Starting phenix.real_space_refine on Fri Mar 6 15:36:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpe_32684/03_2026/7wpe_32684_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpe_32684/03_2026/7wpe_32684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wpe_32684/03_2026/7wpe_32684_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpe_32684/03_2026/7wpe_32684_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wpe_32684/03_2026/7wpe_32684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpe_32684/03_2026/7wpe_32684.map" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 135 5.16 5 C 20408 2.51 5 N 5282 2.21 5 O 6213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32038 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 7701 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 968} Chain breaks: 7 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 9, 'ASN:plan1': 9, 'GLU:plan': 9, 'PHE:plan': 2, 'ARG:plan': 6, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 185 Chain: "B" Number of atoms: 7681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7681 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 52, 'TRANS': 971} Chain breaks: 7 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 430 Unresolved non-hydrogen dihedrals: 293 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 9, 'ASN:plan1': 5, 'GLU:plan': 9, 'PHE:plan': 3, 'ARG:plan': 7, 'TYR:plan': 5, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 194 Chain: "C" Number of atoms: 7642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7642 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 971} Chain breaks: 7 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 14, 'PHE:plan': 2, 'GLN:plan1': 8, 'ASN:plan1': 7, 'ARG:plan': 8, 'TYR:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 226 Chain: "X" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1665 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 212} Chain: "Y" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 202} Chain: "Z" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "U" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1665 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 212} Chain: "V" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Chain: "W" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "D" 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: "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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 7.70, per 1000 atoms: 0.24 Number of scatterers: 32038 At special positions: 0 Unit cell: (194.464, 140.904, 233.192, 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 135 16.00 O 6213 8.00 N 5282 7.00 C 20408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 364 " distance=1.91 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 435 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 491 " distance=2.03 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 593 " distance=2.04 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 652 " distance=2.03 Simple disulfide: pdb=" SG CYS A 665 " - pdb=" SG CYS A 674 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 763 " distance=1.85 Simple disulfide: pdb=" SG CYS A 746 " - pdb=" SG CYS A 752 " distance=2.04 Simple disulfide: pdb=" SG CYS A1035 " - pdb=" SG CYS A1046 " distance=2.03 Simple disulfide: pdb=" SG CYS A1085 " - pdb=" SG CYS A1129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 304 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 364 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 435 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 483 " - pdb=" SG CYS B 491 " distance=2.04 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 593 " distance=2.04 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 652 " distance=2.03 Simple disulfide: pdb=" SG CYS B 665 " - pdb=" SG CYS B 674 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 763 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 752 " distance=2.03 Simple disulfide: pdb=" SG CYS B1035 " - pdb=" SG CYS B1046 " distance=2.03 Simple disulfide: pdb=" SG CYS B1085 " - pdb=" SG CYS B1129 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 294 " - pdb=" SG CYS C 304 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 364 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 435 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 528 " distance=2.03 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 491 " distance=2.03 Simple disulfide: pdb=" SG CYS C 541 " - pdb=" SG CYS C 593 " distance=1.52 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 652 " distance=2.03 Simple disulfide: pdb=" SG CYS C 665 " - pdb=" SG CYS C 674 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 763 " distance=2.03 Simple disulfide: pdb=" SG CYS C 746 " - pdb=" SG CYS C 752 " distance=2.03 Simple disulfide: pdb=" SG CYS C1035 " - pdb=" SG CYS C1046 " distance=2.03 Simple disulfide: pdb=" SG CYS C1085 " - pdb=" SG CYS C1129 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.03 Simple disulfide: pdb=" SG CYS X 150 " - pdb=" SG CYS X 206 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 290 " - pdb=" SG CYS Y 355 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 401 " - pdb=" SG CYS Y 461 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 31 " - pdb=" SG CYS Z 105 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS U 150 " - pdb=" SG CYS U 206 " distance=2.03 Simple disulfide: pdb=" SG CYS V 290 " - pdb=" SG CYS V 355 " distance=2.03 Simple disulfide: pdb=" SG CYS V 401 " - pdb=" SG CYS V 461 " distance=2.03 Simple disulfide: pdb=" SG CYS W 31 " - pdb=" SG CYS W 105 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1301 " - " ASN A 660 " " NAG A1302 " - " ASN A 334 " " NAG A1303 " - " ASN A 237 " " NAG A1304 " - " ASN A 606 " " NAG A1305 " - " ASN A1077 " " NAG A1306 " - " ASN A1137 " " NAG A1307 " - " ASN A1101 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 619 " " NAG A1310 " - " ASN A 712 " " NAG A1311 " - " ASN A 804 " " NAG A1312 " - " ASN A 285 " " NAG B1301 " - " ASN B1077 " " NAG B1302 " - " ASN B 237 " " NAG B1303 " - " ASN B 285 " " NAG B1304 " - " ASN B1101 " " NAG B1305 " - " ASN B 804 " " NAG B1306 " - " ASN B 712 " " NAG B1307 " - " ASN B 660 " " NAG B1308 " - " ASN B 619 " " NAG B1309 " - " ASN B 606 " " NAG B1310 " - " ASN B 334 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B1137 " " NAG C1301 " - " ASN C 606 " " NAG C1302 " - " ASN C 285 " " NAG C1303 " - " ASN C 660 " " NAG C1304 " - " ASN C 334 " " NAG C1305 " - " ASN C1137 " " NAG C1306 " - " ASN C 237 " " NAG C1307 " - " ASN C 712 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C1101 " " NAG C1310 " - " ASN C 804 " " NAG C1311 " - " ASN C1077 " " NAG C1312 " - " ASN C 619 " " NAG D 1 " - " ASN A 720 " " NAG E 1 " - " ASN B 720 " Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.3 seconds 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7802 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 70 sheets defined 20.6% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.728A pdb=" N GLN A 115 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 340 through 346 removed outlier: 3.789A pdb=" N VAL A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 386 through 392 removed outlier: 4.478A pdb=" N ASN A 391 " --> pdb=" O THR A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.997A pdb=" N ARG A 411 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 425 removed outlier: 3.535A pdb=" N ASN A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 574 No H-bonds generated for 'chain 'A' and resid 572 through 574' Processing helix chain 'A' and resid 740 through 747 Processing helix chain 'A' and resid 749 through 757 removed outlier: 3.602A pdb=" N SER A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN A 754 " --> pdb=" O THR A 750 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A 755 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 757 " --> pdb=" O SER A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 760 No H-bonds generated for 'chain 'A' and resid 758 through 760' Processing helix chain 'A' and resid 761 through 786 Processing helix chain 'A' and resid 819 through 829 removed outlier: 3.702A pdb=" N VAL A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 888 Processing helix chain 'A' and resid 889 through 893 Processing helix chain 'A' and resid 900 through 912 removed outlier: 3.611A pdb=" N ILE A 912 " --> pdb=" O ARG A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 922 through 944 removed outlier: 3.691A pdb=" N GLN A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP A 939 " --> pdb=" O GLY A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 968 Processing helix chain 'A' and resid 969 through 971 No H-bonds generated for 'chain 'A' and resid 969 through 971' Processing helix chain 'A' and resid 979 through 987 Processing helix chain 'A' and resid 988 through 1036 removed outlier: 4.493A pdb=" N VAL A 994 " --> pdb=" O PRO A 990 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN A 995 " --> pdb=" O GLU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1148 removed outlier: 4.050A pdb=" N GLU A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 340 through 348 removed outlier: 3.873A pdb=" N ASN B 346 " --> pdb=" O ASP B 342 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR B 348 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 393 removed outlier: 3.865A pdb=" N LEU B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN B 391 " --> pdb=" O PRO B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.801A pdb=" N ILE B 413 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 740 through 746 Processing helix chain 'B' and resid 749 through 757 Processing helix chain 'B' and resid 758 through 760 No H-bonds generated for 'chain 'B' and resid 758 through 760' Processing helix chain 'B' and resid 761 through 786 Processing helix chain 'B' and resid 819 through 829 Processing helix chain 'B' and resid 869 through 888 Processing helix chain 'B' and resid 889 through 893 Processing helix chain 'B' and resid 900 through 912 Processing helix chain 'B' and resid 916 through 921 Processing helix chain 'B' and resid 922 through 944 Processing helix chain 'B' and resid 948 through 968 removed outlier: 4.334A pdb=" N VAL B 954 " --> pdb=" O LYS B 950 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL B 955 " --> pdb=" O LEU B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 971 No H-bonds generated for 'chain 'B' and resid 969 through 971' Processing helix chain 'B' and resid 979 through 987 Processing helix chain 'B' and resid 988 through 1036 removed outlier: 4.591A pdb=" N VAL B 994 " --> pdb=" O PRO B 990 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN B 995 " --> pdb=" O GLU B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1149 removed outlier: 4.251A pdb=" N GLU B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 340 through 346 Processing helix chain 'C' and resid 367 through 374 Processing helix chain 'C' and resid 386 through 392 removed outlier: 4.372A pdb=" N ASN C 391 " --> pdb=" O THR C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 413 removed outlier: 3.811A pdb=" N VAL C 410 " --> pdb=" O GLY C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 425 Processing helix chain 'C' and resid 480 through 484 Processing helix chain 'C' and resid 740 through 747 Processing helix chain 'C' and resid 749 through 757 removed outlier: 3.779A pdb=" N LEU C 755 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU C 757 " --> pdb=" O SER C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 760 No H-bonds generated for 'chain 'C' and resid 758 through 760' Processing helix chain 'C' and resid 761 through 786 removed outlier: 3.546A pdb=" N GLN C 777 " --> pdb=" O ILE C 773 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP C 778 " --> pdb=" O ALA C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 829 removed outlier: 3.775A pdb=" N VAL C 829 " --> pdb=" O LEU C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 887 Processing helix chain 'C' and resid 888 through 893 removed outlier: 3.822A