Starting phenix.real_space_refine on Mon Aug 25 17:23:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y87_39036/08_2025/8y87_39036.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y87_39036/08_2025/8y87_39036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y87_39036/08_2025/8y87_39036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y87_39036/08_2025/8y87_39036.map" model { file = "/net/cci-nas-00/data/ceres_data/8y87_39036/08_2025/8y87_39036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y87_39036/08_2025/8y87_39036.cif" } resolution = 3.26 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= 0.002 sd= 0.033 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 179 5.16 5 C 18832 2.51 5 N 4799 2.21 5 O 5721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29531 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 9117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 9117 Classifications: {'peptide': 1172} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1115} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "T" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1727 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 14, 'TRANS': 222} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "C" Number of atoms: 9121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1184, 9121 Classifications: {'peptide': 1184} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 3, 'PTRANS': 52, 'TRANS': 1128} Chain breaks: 4 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 3, 'TRP:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 9163 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1185, 9152 Classifications: {'peptide': 1185} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1128} Chain breaks: 3 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 3, 'TYR:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 64 Conformer: "B" Number of residues, atoms: 1185, 9152 Classifications: {'peptide': 1185} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1128} Chain breaks: 3 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 3, 'TYR:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 64 bond proxies already assigned to first conformer: 9365 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "F" 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE B 633 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 633 " occ=0.50 Time building chain proxies: 6.60, per 1000 atoms: 0.22 Number of scatterers: 29531 At special positions: 0 Unit cell: (158.26, 142.68, 235.34, 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 179 16.00 O 5721 8.00 N 4799 7.00 C 18832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=69, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.03 Simple disulfide: pdb=" SG CYS T 410 " - pdb=" SG CYS T 426 " distance=2.03 Simple disulfide: pdb=" SG CYS T 437 " - pdb=" SG CYS T 465 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " 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 D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A 188 " " NAG A1302 " - " ASN A 192 " " NAG A1303 " - " ASN A 335 " " NAG A1304 " - " ASN A 664 " " NAG A1305 " - " ASN A 703 " " NAG A1306 " - " ASN A 725 " " NAG A1307 " - " ASN A 793 " " NAG A1308 " - " ASN A 355 " " NAG A1309 " - " ASN A1211 " " NAG B1301 " - " ASN B 664 " " NAG B1302 " - " ASN B 58 " " NAG B1303 " - " ASN B 188 " " NAG B1304 " - " ASN B 192 " " NAG B1305 " - " ASN B 725 " " NAG B1306 " - " ASN B1211 " " NAG C1301 " - " ASN C 58 " " NAG C1302 " - " ASN C 664 " " NAG C1303 " - " ASN C 703 " " NAG C1304 " - " ASN C 771 " " NAG C1305 " - " ASN C 793 " " NAG C1306 " - " ASN C 192 " " NAG C1307 " - " ASN C 355 " " NAG D 1 " - " ASN C 132 " " NAG E 1 " - " ASN C 188 " " NAG F 1 " - " ASN B 132 " Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7104 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 66 sheets defined 23.6% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 Processing helix chain 'A' and resid 285 through 295 Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.557A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 344 removed outlier: 4.113A pdb=" N TRP A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.885A pdb=" N LEU A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.584A pdb=" N SER A 412 " --> pdb=" O PHE A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 removed outlier: 3.661A pdb=" N VAL A 481 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL A 482 " --> pdb=" O PRO A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 478 through 482' Processing helix chain 'A' and resid 696 through 704 removed outlier: 4.756A pdb=" N ASN A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 819 Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.546A pdb=" N HIS A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 862 removed outlier: 3.615A pdb=" N CYS A 836 " --> pdb=" O TYR A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 872 No H-bonds generated for 'chain 'A' and resid 870 through 872' Processing helix chain 'A' and resid 878 through 882 removed outlier: 4.165A pdb=" N ASN A 881 " --> pdb=" O ASP A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 901 through 909 removed outlier: 3.799A pdb=" N LEU A 906 " --> pdb=" O PRO A 902 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 924 removed outlier: 3.885A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 removed outlier: 3.997A pdb=" N VAL A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 965 Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 993 through 1000 removed outlier: 3.794A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1019 removed outlier: 3.565A pdb=" N ASN A1009 " --> pdb=" O ALA A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1045 Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 3.551A pdb=" N ASN A1049 " --> pdb=" O GLN A1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1046 through 1049' Processing helix chain 'A' and resid 1058 through 1063 Processing helix chain 'A' and resid 1066 through 1069 Processing helix chain 'A' and resid 1070 through 1114 removed outlier: 3.696A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'T' and resid 299 through 303 Processing helix