0.4980 chunk 208 optimal weight: 9.9990 chunk 293 optimal weight: 40.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 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 = 0.3954 r_free = 0.3954 target = 0.095249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.065017 restraints weight = 83708.501| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 4.07 r_work: 0.2961 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27080 Z= 0.102 Angle : 0.529 19.595 36907 Z= 0.263 Chirality : 0.044 0.359 4250 Planarity : 0.004 0.046 4713 Dihedral : 5.619 57.334 4068 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.13 % Allowed : 11.86 % Favored : 87.01 % 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: 0.14 (0.15), residues: 3281 helix: 2.39 (0.21), residues: 655 sheet: 0.43 (0.18), residues: 848 loop : -0.99 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 157 HIS 0.003 0.000 HIS B1058 PHE 0.020 0.001 PHE D 219 TYR 0.018 0.001 TYR C 421 ARG 0.002 0.000 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00659 ( 21) link_NAG-ASN : angle 3.70123 ( 63) link_BETA1-4 : bond 0.00297 ( 2) link_BETA1-4 : angle 1.32834 ( 6) hydrogen bonds : bond 0.04869 ( 1019) hydrogen bonds : angle 4.87109 ( 2823) SS BOND : bond 0.00286 ( 42) SS BOND : angle 0.99077 ( 84) covalent geometry : bond 0.00223 (27014) covalent geometry : angle 0.50500 (36754) Misc. bond : bond 0.00184 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 858 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8894 (pp) REVERT: B 392 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6102 (p90) REVERT: C 1100 THR cc_start: 0.7219 (t) cc_final: 0.6983 (m) REVERT: D 35 TRP cc_start: 0.4947 (t-100) cc_final: 0.4490 (t-100) REVERT: D 231 PHE cc_start: 0.5641 (m-80) cc_final: 0.5042 (m-80) outliers start: 33 outliers final: 27 residues processed: 116 average time/residue: 0.3583 time to fit residues: 71.4751 Evaluate side-chains 109 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 83 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 99 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 139 optimal weight: 0.9990 chunk 250 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 308 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 chunk 321 optimal weight: 0.2980 chunk 146 optimal weight: 10.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 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 = 0.3947 r_free = 0.3947 target = 0.101174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.068664 restraints weight = 103956.024| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.71 r_work: 0.2953 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27080 Z= 0.142 Angle : 0.556 19.639 36907 Z= 0.279 Chirality : 0.045 0.287 4250 Planarity : 0.004 0.045 4713 Dihedral : 5.765 59.723 4068 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.09 % Allowed : 11.96 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.04 (0.15), residues: 3281 helix: 2.31 (0.21), residues: 649 sheet: 0.30 (0.18), residues: 856 loop : -1.01 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.002 TRP D 170 HIS 0.005 0.001 HIS B1058 PHE 0.017 0.001 PHE D 219 TYR 0.021 0.001 TYR C 421 ARG 0.005 0.000 ARG D 173 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 21) link_NAG-ASN : angle 3.71680 ( 63) link_BETA1-4 : bond 0.00284 ( 2) link_BETA1-4 : angle 1.40797 ( 6) hydrogen bonds : bond 0.05614 ( 1019) hydrogen bonds : angle 5.00644 ( 2823) SS BOND : bond 0.00391 ( 42) SS BOND : angle 1.07689 ( 84) covalent geometry : bond 0.00329 (27014) covalent geometry : angle 0.53281 (36754) Misc. bond : bond 0.00280 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 3.354 Fit side-chains revert: symmetry clash REVERT: A 858 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8893 (pp) REVERT: B 392 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.6371 (p90) REVERT: C 1100 THR cc_start: 0.7227 (t) cc_final: 0.6974 (m) REVERT: D 35 TRP cc_start: 0.4852 (t-100) cc_final: 0.4394 (t-100) REVERT: D 231 PHE cc_start: 0.5666 (m-80) cc_final: 0.5268 (m-80) outliers start: 32 outliers final: 27 residues processed: 102 average time/residue: 0.3831 time to fit residues: 69.1751 Evaluate side-chains 104 residues out of total 2926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 83 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 31 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 37 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 285 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 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 = 0.3942 r_free = 0.3942 target = 0.098745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.067098 restraints weight = 76717.377| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 4.22 r_work: 0.2931 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 27080 Z= 0.156 Angle : 0.568 19.710 36907 Z= 0.285 Chirality : 0.045 0.289 4250 Planarity : 0.004 0.047 4713 Dihedral : 5.816 59.647 4068 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.06 % Allowed : 12.10 % Favored : 86.84 % 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: -0.05 (0.15), residues: 3281 helix: 2.18 (0.21), residues: 657 sheet: 0.19 (0.18), residues: 860 loop : -1.03 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 436 HIS 0.004 0.001 HIS B1058 PHE 0.020 0.001 PHE D 219 TYR 0.020 0.001 TYR A1067 ARG 0.004 0.000 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 21) link_NAG-ASN : angle 3.75765 ( 63) link_BETA1-4 : bond 0.00308 ( 2) link_BETA1-4 : angle 1.44441 ( 6) hydrogen bonds : bond 0.05770 ( 1019) hydrogen bonds : angle 5.06250 ( 2823) SS BOND : bond 0.00423 ( 42) SS BOND : angle 1.62815 ( 84) covalent geometry : bond 0.00367 (27014) covalent geometry : angle 0.54115 (36754) Misc. bond : bond 0.00304 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17706.98 seconds wall clock time: 306 minutes 0.14 seconds (18360.14 seconds total)