pdb=" N PHE C 891 " --> pdb=" O GLY C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 912 Processing helix chain 'C' and resid 916 through 921 Processing helix chain 'C' and resid 922 through 944 Processing helix chain 'C' and resid 948 through 969 removed outlier: 4.393A pdb=" N VAL C 954 " --> pdb=" O LYS C 950 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 969 " --> pdb=" O LEU C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 987 Processing helix chain 'C' and resid 988 through 1036 removed outlier: 4.360A pdb=" N VAL C 994 " --> pdb=" O PRO C 990 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN C 995 " --> pdb=" O GLU C 991 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 32 Processing helix chain 'X' and resid 62 through 65 removed outlier: 3.671A pdb=" N GLN X 65 " --> pdb=" O GLN X 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 62 through 65' Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'X' and resid 137 through 141 Processing helix chain 'X' and resid 166 through 168 No H-bonds generated for 'chain 'X' and resid 166 through 168' Processing helix chain 'Y' and resid 346 through 350 Processing helix chain 'Y' and resid 388 through 393 Processing helix chain 'Y' and resid 417 through 420 Processing helix chain 'Y' and resid 450 through 456 removed outlier: 3.692A pdb=" N HIS Y 456 " --> pdb=" O ASP Y 452 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 32 Processing helix chain 'U' and resid 87 through 91 Processing helix chain 'U' and resid 137 through 141 Processing helix chain 'U' and resid 166 through 168 No H-bonds generated for 'chain 'U' and resid 166 through 168' Processing helix chain 'U' and resid 197 through 202 removed outlier: 4.486A pdb=" N THR U 201 " --> pdb=" O SER U 197 " (cutoff:3.500A) Processing helix chain 'V' and resid 346 through 350 removed outlier: 3.658A pdb=" N ILE V 350 " --> pdb=" O PRO V 347 " (cutoff:3.500A) Processing helix chain 'V' and resid 388 through 393 Processing helix chain 'V' and resid 417 through 420 Processing helix chain 'V' and resid 450 through 456 removed outlier: 3.730A pdb=" N HIS V 456 " --> pdb=" O ASP V 452 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.239A pdb=" N ASN A 61 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR A 272 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE A 201 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP A 231 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE A 203 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N HIS A 207 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N ALA A 225 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL A 36 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.985A pdb=" N ASP A 290 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.883A pdb=" N GLY A 103 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 314 through 322 removed outlier: 7.317A pdb=" N VAL A 598 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN A 320 " --> pdb=" O GLY A 596 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLY A 596 " --> pdb=" O ASN A 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 327 through 331 removed outlier: 4.222A pdb=" N GLU A 327 " --> pdb=" O CYS A 541 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASP A 577 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA A 578 " --> pdb=" O GLY A 569 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 361 removed outlier: 3.647A pdb=" N ASN A 357 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASN A 397 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 364 through 365 removed outlier: 6.497A pdb=" N CYS A 364 " --> pdb=" O CYS A 528 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 455 through 457 Processing sheet with id=AB1, first strand: chain 'A' and resid 657 through 658 removed outlier: 6.166A pdb=" N GLU A 657 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N THR A 699 " --> pdb=" O GLU A 657 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE A 673 " --> pdb=" O ILE A 669 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 705 through 706 Processing sheet with id=AB3, first strand: chain 'A' and resid 714 through 731 removed outlier: 6.536A pdb=" N SER A 714 " --> pdb=" O THR A1079 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR A1079 " --> pdb=" O SER A 714 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA A 716 " --> pdb=" O ASN A1077 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASN A1077 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLU A1075 " --> pdb=" O PRO A 718 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N TYR A1070 " --> pdb=" O HIS A1051 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N HIS A1051 " --> pdb=" O TYR A1070 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 714 through 731 removed outlier: 6.536A pdb=" N SER A 714 " --> pdb=" O THR A1079 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR A1079 " --> pdb=" O SER A 714 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA A 716 " --> pdb=" O ASN A1077 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASN A1077 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLU A1075 " --> pdb=" O PRO A 718 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 736 through 739 removed outlier: 4.268A pdb=" N LYS A 736 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 791 through 793 Processing sheet with id=AB7, first strand: chain 'A' and resid 1123 through 1128 removed outlier: 5.507A pdb=" N VAL A1125 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N PHE A1092 " --> pdb=" O VAL A1125 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY A1127 " --> pdb=" O ALA A1090 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.211A pdb=" N ASN B 61 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N TYR B 272 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 267 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE B 201 " --> pdb=" O ASP B 231 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP B 231 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 203 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N HIS B 207 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N ALA B 225 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 36 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.976A pdb=" N ASP B 290 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.800A pdb=" N GLY B 103 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 134 through 135 removed outlier: 7.092A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 314 through 322 removed outlier: 7.258A pdb=" N VAL B 598 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASN B 320 " --> pdb=" O GLY B 596 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLY B 596 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY B 597 " --> pdb=" O GLN B 616 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 327 through 328 removed outlier: 6.617A pdb=" N GLU B 327 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP B 577 " --> pdb=" O ILE B 590 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 578 " --> pdb=" O GLY B 569 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 357 through 362 removed outlier: 3.577A pdb=" N ASN B 357 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B 402 " --> pdb=" O ASN B 357 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN B 397 " --> pdb=" O GLU B 519 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N CYS B 435 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 438 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 364 through 365 removed outlier: 6.310A pdb=" N CYS B 364 " --> pdb=" O CYS B 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 455 through 457 Processing sheet with id=AC8, first strand: chain 'B' and resid 657 through 658 removed outlier: 6.692A pdb=" N ILE B 673 " --> pdb=" O ILE B 669 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 704 through 707 Processing sheet with id=AD1, first strand: chain 'B' and resid 714 through 731 removed outlier: 6.791A pdb=" N GLN B1074 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE B 721 " --> pdb=" O PRO B1072 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE B 723 " --> pdb=" O TYR B1070 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TYR B1070 " --> pdb=" O ILE B 723 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL B 725 " --> pdb=" O VAL B1068 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B1068 " --> pdb=" O VAL B 725 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR B 727 " --> pdb=" O LEU B1066 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU B1066 " --> pdb=" O THR B 727 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE B 729 " --> pdb=" O VAL B1064 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL B1064 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLY B1062 " --> pdb=" O PRO B 731 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR B1070 " --> pdb=" O HIS B1051 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS B1051 " --> pdb=" O TYR B1070 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 714 through 731 removed outlier: 6.791A pdb=" N GLN B1074 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE B 721 " --> pdb=" O PRO B1072 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE B 723 " --> pdb=" O TYR B1070 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TYR B1070 " --> pdb=" O ILE B 723 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL B 725 " --> pdb=" O VAL B1068 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B1068 " --> pdb=" O VAL B 725 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR B 727 " --> pdb=" O LEU B1066 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU B1066 " --> pdb=" O THR B 727 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE B 729 " --> pdb=" O VAL B1064 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL B1064 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLY B1062 " --> pdb=" O PRO B 731 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 736 through 739 removed outlier: 4.180A pdb=" N LYS B 736 " --> pdb=" O LEU B 864 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1123 through 1128 removed outlier: 4.390A pdb=" N ALA B1090 " --> pdb=" O SER B1126 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.255A pdb=" N ASN C 61 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR C 272 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE C 201 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP C 231 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE C 203 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.920A pdb=" N ASP C 290 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.236A pdb=" N ASP C 142 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.607A pdb=" N GLY C 103 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA C 246 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE C 101 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 134 through 135 removed outlier: 3.656A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 314 through 322 removed outlier: 5.398A pdb=" N ILE C 315 " --> pdb=" O THR C 602 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR C 602 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLN C 317 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL C 600 " --> pdb=" O GLN C 317 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER C 319 " --> pdb=" O VAL C 598 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY C 597 " --> pdb=" O GLN C 616 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 328 through 331 Processing sheet with id=AE3, first strand: chain 'C' and resid 360 through 361 removed outlier: 4.028A pdb=" N VAL C 398 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASN C 397 " --> pdb=" O GLU C 519 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER C 517 " --> pdb=" O TYR C 399 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 401 " --> pdb=" O VAL C 515 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA C 438 " --> pdb=" O PHE C 378 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 360 through 361 removed outlier: 4.028A pdb=" N VAL C 398 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASN C 397 " --> pdb=" O GLU C 519 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER C 517 " --> pdb=" O TYR C 399 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 401 " --> pdb=" O VAL C 515 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 364 through 365 removed outlier: 6.469A pdb=" N CYS C 364 " --> pdb=" O CYS C 528 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 455 through 457 Processing sheet with id=AE7, first strand: chain 'C' and resid 476 through 477 Processing sheet with id=AE8, first strand: chain 'C' and resid 657 through 658 removed outlier: 6.086A pdb=" N GLU C 657 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N THR C 699 " --> pdb=" O GLU C 657 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE C 673 " --> pdb=" O ILE C 669 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 715 through 731 removed outlier: 6.770A pdb=" N GLN C1074 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE C 721 " --> pdb=" O PRO C1072 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE C 723 " --> pdb=" O TYR C1070 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR C1070 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL C 725 " --> pdb=" O VAL C1068 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL C1068 " --> pdb=" O VAL C 725 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR C 727 " --> pdb=" O LEU C1066 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU C1066 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE C 729 " --> pdb=" O VAL C1064 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL C1064 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLY C1062 " --> pdb=" O PRO C 731 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLY C1062 " --> pdb=" O SER C1058 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N SER C1058 " --> pdb=" O GLY C1062 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL C1064 " --> pdb=" O PRO C1056 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU C1066 " --> pdb=" O SER C1054 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER C1054 " --> pdb=" O LEU C1066 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL C1068 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 736 through 739 removed outlier: 4.266A pdb=" N LYS C 736 " --> pdb=" O LEU C 864 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1123 through 1125 Processing sheet with id=AF3, first strand: chain 'C' and resid 1097 through 1099 Processing sheet with id=AF4, first strand: chain 'X' and resid 3 through 6 removed outlier: 3.526A pdb=" N VAL X 20 " --> pdb=" O MET X 81 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'X' and resid 10 through 12 removed outlier: 3.708A pdb=" N THR X 120 " --> pdb=" O GLU X 10 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS X 12 " --> pdb=" O THR X 120 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE X 34 " --> pdb=" O ARG X 50 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ARG X 50 " --> pdb=" O ILE X 34 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TRP X 36 " --> pdb=" O MET X 48 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N MET X 48 " --> pdb=" O TRP X 36 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 130 through 133 removed outlier: 6.244A pdb=" N TYR X 186 " --> pdb=" O ASP X 154 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER X 187 " --> pdb=" O ALA X 178 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA X 178 " --> pdb=" O SER X 187 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER X 189 " --> pdb=" O PHE X 176 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'X' and resid 161 through 164 Processing sheet with id=AF8, first strand: chain 'Y' and resid 272 through 274 removed outlier: 3.628A pdb=" N THR Y 289 " --> pdb=" O SER Y 274 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N THR Y 336 " --> pdb=" O ALA Y 292 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N GLN Y 294 " --> pdb=" O SER Y 334 " (cutoff:3.500A) removed outlier: 9.564A pdb=" N SER Y 334 " --> pdb=" O GLN Y 294 " (cutoff:3.500A) removed outlier: 11.252A pdb=" N ILE Y 296 " --> pdb=" O SER Y 332 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N SER Y 332 " --> pdb=" O ILE Y 296 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Y' and resid 277 through 280 removed outlier: 5.775A pdb=" N LEU Y 300 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP Y 317 " --> pdb=" O LEU Y 300 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLN Y 304 " --> pdb=" O LEU Y 313 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU Y 313 " --> pdb=" O GLN Y 304 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP Y 317 " --> pdb=" O ASN Y 320 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Y' and resid 277 through 280 removed outlier: 3.727A pdb=" N THR Y 364 " --> pdb=" O GLN Y 357 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Y' and resid 381 through 385 removed outlier: 5.489A pdb=" N TYR Y 440 " --> pdb=" O ASN Y 405 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Y' and resid 413 through 415 Processing sheet with id=AG4, first strand: chain 'Z' and resid 14 through 17 removed outlier: 3.642A pdb=" N GLN Z 14 " --> pdb=" O ALA Z 32 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU Z 29 " --> pdb=" O LEU Z 90 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU Z 90 " --> pdb=" O LEU Z 29 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR Z 78 " --> pdb=" O GLN Z 91 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Z' and resid 19 through 21 removed outlier: 5.778A pdb=" N TRP Z 120 " --> pdb=" O ILE Z 107 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE Z 107 " --> pdb=" O TRP Z 120 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN Z 122 " --> pdb=" O CYS Z 105 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA Z 42 " --> pdb=" O ASP Z 108 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N MET Z 43 " --> pdb=" O VAL Z 59 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL Z 59 " --> pdb=" O MET Z 43 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP Z 45 " --> pdb=" O VAL Z 57 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE Z 68 " --> pdb=" O VAL Z 59 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'U' and resid 2 through 6 removed outlier: 3.515A pdb=" N CYS U 22 " --> pdb=" O ALA U 79 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA U 79 " --> pdb=" O CYS U 22 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'U' and resid 10 through 12 removed outlier: 3.698A pdb=" N THR U 120 " --> pdb=" O GLU U 10 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS U 12 " --> pdb=" O THR U 120 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE U 34 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ARG U 50 " --> pdb=" O ILE U 34 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TRP U 36 " --> pdb=" O MET U 48 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 130 through 133 removed outlier: 5.977A pdb=" N TYR U 186 " --> pdb=" O ASP U 154 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER U 187 " --> pdb=" O ALA U 178 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA U 178 " --> pdb=" O SER U 187 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER U 189 " --> pdb=" O PHE U 176 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'U' and resid 161 through 164 Processing sheet with id=AH1, first strand: chain 'V' and resid 271 through 274 removed outlier: 5.819A pdb=" N THR V 336 " --> pdb=" O ALA V 292 " (cutoff:3.500A) removed outlier: 10.065A pdb=" N GLN V 294 " --> pdb=" O SER V 334 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N SER V 334 " --> pdb=" O GLN V 294 " (cutoff:3.500A) removed outlier: 12.098A pdb=" N ILE V 296 " --> pdb=" O SER V 332 " (cutoff:3.500A) removed outlier: 12.508A pdb=" N SER V 332 " --> pdb=" O ILE V 296 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'V' and resid 277 through 280 removed outlier: 3.742A pdb=" N ALA V 351 " --> pdb=" O VAL V 371 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP V 302 " --> pdb=" O LEU V 314 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'V' and resid 277 through 280 removed outlier: 3.742A pdb=" N ALA V 351 " --> pdb=" O VAL V 371 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN V 357 " --> pdb=" O THR V 364 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR V 364 " --> pdb=" O GLN V 357 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'V' and resid 381 through 385 removed outlier: 5.204A pdb=" N TYR V 440 " --> pdb=" O ASN V 405 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'V' and resid 412 through 415 removed outlier: 3.916A pdb=" N LYS V 412 " --> pdb=" O THR V 464 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR V 464 " --> pdb=" O LYS V 412 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'W' and resid 14 through 17 removed outlier: 3.528A pdb=" N GLN W 14 " --> pdb=" O ALA W 32 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'W' and resid 19 through 21 removed outlier: 5.810A pdb=" N TRP W 120 " --> pdb=" O ILE W 107 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE W 107 " --> pdb=" O TRP W 120 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN W 122 " --> pdb=" O CYS W 105 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA W 42 " --> pdb=" O ASP W 108 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N MET W 43 " --> pdb=" O VAL W 59 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL W 59 " --> pdb=" O MET W 43 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP W 45 " --> pdb=" O VAL W 57 " (cutoff:3.500A) 1337 hydrogen bonds defined for protein. 3570 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: 9.18 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10211 1.34 - 1.47: 8383 1.47 - 1.59: 14004 1.59 - 1.72: 1 1.72 - 1.85: 170 Bond restraints: 32769 Sorted by residual: bond pdb=" CA SER U 104 " pdb=" CB SER U 104 " ideal model delta sigma weight residual 1.524 1.471 0.054 1.22e-02 6.72e+03 1.93e+01 bond pdb=" N SER U 101 " pdb=" CA SER U 101 " ideal model delta sigma weight residual 1.457 1.513 -0.055 1.29e-02 6.01e+03 1.83e+01 bond pdb=" N GLU U 107 " pdb=" CA GLU U 107 " ideal model delta sigma weight residual 1.454 1.500 -0.046 1.18e-02 7.18e+03 1.52e+01 bond pdb=" CA SER U 103 " pdb=" CB SER U 103 " ideal model delta sigma weight residual 1.538 1.498 0.040 1.22e-02 6.72e+03 1.06e+01 bond pdb=" N ASP U 108 " pdb=" CA ASP U 108 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.69e+00 ... (remaining 32764 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 44435 3.11 - 6.23: 244 6.23 - 9.34: 16 9.34 - 12.46: 7 12.46 - 15.57: 2 Bond angle restraints: 44704 Sorted by residual: angle pdb=" N PRO X 177 " pdb=" CA PRO X 177 " pdb=" C PRO X 177 " ideal model delta sigma weight residual 111.33 121.41 -10.08 1.43e+00 4.89e-01 4.97e+01 angle pdb=" CA PRO Y 326 " pdb=" N PRO Y 326 " pdb=" CD PRO Y 326 " ideal model delta sigma weight residual 112.00 103.96 8.04 1.40e+00 5.10e-01 3.30e+01 angle pdb=" OG1 THR X 28 " pdb=" CB THR X 28 " pdb=" CG2 THR X 28 " ideal model delta sigma weight residual 109.30 120.57 -11.27 2.00e+00 2.50e-01 3.17e+01 angle pdb=" OG1 THR X 126 " pdb=" CB THR X 126 " pdb=" CG2 THR X 126 " ideal model delta sigma weight residual 109.30 120.45 -11.15 2.00e+00 2.50e-01 3.11e+01 angle pdb=" O LEU U 99 " pdb=" C LEU U 99 " pdb=" N ALA U 100 " ideal model delta sigma weight residual 122.82 115.89 6.93 1.28e+00 6.10e-01 2.93e+01 ... (remaining 44699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 18271 17.86 - 35.72: 1273 35.72 - 53.59: 266 53.59 - 71.45: 68 71.45 - 89.31: 19 Dihedral angle restraints: 19897 sinusoidal: 7755 harmonic: 12142 Sorted by residual: dihedral pdb=" CB CYS A 746 " pdb=" SG CYS A 746 " pdb=" SG CYS A 752 " pdb=" CB CYS A 752 " ideal model delta sinusoidal sigma weight residual -86.00 -159.08 73.08 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CB CYS C 741 " pdb=" SG CYS C 741 " pdb=" SG CYS C 763 " pdb=" CB CYS C 763 " ideal model delta sinusoidal sigma weight residual -86.00 -146.01 60.01 1 1.00e+01 1.00e-02 4.80e+01 dihedral pdb=" CB CYS C 541 " pdb=" SG CYS C 541 " pdb=" SG CYS C 593 " pdb=" CB CYS C 593 " ideal model delta sinusoidal sigma weight residual -86.00 -31.69 -54.31 1 1.00e+01 1.00e-02 4.00e+01 ... (remaining 19894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.340: 5224 0.340 - 0.680: 22 0.680 - 1.021: 1 1.021 - 1.361: 0 1.361 - 1.701: 7 Chirality restraints: 5254 Sorted by residual: chirality pdb=" CG LEU Z 29 " pdb=" CB LEU Z 29 " pdb=" CD1 LEU Z 29 " pdb=" CD2 LEU Z 29 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.23e+01 chirality pdb=" CB ILE Y 384 " pdb=" CA ILE Y 384 " pdb=" CG1 ILE Y 384 " pdb=" CG2 ILE Y 384 " both_signs ideal model delta sigma weight residual False 2.64 1.00 1.64 2.00e-01 2.50e+01 6.75e+01 chirality pdb=" CB ILE X 112 " pdb=" CA ILE X 112 " pdb=" CG1 ILE X 112 " pdb=" CG2 ILE X 112 " both_signs ideal model delta sigma weight residual False 2.64 1.01 1.63 2.00e-01 2.50e+01 6.67e+01 ... (remaining 5251 not shown) Planarity restraints: 5763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1137 " 0.148 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" CG ASN B1137 " -0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN B1137 " 0.125 2.00e-02 2.50e+03 pdb=" ND2 ASN B1137 " -0.532 2.00e-02 2.50e+03 pdb=" C1 NAG B1312 " 0.337 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 712 " 0.076 2.00e-02 2.50e+03 1.29e-01 2.08e+02 pdb=" CG ASN A 712 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A 712 " 0.050 2.00e-02 2.50e+03 pdb=" ND2 ASN A 712 " -0.231 2.00e-02 2.50e+03 pdb=" C1 NAG A1310 " 0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU U 99 " -0.040 2.00e-02 2.50e+03 7.65e-02 5.85e+01 pdb=" C LEU U 99 " 0.132 2.00e-02 2.50e+03 pdb=" O LEU U 99 " -0.050 2.00e-02 2.50e+03 pdb=" N ALA U 100 " -0.042 2.00e-02 2.50e+03 ... (remaining 5760 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 130 2.49 - 3.09: 23219 3.09 - 3.70: 46999 3.70 - 4.30: 69192 4.30 - 4.90: 116918 Nonbonded interactions: 256458 Sorted by model distance: nonbonded pdb=" OG SER U 17 " pdb=" OE2 GLU U 82 " model vdw 1.889 3.040 nonbonded pdb=" O LYS X 63 " pdb=" NH1 ARG X 67 " model vdw 1.983 3.120 nonbonded pdb=" OH TYR A 759 " pdb=" OD1 ASP A 997 " model vdw 1.991 3.040 nonbonded pdb=" OG SER V 281 " pdb=" OD2 ASP V 284 " model vdw 2.039 3.040 nonbonded pdb=" NH2 ARG W 47 " pdb=" O GLU W 98 " model vdw 2.083 3.120 ... (remaining 256453 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 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 81 through 95 or (resid 96 through 98 and (na \ me N or name CA or name C or name O or name CB )) or resid 99 through 107 or (re \ sid 108 through 113 and (name N or name CA or name C or name O or name CB )) or \ resid 114 through 123 or (resid 124 and (name N or name CA or name C or name O o \ r name CB )) or resid 125 through 135 or (resid 136 through 138 and (name N or n \ ame CA or name C or name O or name CB )) or resid 139 through 142 or resid 158 t \ hrough 175 or (resid 176 through 187 and (name N or name CA or name C or name O \ or name CB )) or resid 188 through 199 or (resid 200 and (name N or name CA or n \ ame C or name O or name CB )) or resid 201 through 205 or (resid 206 and (name N \ or name CA or name C or name O or name CB )) or resid 207 through 220 or (resid \ 221 and (name N or name CA or name C or name O or name CB )) or resid 222 throu \ gh 226 or (resid 227 and (name N or name CA or name C or name O or name CB )) or \ resid 228 through 247 or (resid 248 through 249 and (name N or name CA or name \ C or name O or name CB )) or resid 250 through 251 or (resid 252 through 253 and \ (name N or name CA or name C or name O or name CB )) or resid 254 through 283 o \ r (resid 284 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 85 through 289 or (resid 290 through 291 and (name N or name CA or name C or nam \ e O or name CB )) or resid 292 through 306 or (resid 307 and (name N or name CA \ or name C or name O or name CB )) or resid 308 through 311 or (resid 312 through \ 313 and (name N or name CA or name C or name O or name CB )) or resid 314 throu \ gh 323 or (resid 324 and (name N or name CA or name C or name O or name CB )) or \ resid 325 through 326 or (resid 327 and (name N or name CA or name C or name O \ or name CB )) or resid 328 through 348 or (resid 349 and (name N or name CA or n \ ame C or name O or name CB )) or resid 350 through 371 or (resid 372 and (name N \ or name CA or name C or name O or name CB )) or resid 373 through 388 or (resid \ 389 and (name N or name CA or name C or name O or name CB )) or resid 390 throu \ gh 405 or (resid 406 and (name N or name CA or name C or name O or name CB )) or \ (resid 407 through 409 and (name N or name CA or name C or name O or name CB )) \ or resid 410 or (resid 411 and (name N or name CA or name C or name O or name C \ B )) or resid 412 through 426 or (resid 427 and (name N or name CA or name C or \ name O or name CB )) or resid 428 through 430 or (resid 431 and (name N or name \ CA or name C or name O or name CB )) or resid 432 through 441 or (resid 442 and \ (name N or name CA or name C or name O or name CB )) or resid 443 or (resid 444 \ through 445 and (name N or name CA or name C or name O or name CB )) or resid 44 \ 6 or (resid 447 through 448 and (name N or name CA or name C or name O or name C \ B )) or resid 449 through 464 or (resid 465 and (name N or name CA or name C or \ name O or name CB )) or resid 466 through 511 or (resid 512 and (name N or name \ CA or name C or name O or name CB )) or resid 513 through 517 or (resid 518 thro \ ugh 519 and (name N or name CA or name C or name O or name CB )) or resid 520 th \ rough 534 or (resid 535 and (name N or name CA or name C or name O or name CB )) \ or resid 536 through 539 or (resid 540 and (name N or name CA or name C or name \ O or name CB )) or resid 541 through 559 or (resid 560 through 561 and (name N \ or name CA or name C or name O or name CB )) or resid 562 through 571 or (resid \ 572 through 575 and (name N or name CA or name C or name O or name CB )) or resi \ d 576 through 615 or (resid 616 and (name N or name CA or name C or name O or na \ me CB )) or resid 617 through 665 or (resid 666 and (name N or name CA or name C \ or name O or name CB )) or resid 667 through 704 or (resid 705 and (name N or n \ ame CA or name C or name O or name CB )) or resid 706 through 739 or (resid 740 \ and (name N or name CA or name C or name O or name CB )) or resid 741 through 74 \ 2 or (resid 743 and (name N or name CA or name C or name O or name CB )) or resi \ d 744 through 747 or (resid 748 and (name N or name CA or name C or name O or na \ me CB )) or resid 749 through 778 or (resid 779 and (name N or name CA or name C \ or name O or name CB )) or resid 780 through 781 or (resid 782 through 783 and \ (name N or name CA or name C or name O or name CB )) or resid 784 through 797 or \ (resid 798 and (name N or name CA or name C or name O or name CB )) or resid 79 \ 9 through 810 or (resid 811 and (name N or name CA or name C or name O or name C \ B )) or resid 812 through 813 or (resid 814 and (name N or name CA or name C or \ name O or name CB )) or resid 815 through 821 or (resid 822 and (name N or name \ CA or name C or name O or name CB )) or resid 823 through 827 or (resid 828 and \ (name N or name CA or name C or name O or name CB )) or resid 829 through 831 or \ (resid 858 and (name N or name CA or name C or name O or name CB )) or resid 85 \ 9 through 870 or (resid 871 and (name N or name CA or name C or name O or name C \ B )) or resid 872 through 920 or (resid 921 and (name N or name CA or name C or \ name O or name CB )) or resid 922 through 941 or (resid 942 through 947 and (nam \ e N or name CA or name C or name O or name CB )) or resid 948 through 949 or (re \ sid 950 and (name N or name CA or name C or name O or name CB )) or resid 951 th \ rough 966 or (resid 967 and (name N or name CA or name C or name O or name CB )) \ or resid 968 through 997 or (resid 998 and (name N or name CA or name C or name \ O or name CB )) or resid 999 through 1016 or (resid 1017 through 1019 and (name \ N or name CA or name C or name O or name CB )) or resid 1020 through 1021 or (r \ esid 1022 through 1023 and (name N or name CA or name C or name O or name CB )) \ or resid 1024 through 1075 or (resid 1076 and (name N or name CA or name C or na \ me O or name CB )) or resid 1077 through 1094 or (resid 1095 and (name N or name \ CA or name C or name O or name CB )) or resid 1096 through 1140 or (resid 1141 \ and (name N or name CA or name C or name O or name CB )) or resid 1142 through 1 \ 143 or (resid 1144 through 1145 and (name N or name CA or name C or name O or na \ me CB )) or resid 1146 through 1148 or (resid 1149 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1301 through 1312)) selection = (chain 'B' and (resid 27 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 45 or (resid 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 51 or (resid 52 throu \ gh 53 and (name N or name CA or name C or name O or name CB )) or resid 54 throu \ gh 68 or resid 81 through 86 or (resid 87 and (name N or name CA or name C or na \ me O or name CB )) or resid 88 through 95 or (resid 96 through 98 and (name N or \ name CA or name C or name O or name CB )) or resid 99 through 114 or (resid 115 \ and (name N or name CA or name C or name O or name CB )) or resid 116 through 1 \ 23 or (resid 124 and (name N or name CA or name C or name O or name CB )) or res \ id 125 through 133 or (resid 134 and (name N or name CA or name C or name O or n \ ame CB )) or resid 135 or (resid 136 through 138 and (name N or name CA or name \ C or name O or name CB )) or resid 139 through 142 or resid 158 through 160 or ( \ resid 161 through 164 and (name N or name CA or name C or name O or name CB )) o \ r resid 165 through 205 or (resid 206 and (name N or name CA or name C or name O \ or name CB )) or resid 207 through 209 or (resid 210 and (name N or name CA or \ name C or name O or name CB )) or resid 218 through 247 or (resid 248 through 24 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 250 through \ 256 or (resid 257 and (name N or name CA or name C or name O or name CB )) or re \ sid 258 through 283 or (resid 284 and (name N or name CA or name C or name O or \ name CB )) or resid 285 through 289 or (resid 290 through 291 and (name N or nam \ e CA or name C or name O or name CB )) or resid 292 through 311 or (resid 312 th \ rough 313 and (name N or name CA or name C or name O or name CB )) or resid 314 \ through 321 or (resid 322 and (name N or name CA or name C or name O or name CB \ )) or resid 323 through 326 or (resid 327 and (name N or name CA or name C or na \ me O or name CB )) or resid 328 through 334 or (resid 335 and (name N or name CA \ or name C or name O or name CB )) or resid 336 through 348 or (resid 349 and (n \ ame N or name CA or name C or name O or name CB )) or resid 350 through 358 or ( \ resid 359 through 360 and (name N or name CA or name C or name O or name CB )) o \ r resid 361 through 388 or (resid 389 and (name N or name CA or name C or name O \ or name CB )) or resid 390 or (resid 391 and (name N or name CA or name C or na \ me O or name CB )) or resid 392 through 407 or (resid 408 through 409 and (name \ N or name CA or name C or name O or name CB )) or resid 410 through 443 or (resi \ d 444 through 445 and (name N or name CA or name C or name O or name CB )) or re \ sid 446 through 461 or (resid 462 and (name N or name CA or name C or name O or \ name CB )) or resid 463 through 530 or (resid 531 through 532 and (name N or nam \ e CA or name C or name O or name CB )) or resid 533 through 534 or (resid 535 an \ d (name N or name CA or name C or name O or name CB )) or resid 536 through 539 \ or (resid 540 and (name N or name CA or name C or name O or name CB )) or resid \ 541 through 556 or (resid 557 and (name N or name CA or name C or name O or name \ CB )) or resid 558 or (resid 559 through 561 and (name N or name CA or name C o \ r name O or name CB )) or resid 562 through 566 or (resid 567 and (name N or nam \ e CA or name C or name O or name CB )) or resid 568 through 573 or (resid 574 th \ rough 575 and (name N or name CA or name C or name O or name CB )) or resid 576 \ through 615 or (resid 616 and (name N or name CA or name C or name O or name CB \ )) or resid 617 through 623 or resid 644 through 679 or resid 694 through 739 or \ (resid 740 and (name N or name CA or name C or name O or name CB )) or resid 74 \ 1 through 747 or (resid 748 and (name N or name CA or name C or name O or name C \ B )) or resid 749 through 750 or (resid 751 and (name N or name CA or name C or \ name O or name CB )) or resid 752 through 778 or (resid 779 and (name N or name \ CA or name C or name O or name CB )) or resid 780 through 781 or (resid 782 thro \ ugh 783 and (name N or name CA or name C or name O or name CB )) or resid 784 th \ rough 813 or (resid 814 and (name N or name CA or name C or name O or name CB )) \ or resid 815 through 830 or (resid 831 and (name N or name CA or name C or name \ O or name CB )) or (resid 858 and (name N or name CA or name C or name O or nam \ e CB )) or resid 859 through 870 or (resid 871 and (name N or name CA or name C \ or name O or name CB )) or resid 872 through 941 or (resid 942 through 947 and ( \ name N or name CA or name C or name O or name CB )) or resid 948 through 987 or \ (resid 988 and (name N or name CA or name C or name O or name CB )) or resid 989 \ through 990 or (resid 991 through 992 and (name N or name CA or name C or name \ O or name CB )) or resid 993 through 997 or (resid 998 and (name N or name CA or \ name C or name O or name CB )) or resid 999 through 1016 or (resid 1017 through \ 1019 and (name N or name CA or name C or name O or name CB )) or resid 1020 thr \ ough 1021 or (resid 1022 through 1023 and (name N or name CA or name C or name O \ or name CB )) or resid 1024 through 1040 or (resid 1041 and (name N or name CA \ or name C or name O or name CB )) or resid 1042 through 1053 or (resid 1054 and \ (name N or name CA or name C or name O or name CB )) or resid 1055 through 1094 \ or (resid 1095 and (name N or name CA or name C or name O or name CB )) or resid \ 1096 through 1113 or (resid 1114 and (name N or name CA or name C or name O or \ name CB )) or resid 1115 through 1146 or (resid 1147 through 1149 and (name N or \ name CA or name C or name O or name CB )) or resid 1301 through 1312)) selection = (chain 'C' and (resid 27 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 51 or (resid 52 through 53 and (na \ me N or name CA or name C or name O or name CB )) or resid 54 through 67 or (res \ id 68 and (name N or name CA or name C or name O or name CB )) or resid 81 throu \ gh 86 or (resid 87 and (name N or name CA or name C or name O or name CB )) or r \ esid 88 through 107 or (resid 108 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 114 or (resid 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 through 120 or (resid 121 through 124 an \ d (name N or name CA or name C or name O or name CB )) or resid 125 through 160 \ or (resid 161 through 164 and (name N or name CA or name C or name O or name CB \ )) or resid 165 through 199 or (resid 200 and (name N or name CA or name C or na \ me O or name CB )) or resid 201 through 220 or (resid 221 and (name N or name CA \ or name C or name O or name CB )) or resid 222 through 226 or (resid 227 and (n \ ame N or name CA or name C or name O or name CB )) or resid 228 through 251 or ( \ resid 252 through 253 and (name N or name CA or name C or name O or name CB )) o \ r resid 254 through 256 or (resid 257 and (name N or name CA or name C or name O \ or name CB )) or resid 258 through 323 or (resid 324 and (name N or name CA or \ name C or name O or name CB )) or resid 325 or (resid 326 through 327 and (name \ N or name CA or name C or name O or name CB )) or resid 328 through 334 or (resi \ d 335 and (name N or name CA or name C or name O or name CB )) or resid 336 thro \ ugh 359 or (resid 360 and (name N or name CA or name C or name O or name CB )) o \ r resid 361 through 405 or (resid 406 and (name N or name CA or name C or name O \ or name CB )) or resid 407 or (resid 408 through 409 and (name N or name CA or \ name C or name O or name CB )) or resid 410 or (resid 411 and (name N or name CA \ or name C or name O or name CB )) or resid 412 through 417 or (resid 418 and (n \ ame N or name CA or name C or name O or name CB )) or resid 419 through 426 or ( \ resid 427 and (name N or name CA or name C or name O or name CB )) or resid 428 \ through 447 or (resid 448 and (name N or name CA or name C or name O or name CB \ )) or resid 449 through 460 or (resid 461 through 462 and (name N or name CA or \ name C or name O or name CB )) or resid 463 through 467 or (resid 468 and (name \ N or name CA or name C or name O or name CB )) or resid 469 through 489 or (resi \ d 490 and (name N or name CA or name C or name O or name CB )) or resid 491 thro \ ugh 502 or (resid 503 and (name N or name CA or name C or name O or name CB )) o \ r resid 504 through 511 or (resid 512 and (name N or name CA or name C or name O \ or name CB )) or resid 513 through 517 or (resid 518 through 519 and (name N or \ name CA or name C or name O or name CB )) or resid 520 through 566 or (resid 56 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 568 through \ 571 or (resid 572 through 575 and (name N or name CA or name C or name O or name \ CB )) or resid 576 through 582 or (resid 583 and (name N or name CA or name C o \ r name O or name CB )) or resid 584 through 620 or (resid 621 and (name N or nam \ e CA or name C or name O or name CB )) or resid 622 through 623 or resid 644 thr \ ough 679 or resid 694 through 742 or (resid 743 and (name N or name CA or name C \ or name O or name CB )) or resid 744 through 750 or (resid 751 and (name N or n \ ame CA or name C or name O or name CB )) or resid 752 through 810 or (resid 811 \ and (name N or name CA or name C or name O or name CB )) or resid 812 through 82 \ 1 or (resid 822 and (name N or name CA or name C or name O or name CB )) or resi \ d 823 through 827 or (resid 828 and (name N or name CA or name C or name O or na \ me CB )) or resid 829 through 831 or resid 858 through 920 or (resid 921 and (na \ me N or name CA or name C or name O or name CB )) or resid 922 through 923 or (r \ esid 924 and (name N or name CA or name C or name O or name CB )) or resid 925 t \ hrough 935 or (resid 936 and (name N or name CA or name C or name O or name CB ) \ ) or resid 937 through 938 or (resid 939 and (name N or name CA or name C or nam \ e O or name CB )) or resid 940 through 943 or (resid 944 through 947 and (name N \ or name CA or name C or name O or name CB )) or resid 948 through 949 or (resid \ 950 and (name N or name CA or name C or name O or name CB )) or resid 951 throu \ gh 966 or (resid 967 and (name N or name CA or name C or name O or name CB )) or \ resid 968 through 1053 or (resid 1054 and (name N or name CA or name C or name \ O or name CB )) or resid 1055 through 1109 or (resid 1110 and (name N or name CA \ or name C or name O or name CB )) or resid 1111 through 1113 or (resid 1114 and \ (name N or name CA or name C or name O or name CB )) or resid 1115 through 1140 \ or (resid 1141 and (name N or name CA or name C or name O or name CB )) or resi \ d 1142 through 1146 or (resid 1147 through 1149 and (name N or name CA or name C \ or name O or name CB )) or resid 1301 through 1312)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'U' selection = chain 'X' } ncs_group { reference = chain 'V' selection = chain 'Y' } ncs_group { reference = chain 'W' selection = chain 'Z' } 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: 9.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.640 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 32.160 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 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 0.513 32858 Z= 0.220 Angle : 0.688 33.665 44922 Z= 0.352 Chirality : 0.077 1.701 5254 Planarity : 0.004 0.095 5725 Dihedral : 13.022 89.309 11948 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.17 % Favored : 96.78 % Rotamer: Outliers : 0.12 % Allowed : 9.08 % Favored : 90.80 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.13), residues: 4127 helix: 1.95 (0.21), residues: 688 sheet: 0.54 (0.14), residues: 1226 loop : -0.51 (0.13), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG W 61 TYR 0.019 0.001 TYR X 94 PHE 0.029 0.001 PHE B 168 TRP 0.041 0.001 TRP X 106 HIS 0.001 0.000 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00303 (32769) covalent geometry : angle 0.60720 (44704) SS BOND : bond 0.07963 ( 49) SS BOND : angle 5.62894 ( 98) hydrogen bonds : bond 0.20568 ( 1291) hydrogen bonds : angle 8.40305 ( 3570) link_BETA1-4 : bond 0.00289 ( 2) link_BETA1-4 : angle 1.29608 ( 6) link_NAG-ASN : bond 0.01595 ( 38) link_NAG-ASN : angle 3.80668 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 523 time to evaluate : 1.000 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 312 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7372 (mp0) REVERT: A 511 TYR cc_start: 0.7954 (m-80) cc_final: 0.7554 (m-80) REVERT: A 584 THR cc_start: 0.8711 (p) cc_final: 0.8395 (t) REVERT: A 606 ASN cc_start: 0.7087 (t0) cc_final: 0.6785 (t160) REVERT: A 907 TYR cc_start: 0.8046 (m-10) cc_final: 0.7544 (m-10) REVERT: A 1076 LYS cc_start: 0.8490 (ttmm) cc_final: 0.8231 (mttp) REVERT: B 1034 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7441 (mt-10) REVERT: C 190 ARG cc_start: 0.7676 (mtm-85) cc_final: 0.7443 (mtt-85) REVERT: C 606 ASN cc_start: 0.7393 (t0) cc_final: 0.7190 (t0) REVERT: Y 344 SER cc_start: 0.4980 (t) cc_final: 0.4641 (m) REVERT: U 48 MET cc_start: 0.4336 (mpp) cc_final: 0.3937 (mpp) REVERT: U 57 THR cc_start: 0.6665 (p) cc_final: 0.6404 (p) outliers start: 4 outliers final: 2 residues processed: 524 average time/residue: 0.5246 time to fit residues: 333.9392 Evaluate side-chains 487 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 484 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1034 GLU Chi-restraints excluded: chain U residue 106 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.0060 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.0470 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.4980 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 0.0670 overall best weight: 0.2032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN A 337 ASN A 609 ASN A 782 GLN A 963 ASN A1008 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 196 ASN Y 346 GLN V 391 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.210192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.151502 restraints weight = 52003.646| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.61 r_work: 0.3666 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32858 Z= 0.130 Angle : 0.610 19.088 44922 Z= 0.315 Chirality : 0.046 0.262 5254 Planarity : 0.004 0.055 5725 Dihedral : 5.545 68.954 5309 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.62 % Allowed : 10.28 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.13), residues: 4127 helix: 2.04 (0.21), residues: 678 sheet: 0.59 (0.14), residues: 1240 loop : -0.51 (0.13), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 67 TYR 0.019 0.001 TYR A1070 PHE 0.019 0.001 PHE C 168 TRP 0.029 0.001 TRP X 106 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00278 (32769) covalent geometry : angle 0.58249 (44704) SS BOND : bond 0.00437 ( 49) SS BOND : angle 1.23472 ( 98) hydrogen bonds : bond 0.04740 ( 1291) hydrogen bonds : angle 6.33623 ( 3570) link_BETA1-4 : bond 0.00213 ( 2) link_BETA1-4 : angle 1.02910 ( 6) link_NAG-ASN : bond 0.00650 ( 38) link_NAG-ASN : angle 3.46633 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 507 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8031 (tp) cc_final: 0.7770 (tm) REVERT: A 386 SER cc_start: 0.8033 (p) cc_final: 0.7819 (t) REVERT: A 412 GLN cc_start: 0.8594 (mt0) cc_final: 0.7943 (tt0) REVERT: A 454 TYR cc_start: 0.8394 (m-80) cc_final: 0.8105 (m-80) REVERT: A 511 TYR cc_start: 0.8146 (m-80) cc_final: 0.7720 (m-80) REVERT: A 584 THR cc_start: 0.8697 (p) cc_final: 0.8397 (t) REVERT: A 606 ASN cc_start: 0.7431 (t0) cc_final: 0.7140 (t160) REVERT: A 646 PHE cc_start: 0.7839 (t80) cc_final: 0.7638 (t80) REVERT: A 743 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8217 (ttt) REVERT: A 907 TYR cc_start: 0.8295 (m-10) cc_final: 0.7796 (m-10) REVERT: A 1076 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8410 (mttp) REVERT: B 648 THR cc_start: 0.8379 (m) cc_final: 0.8164 (p) REVERT: B 780 ASN cc_start: 0.8289 (m-40) cc_final: 0.8023 (m110) REVERT: C 28 TYR cc_start: 0.8083 (m-10) cc_final: 0.7830 (m-80) REVERT: C 602 THR cc_start: 0.8661 (p) cc_final: 0.8401 (p) REVERT: C 606 ASN cc_start: 0.7755 (t0) cc_final: 0.7473 (t0) REVERT: C 878 SER cc_start: 0.8895 (t) cc_final: 0.8675 (m) REVERT: X 118 MET cc_start: 0.3234 (tpt) cc_final: 0.0928 (tpt) REVERT: Y 271 MET cc_start: 0.3965 (OUTLIER) cc_final: 0.3414 (mpp) REVERT: Y 344 SER cc_start: 0.5337 (t) cc_final: 0.4913 (m) REVERT: U 48 MET cc_start: 0.5393 (mpp) cc_final: 0.4982 (mpp) REVERT: U 118 MET cc_start: 0.6579 (tpt) cc_final: 0.6114 (tpt) REVERT: U 119 VAL cc_start: 0.3862 (p) cc_final: 0.3038 (m) outliers start: 54 outliers final: 29 residues processed: 528 average time/residue: 0.5027 time to fit residues: 326.6026 Evaluate side-chains 508 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 477 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 1126 SER Chi-restraints excluded: chain C residue 1128 ASN Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Y residue 271 MET Chi-restraints excluded: chain Y residue 398 SER Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 106 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 413 optimal weight: 20.0000 chunk 141 optimal weight: 6.9990 chunk 277 optimal weight: 1.9990 chunk 205 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 297 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 246 optimal weight: 50.0000 chunk 115 optimal weight: 0.9990 chunk 237 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 324 GLN A 440 ASN A 782 GLN A 960 GLN A1104 HIS B 543 ASN B 567 GLN B 706 ASN B 807 GLN B 875 GLN B 904 GLN B1091 HIS C 188 ASN C 196 ASN C 910 ASN ** Z 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.206693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.146900 restraints weight = 51254.279| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.70 r_work: 0.3558 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 32858 Z= 0.219 Angle : 0.629 11.072 44922 Z= 0.324 Chirality : 0.049 0.440 5254 Planarity : 0.005 0.054 5725 Dihedral : 5.545 59.700 5306 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.64 % Allowed : 10.96 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.13), residues: 4127 helix: 1.68 (0.20), residues: 681 sheet: 0.58 (0.14), residues: 1197 loop : -0.67 (0.13), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1042 TYR 0.033 0.002 TYR A 268 PHE 0.025 0.002 PHE A 546 TRP 0.026 0.002 TRP X 106 HIS 0.006 0.001 HIS C1067 Details of bonding type rmsd covalent geometry : bond 0.00528 (32769) covalent geometry : angle 0.60761 (44704) SS BOND : bond 0.00462 ( 49) SS BOND : angle 1.73014 ( 98) hydrogen bonds : bond 0.04663 ( 1291) hydrogen bonds : angle 5.95179 ( 3570) link_BETA1-4 : bond 0.00421 ( 2) link_BETA1-4 : angle 1.20884 ( 6) link_NAG-ASN : bond 0.00867 ( 38) link_NAG-ASN : angle 2.89002 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 497 time to evaluate : 1.123 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 99 ASN cc_start: 0.7907 (t0) cc_final: 0.7684 (t0) REVERT: A 412 GLN cc_start: 0.8710 (mt0) cc_final: 0.8143 (tt0) REVERT: A 511 TYR cc_start: 0.8125 (m-80) cc_final: 0.7697 (m-80) REVERT: A 577 ASP cc_start: 0.7967 (t0) cc_final: 0.7633 (t0) REVERT: A 584 THR cc_start: 0.8630 (p) cc_final: 0.8422 (t) REVERT: A 606 ASN cc_start: 0.7464 (t0) cc_final: 0.7216 (t160) REVERT: A 743 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8278 (ttt) REVERT: A 1076 LYS cc_start: 0.8616 (ttmm) cc_final: 0.8371 (mtpt) REVERT: B 188 ASN cc_start: 0.6537 (m110) cc_final: 0.6333 (m110) REVERT: B 780 ASN cc_start: 0.8586 (m-40) cc_final: 0.8233 (m110) REVERT: B 903 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8571 (mtm) REVERT: B 1097 VAL cc_start: 0.7748 (OUTLIER) cc_final: 0.7509 (p) REVERT: C 52 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: C 188 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7568 (p0) REVERT: C 602 THR cc_start: 0.8726 (p) cc_final: 0.8467 (p) REVERT: C 606 ASN cc_start: 0.7830 (t0) cc_final: 0.7606 (t0) REVERT: C 878 SER cc_start: 0.8934 (t) cc_final: 0.8729 (m) REVERT: C 903 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8404 (mtm) REVERT: X 118 MET cc_start: 0.3071 (tpt) cc_final: 0.1274 (tpt) REVERT: Y 271 MET cc_start: 0.3602 (OUTLIER) cc_final: 0.3101 (mpp) REVERT: U 48 MET cc_start: 0.5920 (mpp) cc_final: 0.5474 (mpp) REVERT: U 118 MET cc_start: 0.6606 (tpt) cc_final: 0.5959 (tpt) outliers start: 88 outliers final: 45 residues processed: 531 average time/residue: 0.5272 time to fit residues: 342.1761 Evaluate side-chains 539 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 487 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 938 GLN Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 859 LYS Chi-restraints excluded: chain B residue 903 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1041 LYS Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1136 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 321 PHE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 743 MET Chi-restraints excluded: chain C residue 757 LEU Chi-restraints excluded: chain C residue 811 ASP Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 903 MET Chi-restraints excluded: chain C residue 1126 SER Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Y residue 271 MET Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 343 SER Chi-restraints excluded: chain U residue 106 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 347 optimal weight: 50.0000 chunk 247 optimal weight: 0.1980 chunk 329 optimal weight: 9.9990 chunk 325 optimal weight: 30.0000 chunk 57 optimal weight: 0.7980 chunk 309 optimal weight: 20.0000 chunk 178 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 173 optimal weight: 0.5980 chunk 7 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN A 765 GLN A 782 GLN A 904 GLN A1008 GLN B 661 ASN C 196 ASN C 952 GLN ** W 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.206228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.147301 restraints weight = 51005.612| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.47 r_work: 0.3579 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 32858 Z= 0.185 Angle : 0.598 9.413 44922 Z= 0.306 Chirality : 0.047 0.511 5254 Planarity : 0.005 0.058 5725 Dihedral : 5.457 53.381 5304 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.55 % Allowed : 12.76 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.13), residues: 4127 helix: 1.65 (0.20), residues: 679 sheet: 0.60 (0.14), residues: 1208 loop : -0.70 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 190 TYR 0.027 0.001 TYR A 268 PHE 0.023 0.002 PHE B 595 TRP 0.022 0.001 TRP X 106 HIS 0.004 0.001 HIS C1067 Details of bonding type rmsd covalent geometry : bond 0.00443 (32769) covalent geometry : angle 0.57393 (44704) SS BOND : bond 0.00433 ( 49) SS BOND : angle 1.59743 ( 98) hydrogen bonds : bond 0.04175 ( 1291) hydrogen bonds : angle 5.74241 ( 3570) link_BETA1-4 : bond 0.00285 ( 2) link_BETA1-4 : angle 1.10233 ( 6) link_NAG-ASN : bond 0.00798 ( 38) link_NAG-ASN : angle 3.09179 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 499 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7872 (t0) cc_final: 0.7629 (t0) REVERT: A 412 GLN cc_start: 0.8720 (mt0) cc_final: 0.8152 (tt0) REVERT: A 491 CYS cc_start: 0.4309 (OUTLIER) cc_final: 0.3911 (m) REVERT: A 511 TYR cc_start: 0.8108 (m-80) cc_final: 0.7707 (m-80) REVERT: A 577 ASP cc_start: 0.7931 (t0) cc_final: 0.7613 (t0) REVERT: A 606 ASN cc_start: 0.7548 (t0) cc_final: 0.7293 (t160) REVERT: A 727 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8444 (m) REVERT: A 743 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8219 (ttt) REVERT: A 1076 LYS cc_start: 0.8595 (ttmm) cc_final: 0.8341 (mtpt) REVERT: B 780 ASN cc_start: 0.8574 (m-40) cc_final: 0.8349 (m110) REVERT: B 903 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8456 (mtm) REVERT: B 1017 ARG cc_start: 0.8748 (mtm-85) cc_final: 0.8544 (mtm-85) REVERT: B 1075 GLU cc_start: 0.8410 (pm20) cc_final: 0.8052 (pm20) REVERT: C 52 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7625 (tm-30) REVERT: C 606 ASN cc_start: 0.7929 (t0) cc_final: 0.7720 (t0) REVERT: C 878 SER cc_start: 0.8918 (t) cc_final: 0.8707 (m) REVERT: C 903 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8370 (mtm) REVERT: X 118 MET cc_start: 0.3014 (tpt) cc_final: 0.1063 (tpt) REVERT: Y 271 MET cc_start: 0.3323 (mpt) cc_final: 0.2893 (mpp) REVERT: U 86 LEU cc_start: 0.5025 (OUTLIER) cc_final: 0.4809 (pt) REVERT: U 118 MET cc_start: 0.6569 (tpt) cc_final: 0.6099 (tpt) REVERT: U 119 VAL cc_start: 0.4089 (p) cc_final: 0.3298 (m) REVERT: V 271 MET cc_start: 0.4720 (pmt) cc_final: 0.2818 (mtp) outliers start: 85 outliers final: 51 residues processed: 535 average time/residue: 0.5155 time to fit residues: 336.9267 Evaluate side-chains 538 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 480 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 859 LYS Chi-restraints excluded: chain B residue 903 MET Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 321 PHE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 757 LEU Chi-restraints excluded: chain C residue 811 ASP Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 903 MET Chi-restraints excluded: chain C residue 996 ILE Chi-restraints excluded: chain C residue 1126 SER Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 343 SER Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 86 LEU Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 106 TRP Chi-restraints excluded: chain V residue 339 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 339 optimal weight: 30.0000 chunk 9 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 316 optimal weight: 8.9990 chunk 248 optimal weight: 20.0000 chunk 148 optimal weight: 3.9990 chunk 143 optimal weight: 0.2980 chunk 266 optimal weight: 0.7980 chunk 385 optimal weight: 0.0870 chunk 279 optimal weight: 0.9980 chunk 379 optimal weight: 0.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN A 644 ASN A 782 GLN A1008 GLN B 706 ASN C 196 ASN C 904 GLN ** W 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.206512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.148117 restraints weight = 51132.891| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.48 r_work: 0.3585 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 32858 Z= 0.132 Angle : 0.594 18.531 44922 Z= 0.299 Chirality : 0.048 0.739 5254 Planarity : 0.004 0.055 5725 Dihedral : 5.392 59.350 5304 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.25 % Allowed : 13.96 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.13), residues: 4127 helix: 1.68 (0.21), residues: 682 sheet: 0.66 (0.14), residues: 1209 loop : -0.69 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 331 TYR 0.023 0.001 TYR A 268 PHE 0.026 0.001 PHE A 646 TRP 0.025 0.001 TRP U 36 HIS 0.003 0.001 HIS C1067 Details of bonding type rmsd covalent geometry : bond 0.00303 (32769) covalent geometry : angle 0.55472 (44704) SS BOND : bond 0.00368 ( 49) SS BOND : angle 1.63505 ( 98) hydrogen bonds : bond 0.03794 ( 1291) hydrogen bonds : angle 5.59163 ( 3570) link_BETA1-4 : bond 0.00270 ( 2) link_BETA1-4 : angle 1.09057 ( 6) link_NAG-ASN : bond 0.00847 ( 38) link_NAG-ASN : angle 4.00227 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 489 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7844 (t0) cc_final: 0.7593 (t0) REVERT: A 412 GLN cc_start: 0.8682 (mt0) cc_final: 0.8048 (tt0) REVERT: A 454 TYR cc_start: 0.8389 (m-80) cc_final: 0.8093 (m-80) REVERT: A 491 CYS cc_start: 0.4395 (OUTLIER) cc_final: 0.3981 (m) REVERT: A 577 ASP cc_start: 0.7940 (t0) cc_final: 0.7582 (t0) REVERT: A 606 ASN cc_start: 0.7500 (t0) cc_final: 0.7237 (t160) REVERT: A 727 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8451 (m) REVERT: A 743 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8167 (ttt) REVERT: A 1076 LYS cc_start: 0.8566 (ttmm) cc_final: 0.8286 (mtpt) REVERT: B 53 ASP cc_start: 0.8106 (t0) cc_final: 0.7878 (t70) REVERT: B 1017 ARG cc_start: 0.8745 (mtm-85) cc_final: 0.8525 (mtm-85) REVERT: B 1032 MET cc_start: 0.8826 (tpp) cc_final: 0.8064 (tpp) REVERT: B 1075 GLU cc_start: 0.8394 (pm20) cc_final: 0.8037 (pm20) REVERT: B 1097 VAL cc_start: 0.7675 (OUTLIER) cc_final: 0.7378 (p) REVERT: C 170 TYR cc_start: 0.7672 (t80) cc_final: 0.6774 (t80) REVERT: C 878 SER cc_start: 0.8879 (t) cc_final: 0.8655 (m) REVERT: C 903 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8276 (mtm) REVERT: X 118 MET cc_start: 0.3039 (tpt) cc_final: 0.1162 (tpt) REVERT: Y 271 MET cc_start: 0.3442 (OUTLIER) cc_final: 0.2973 (mpp) REVERT: U 86 LEU cc_start: 0.4934 (OUTLIER) cc_final: 0.4695 (pt) REVERT: U 118 MET cc_start: 0.6555 (tpt) cc_final: 0.5900 (tpt) REVERT: V 271 MET cc_start: 0.4633 (pmt) cc_final: 0.2997 (mtp) outliers start: 75 outliers final: 45 residues processed: 522 average time/residue: 0.5163 time to fit residues: 329.9303 Evaluate side-chains 527 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 475 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 859 LYS Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 321 PHE Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 903 MET Chi-restraints excluded: chain C residue 996 ILE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1126 SER Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Y residue 271 MET Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 343 SER Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain U residue 86 LEU Chi-restraints excluded: chain U residue 106 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 62 optimal weight: 0.9980 chunk 375 optimal weight: 40.0000 chunk 34 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 244 optimal weight: 50.0000 chunk 39 optimal weight: 0.0470 chunk 287 optimal weight: 1.9990 chunk 390 optimal weight: 5.9990 chunk 331 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN A 357 ASN A 440 ASN A 765 GLN A1008 GLN B 706 ASN B 780 ASN B 807 GLN B 938 GLN C 125 ASN C 196 ASN C 904 GLN ** W 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.206755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.148382 restraints weight = 51004.744| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.51 r_work: 0.3584 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 32858 Z= 0.148 Angle : 0.575 14.619 44922 Z= 0.292 Chirality : 0.046 0.574 5254 Planarity : 0.004 0.056 5725 Dihedral : 5.299 55.310 5304 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.73 % Allowed : 14.11 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.13), residues: 4127 helix: 1.67 (0.21), residues: 679 sheet: 0.71 (0.14), residues: 1207 loop : -0.68 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 331 TYR 0.025 0.001 TYR A 268 PHE 0.029 0.001 PHE A 646 TRP 0.019 0.001 TRP X 106 HIS 0.003 0.001 HIS C1067 Details of bonding type rmsd covalent geometry : bond 0.00348 (32769) covalent geometry : angle 0.54749 (44704) SS BOND : bond 0.00452 ( 49) SS BOND : angle 1.59654 ( 98) hydrogen bonds : bond 0.03798 ( 1291) hydrogen bonds : angle 5.51656 ( 3570) link_BETA1-4 : bond 0.00301 ( 2) link_BETA1-4 : angle 1.08790 ( 6) link_NAG-ASN : bond 0.00830 ( 38) link_NAG-ASN : angle 3.25324 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 479 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7913 (t0) cc_final: 0.7661 (t0) REVERT: A 454 TYR cc_start: 0.8392 (m-80) cc_final: 0.8088 (m-80) REVERT: A 491 CYS cc_start: 0.4372 (OUTLIER) cc_final: 0.3974 (m) REVERT: A 577 ASP cc_start: 0.7942 (t0) cc_final: 0.7628 (t0) REVERT: A 606 ASN cc_start: 0.7550 (t0) cc_final: 0.7290 (t160) REVERT: A 727 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8469 (m) REVERT: A 743 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8068 (ttt) REVERT: A 817 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7890 (mtmm) REVERT: A 986 ARG cc_start: 0.8440 (ptm-80) cc_final: 0.8204 (ptt90) REVERT: A 1076 LYS cc_start: 0.8592 (ttmm) cc_final: 0.8328 (mtpt) REVERT: B 53 ASP cc_start: 0.8104 (t0) cc_final: 0.7890 (t70) REVERT: B 824 LEU cc_start: 0.8331 (tt) cc_final: 0.7918 (mp) REVERT: B 1075 GLU cc_start: 0.8403 (pm20) cc_final: 0.8117 (pm20) REVERT: B 1097 VAL cc_start: 0.7670 (OUTLIER) cc_final: 0.7371 (p) REVERT: C 125 ASN cc_start: 0.7390 (m-40) cc_final: 0.6620 (t0) REVERT: C 903 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8315 (mtm) REVERT: X 118 MET cc_start: 0.3024 (tpt) cc_final: 0.1119 (tpt) REVERT: Y 271 MET cc_start: 0.3283 (OUTLIER) cc_final: 0.2882 (mpp) REVERT: U 118 MET cc_start: 0.6551 (tpt) cc_final: 0.5884 (tpt) REVERT: V 271 MET cc_start: 0.4655 (pmt) cc_final: 0.3346 (mtp) outliers start: 91 outliers final: 62 residues processed: 521 average time/residue: 0.4948 time to fit residues: 318.0590 Evaluate side-chains 540 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 471 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1139 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 859 LYS Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 938 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 321 PHE Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 903 MET Chi-restraints excluded: chain C residue 996 ILE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1126 SER Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain X residue 191 VAL Chi-restraints excluded: chain Y residue 271 MET Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 343 SER Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 106 TRP Chi-restraints excluded: chain V residue 339 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 26 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 190 optimal weight: 0.6980 chunk 320 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 305 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 308 optimal weight: 6.9990 chunk 156 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN A1008 GLN B 706 ASN C 196 ASN C 904 GLN ** Z 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 65 GLN ** W 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.205905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.148111 restraints weight = 50928.071| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.24 r_work: 0.3585 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 32858 Z= 0.170 Angle : 0.606 19.279 44922 Z= 0.306 Chirality : 0.050 1.232 5254 Planarity : 0.005 0.072 5725 Dihedral : 5.269 55.204 5304 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.64 % Allowed : 14.26 % Favored : 83.10 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.13), residues: 4127 helix: 1.67 (0.21), residues: 684 sheet: 0.68 (0.14), residues: 1246 loop : -0.69 (0.13), residues: 2197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 331 TYR 0.027 0.001 TYR A 268 PHE 0.034 0.001 PHE A 646 TRP 0.018 0.001 TRP X 106 HIS 0.004 0.001 HIS B1067 Details of bonding type rmsd covalent geometry : bond 0.00405 (32769) covalent geometry : angle 0.57035 (44704) SS BOND : bond 0.00393 ( 49) SS BOND : angle 1.65693 ( 98) hydrogen bonds : bond 0.03947 ( 1291) hydrogen bonds : angle 5.48818 ( 3570) link_BETA1-4 : bond 0.00312 ( 2) link_BETA1-4 : angle 1.08971 ( 6) link_NAG-ASN : bond 0.00711 ( 38) link_NAG-ASN : angle 3.82559 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 479 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7911 (t0) cc_final: 0.7684 (t0) REVERT: A 454 TYR cc_start: 0.8366 (m-80) cc_final: 0.8052 (m-80) REVERT: A 491 CYS cc_start: 0.4440 (OUTLIER) cc_final: 0.4030 (m) REVERT: A 577 ASP cc_start: 0.7956 (t0) cc_final: 0.7616 (t0) REVERT: A 606 ASN cc_start: 0.7569 (t0) cc_final: 0.7295 (t160) REVERT: A 727 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8469 (m) REVERT: A 743 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8038 (ttt) REVERT: A 817 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7822 (mtmm) REVERT: A 1076 LYS cc_start: 0.8549 (ttmm) cc_final: 0.8255 (mtpt) REVERT: B 53 ASP cc_start: 0.8072 (t0) cc_final: 0.7850 (t70) REVERT: B 129 LYS cc_start: 0.7982 (ttmt) cc_final: 0.7597 (tppp) REVERT: B 312 GLU cc_start: 0.8067 (mp0) cc_final: 0.7809 (mp0) REVERT: B 1075 GLU cc_start: 0.8379 (pm20) cc_final: 0.8069 (pm20) REVERT: B 1097 VAL cc_start: 0.7731 (OUTLIER) cc_final: 0.7463 (p) REVERT: C 125 ASN cc_start: 0.7407 (m-40) cc_final: 0.6641 (t0) REVERT: C 170 TYR cc_start: 0.7682 (t80) cc_final: 0.7001 (t80) REVERT: C 172 SER cc_start: 0.7586 (OUTLIER) cc_final: 0.6502 (m) REVERT: C 903 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8271 (mtm) REVERT: X 118 MET cc_start: 0.3039 (tpt) cc_final: 0.1289 (tpt) REVERT: Y 271 MET cc_start: 0.3507 (OUTLIER) cc_final: 0.3080 (mpp) REVERT: U 118 MET cc_start: 0.6561 (tpt) cc_final: 0.5936 (tpt) REVERT: V 271 MET cc_start: 0.4713 (pmt) cc_final: 0.3554 (mtp) outliers start: 88 outliers final: 65 residues processed: 525 average time/residue: 0.5059 time to fit residues: 325.9875 Evaluate side-chains 552 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 479 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1139 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 859 LYS Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1136 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 321 PHE Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 811 ASP Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 903 MET Chi-restraints excluded: chain C residue 996 ILE Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1126 SER Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain X residue 191 VAL Chi-restraints excluded: chain Y residue 271 MET Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 343 SER Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain U residue 106 TRP Chi-restraints excluded: chain U residue 121 VAL Chi-restraints excluded: chain V residue 339 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 206 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 246 optimal weight: 20.0000 chunk 287 optimal weight: 1.9990 chunk 307 optimal weight: 0.9990 chunk 342 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 297 optimal weight: 0.0270 overall best weight: 0.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN A 765 GLN A1008 GLN B 706 ASN B 807 GLN C 196 ASN C 706 ASN C 904 GLN ** Z 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.205974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.148309 restraints weight = 51243.659| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.26 r_work: 0.3593 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32858 Z= 0.149 Angle : 0.600 23.175 44922 Z= 0.299 Chirality : 0.047 0.691 5254 Planarity : 0.004 0.067 5725 Dihedral : 5.193 55.614 5304 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.85 % Allowed : 14.38 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.13), residues: 4127 helix: 1.77 (0.21), residues: 673 sheet: 0.71 (0.14), residues: 1250 loop : -0.70 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 331 TYR 0.024 0.001 TYR A 268 PHE 0.035 0.001 PHE A 646 TRP 0.019 0.001 TRP X 106 HIS 0.003 0.001 HIS B1067 Details of bonding type rmsd covalent geometry : bond 0.00353 (32769) covalent geometry : angle 0.55338 (44704) SS BOND : bond 0.00391 ( 49) SS BOND : angle 1.65142 ( 98) hydrogen bonds : bond 0.03758 ( 1291) hydrogen bonds : angle 5.41575 ( 3570) link_BETA1-4 : bond 0.00226 ( 2) link_BETA1-4 : angle 1.03282 ( 6) link_NAG-ASN : bond 0.00717 ( 38) link_NAG-ASN : angle 4.38953 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 483 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 TYR cc_start: 0.8367 (m-80) cc_final: 0.8006 (m-80) REVERT: A 491 CYS cc_start: 0.4317 (OUTLIER) cc_final: 0.3918 (m) REVERT: A 577 ASP cc_start: 0.7942 (t0) cc_final: 0.7656 (t0) REVERT: A 606 ASN cc_start: 0.7548 (t0) cc_final: 0.7302 (t160) REVERT: A 743 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8019 (ttt) REVERT: A 817 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7858 (mtmm) REVERT: A 1076 LYS cc_start: 0.8560 (ttmm) cc_final: 0.8315 (mtpt) REVERT: B 53 ASP cc_start: 0.8042 (t0) cc_final: 0.7839 (t70) REVERT: B 312 GLU cc_start: 0.8064 (mp0) cc_final: 0.7846 (mp0) REVERT: B 338 LEU cc_start: 0.8586 (mm) cc_final: 0.8361 (mp) REVERT: B 824 LEU cc_start: 0.8263 (tt) cc_final: 0.8003 (mp) REVERT: B 1032 MET cc_start: 0.8806 (tpp) cc_final: 0.8096 (tpp) REVERT: B 1075 GLU cc_start: 0.8377 (pm20) cc_final: 0.8102 (pm20) REVERT: B 1097 VAL cc_start: 0.7712 (OUTLIER) cc_final: 0.7460 (p) REVERT: C 52 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: C 125 ASN cc_start: 0.7332 (m-40) cc_final: 0.6690 (t0) REVERT: C 170 TYR cc_start: 0.7651 (t80) cc_final: 0.6917 (t80) REVERT: C 172 SER cc_start: 0.7647 (OUTLIER) cc_final: 0.6721 (m) REVERT: C 903 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8221 (mtm) REVERT: X 118 MET cc_start: 0.3064 (tpt) cc_final: 0.1263 (tpt) REVERT: Y 271 MET cc_start: 0.3347 (OUTLIER) cc_final: 0.2970 (mpp) REVERT: U 118 MET cc_start: 0.6443 (tpt) cc_final: 0.5790 (tpt) REVERT: V 271 MET cc_start: 0.4635 (pmt) cc_final: 0.3806 (mtp) outliers start: 95 outliers final: 72 residues processed: 532 average time/residue: 0.5009 time to fit residues: 327.6648 Evaluate side-chains 550 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 470 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1139 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 859 LYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 321 PHE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 903 MET Chi-restraints excluded: chain C residue 996 ILE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1126 SER Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain X residue 191 VAL Chi-restraints excluded: chain Y residue 271 MET Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 343 SER Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 106 TRP Chi-restraints excluded: chain U residue 121 VAL Chi-restraints excluded: chain V residue 298 SER Chi-restraints excluded: chain V residue 339 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 351 optimal weight: 30.0000 chunk 312 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 158 optimal weight: 0.4980 chunk 313 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 261 optimal weight: 0.7980 chunk 409 optimal weight: 9.9990 chunk 177 optimal weight: 0.9980 chunk 352 optimal weight: 40.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN A 440 ASN A1008 GLN B 706 ASN C 196 ASN C 706 ASN C 904 GLN ** W 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.205190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.146897 restraints weight = 50581.953| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.24 r_work: 0.3575 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 32858 Z= 0.219 Angle : 0.643 15.062 44922 Z= 0.323 Chirality : 0.048 0.541 5254 Planarity : 0.005 0.064 5725 Dihedral : 5.416 55.740 5304 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.73 % Allowed : 14.80 % Favored : 82.47 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.13), residues: 4127 helix: 1.58 (0.20), residues: 684 sheet: 0.69 (0.14), residues: 1225 loop : -0.72 (0.13), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 331 TYR 0.032 0.002 TYR A 268 PHE 0.046 0.002 PHE A 646 TRP 0.019 0.002 TRP X 106 HIS 0.005 0.001 HIS C1051 Details of bonding type rmsd covalent geometry : bond 0.00529 (32769) covalent geometry : angle 0.59867 (44704) SS BOND : bond 0.00417 ( 49) SS BOND : angle 1.80382 ( 98) hydrogen bonds : bond 0.04158 ( 1291) hydrogen bonds : angle 5.47505 ( 3570) link_BETA1-4 : bond 0.00258 ( 2) link_BETA1-4 : angle 1.13745 ( 6) link_NAG-ASN : bond 0.00776 ( 38) link_NAG-ASN : angle 4.41905 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 491 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ARG cc_start: 0.7739 (mtt180) cc_final: 0.7372 (mtt180) REVERT: A 412 GLN cc_start: 0.8710 (mt0) cc_final: 0.8201 (tt0) REVERT: A 454 TYR cc_start: 0.8341 (m-80) cc_final: 0.8000 (m-80) REVERT: A 491 CYS cc_start: 0.4433 (OUTLIER) cc_final: 0.4036 (m) REVERT: A 577 ASP cc_start: 0.7904 (t0) cc_final: 0.7632 (t0) REVERT: A 646 PHE cc_start: 0.7740 (t80) cc_final: 0.7480 (t80) REVERT: A 743 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8023 (ttt) REVERT: A 817 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7864 (mtmm) REVERT: A 1076 LYS cc_start: 0.8554 (ttmm) cc_final: 0.8286 (mtpt) REVERT: B 53 ASP cc_start: 0.8006 (t0) cc_final: 0.7799 (t70) REVERT: B 129 LYS cc_start: 0.8023 (ttmt) cc_final: 0.7656 (tppp) REVERT: B 312 GLU cc_start: 0.8097 (mp0) cc_final: 0.7867 (mp0) REVERT: B 1032 MET cc_start: 0.8817 (tpp) cc_final: 0.8089 (tpp) REVERT: B 1075 GLU cc_start: 0.8355 (pm20) cc_final: 0.8072 (pm20) REVERT: C 125 ASN cc_start: 0.7341 (m-40) cc_final: 0.6656 (t0) REVERT: C 170 TYR cc_start: 0.7683 (t80) cc_final: 0.6925 (t80) REVERT: C 172 SER cc_start: 0.7709 (OUTLIER) cc_final: 0.6864 (m) REVERT: C 903 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8316 (mtm) REVERT: X 118 MET cc_start: 0.3059 (tpt) cc_final: 0.1296 (tpt) REVERT: Y 271 MET cc_start: 0.3801 (OUTLIER) cc_final: 0.3186 (mpp) REVERT: U 118 MET cc_start: 0.6479 (tpt) cc_final: 0.5834 (tpt) REVERT: V 271 MET cc_start: 0.4430 (pmt) cc_final: 0.4057 (mtm) outliers start: 91 outliers final: 74 residues processed: 534 average time/residue: 0.5123 time to fit residues: 336.1501 Evaluate side-chains 561 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 481 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1139 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 859 LYS Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1136 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 321 PHE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 811 ASP Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 903 MET Chi-restraints excluded: chain C residue 996 ILE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1126 SER Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain X residue 191 VAL Chi-restraints excluded: chain Y residue 271 MET Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 343 SER Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 106 TRP Chi-restraints excluded: chain U residue 121 VAL Chi-restraints excluded: chain V residue 298 SER Chi-restraints excluded: chain V residue 330 SER Chi-restraints excluded: chain V residue 339 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 395 optimal weight: 20.0000 chunk 56 optimal weight: 0.6980 chunk 280 optimal weight: 0.6980 chunk 385 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN A 910 ASN A1008 GLN B 706 ASN B 938 GLN C 196 ASN ** W 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.205235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.146825 restraints weight = 50859.264| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.26 r_work: 0.3576 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 32858 Z= 0.179 Angle : 0.628 17.561 44922 Z= 0.314 Chirality : 0.047 0.533 5254 Planarity : 0.005 0.066 5725 Dihedral : 5.391 55.718 5304 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.31 % Allowed : 15.19 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.13), residues: 4127 helix: 1.63 (0.20), residues: 679 sheet: 0.70 (0.14), residues: 1226 loop : -0.73 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 331 TYR 0.027 0.001 TYR A 268 PHE 0.042 0.002 PHE A 646 TRP 0.019 0.001 TRP X 106 HIS 0.004 0.001 HIS C1067 Details of bonding type rmsd covalent geometry : bond 0.00428 (32769) covalent geometry : angle 0.58617 (44704) SS BOND : bond 0.00404 ( 49) SS BOND : angle 1.76331 ( 98) hydrogen bonds : bond 0.03921 ( 1291) hydrogen bonds : angle 5.43420 ( 3570) link_BETA1-4 : bond 0.00345 ( 2) link_BETA1-4 : angle 1.08844 ( 6) link_NAG-ASN : bond 0.00790 ( 38) link_NAG-ASN : angle 4.23821 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 488 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ARG cc_start: 0.7724 (mtt180) cc_final: 0.7360 (mtt180) REVERT: A 454 TYR cc_start: 0.8337 (m-80) cc_final: 0.8013 (m-80) REVERT: A 491 CYS cc_start: 0.4403 (OUTLIER) cc_final: 0.3994 (m) REVERT: A 577 ASP cc_start: 0.7878 (t0) cc_final: 0.7614 (t0) REVERT: A 646 PHE cc_start: 0.7713 (t80) cc_final: 0.7460 (t80) REVERT: A 743 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7823 (ttt) REVERT: A 817 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7849 (mtmm) REVERT: A 1076 LYS cc_start: 0.8545 (ttmm) cc_final: 0.8293 (mtpt) REVERT: B 53 ASP cc_start: 0.8001 (t0) cc_final: 0.7790 (t70) REVERT: B 96 GLU cc_start: 0.7383 (pm20) cc_final: 0.7147 (pm20) REVERT: B 312 GLU cc_start: 0.8088 (mp0) cc_final: 0.7874 (mp0) REVERT: B 824 LEU cc_start: 0.8329 (tt) cc_final: 0.7937 (mp) REVERT: B 1032 MET cc_start: 0.8811 (tpp) cc_final: 0.8083 (tpp) REVERT: B 1075 GLU cc_start: 0.8347 (pm20) cc_final: 0.8068 (pm20) REVERT: C 125 ASN cc_start: 0.7326 (m-40) cc_final: 0.6637 (t0) REVERT: C 393 LEU cc_start: 0.8169 (mt) cc_final: 0.7959 (mp) REVERT: X 118 MET cc_start: 0.3063 (tpt) cc_final: 0.1330 (tpt) REVERT: Y 271 MET cc_start: 0.3716 (mpt) cc_final: 0.3150 (mpp) REVERT: U 118 MET cc_start: 0.6573 (tpt) cc_final: 0.5951 (tpt) outliers start: 77 outliers final: 72 residues processed: 525 average time/residue: 0.5149 time to fit residues: 332.4992 Evaluate side-chains 562 residues out of total 3621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 487 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1139 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 859 LYS Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 938 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1136 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 321 PHE Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 811 ASP Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 996 ILE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1126 SER Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain X residue 191 VAL Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 343 SER Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 106 TRP Chi-restraints excluded: chain U residue 121 VAL Chi-restraints excluded: chain V residue 298 SER Chi-restraints excluded: chain V residue 339 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 251 optimal weight: 1.9990 chunk 322 optimal weight: 3.9990 chunk 290 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 146 optimal weight: 5.9990 chunk 323 optimal weight: 8.9990 chunk 319 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 294 optimal weight: 0.9980 chunk 136 optimal weight: 20.0000 chunk 23 optimal weight: 0.0970 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN A 910 ASN A1008 GLN B 337 ASN B 609 ASN B 706 ASN ** B 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 706 ASN ** V 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.204917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.146483 restraints weight = 50752.105| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.25 r_work: 0.3565 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 32858 Z= 0.200 Angle : 0.642 17.825 44922 Z= 0.322 Chirality : 0.051 1.334 5254 Planarity : 0.005 0.068 5725 Dihedral : 5.371 55.775 5304 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.40 % Allowed : 15.10 % Favored : 82.50 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.13), residues: 4127 helix: 1.58 (0.20), residues: 678 sheet: 0.69 (0.14), residues: 1227 loop : -0.75 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 331 TYR 0.029 0.002 TYR A 268 PHE 0.043 0.002 PHE A 646 TRP 0.018 0.002 TRP X 106 HIS 0.005 0.001 HIS C1067 Details of bonding type rmsd covalent geometry : bond 0.00482 (32769) covalent geometry : angle 0.59715 (44704) SS BOND : bond 0.00396 ( 49) SS BOND : angle 1.82584 ( 98) hydrogen bonds : bond 0.04042 ( 1291) hydrogen bonds : angle 5.44174 ( 3570) link_BETA1-4 : bond 0.00292 ( 2) link_BETA1-4 : angle 1.10741 ( 6) link_NAG-ASN : bond 0.00675 ( 38) link_NAG-ASN : angle 4.45423 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17152.72 seconds wall clock time: 290 minutes 48.75 seconds (17448.75 seconds total)