chain 'T' and resid 304 through 307 Processing helix chain 'T' and resid 406 through 411 Processing helix chain 'T' and resid 480 through 492 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 335 removed outlier: 3.572A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 344 removed outlier: 4.000A pdb=" N TRP C 344 " --> pdb=" O PRO C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 removed outlier: 3.546A pdb=" N VAL C 363 " --> pdb=" O LEU C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 Processing helix chain 'C' and resid 398 through 402 removed outlier: 3.902A pdb=" N GLN C 402 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 443 through 448 removed outlier: 3.866A pdb=" N TYR C 448 " --> pdb=" O TRP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 568 through 572 removed outlier: 3.541A pdb=" N PHE C 572 " --> pdb=" O PRO C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 701 removed outlier: 3.530A pdb=" N LEU C 701 " --> pdb=" O CYS C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 818 removed outlier: 3.619A pdb=" N VAL C 818 " --> pdb=" O CYS C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 830 removed outlier: 3.508A pdb=" N HIS C 826 " --> pdb=" O TYR C 822 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 828 " --> pdb=" O ALA C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 862 removed outlier: 3.537A pdb=" N ASN C 840 " --> pdb=" O CYS C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 909 Processing helix chain 'C' and resid 914 through 924 removed outlier: 3.966A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN C 924 " --> pdb=" O GLU C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 935 through 940 Processing helix chain 'C' and resid 953 through 965 Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.748A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1018 removed outlier: 3.512A pdb=" N ALA C1005 " --> pdb=" O GLN C1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1021 No H-bonds generated for 'chain 'C' and resid 1019 through 1021' Processing helix chain 'C' and resid 1023 through 1045 removed outlier: 3.882A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1049 removed outlier: 3.528A pdb=" N ASN C1049 " --> pdb=" O GLN C1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1046 through 1049' Processing helix chain 'C' and resid 1057 through 1063 Processing helix chain 'C' and resid 1066 through 1114 removed outlier: 5.083A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C1077 " --> pdb=" O GLN C1073 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 91 Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.893A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.787A pdb=" N ILE B 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 379 " --> pdb=" O SER B 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 375 through 379' Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.576A pdb=" N LEU B 401 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B 402 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 442 through 448 removed outlier: 4.004A pdb=" N ARG B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR B 448 " --> pdb=" O TRP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.509A pdb=" N ASN B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 556 removed outlier: 3.590A pdb=" N CYS B 556 " --> pdb=" O GLU B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 696 through 701 Processing helix chain 'B' and resid 825 through 830 Processing helix chain 'B' and resid 831 through 833 No H-bonds generated for 'chain 'B' and resid 831 through 833' Processing helix chain 'B' and resid 835 through 862 removed outlier: 4.077A pdb=" N ILE B 839 " --> pdb=" O PHE B 835 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 843 " --> pdb=" O ILE B 839 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 844 " --> pdb=" O ASN B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 901 through 910 removed outlier: 3.679A pdb=" N LEU B 906 " --> pdb=" O PRO B 902 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS B 910 " --> pdb=" O LEU B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 923 removed outlier: 3.562A pdb=" N PHE B 918 " --> pdb=" O SER B 914 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN B 923 " --> pdb=" O VAL B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 928 removed outlier: 4.593A pdb=" N GLY B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 941 removed outlier: 4.176A pdb=" N VAL B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 964 removed outlier: 3.797A pdb=" N ALA B 962 " --> pdb=" O TYR B 958 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 964 " --> pdb=" O THR B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.893A pdb=" N PHE B 968 " --> pdb=" O ALA B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 978 through 989 removed outlier: 3.622A pdb=" N GLY B 989 " --> pdb=" O TYR B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 998 removed outlier: 3.512A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1018 Processing helix chain 'B' and resid 1023 through 1045 removed outlier: 3.847A pdb=" N LYS B1028 " --> pdb=" O SER B1024 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE B1029 " --> pdb=" O ALA B1025 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 Processing helix chain 'B' and resid 1057 through 1063 removed outlier: 3.541A pdb=" N ILE B1061 " --> pdb=" O SER B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1069 Processing helix chain 'B' and resid 1070 through 1114 removed outlier: 4.248A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B1077 " --> pdb=" O GLN B1073 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B1114 " --> pdb=" O VAL B1110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 67 removed outlier: 3.527A pdb=" N PHE A 67 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 262 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASN A 278 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.527A pdb=" N ARG A 75 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 211 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A 224 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.709A pdb=" N GLY A 81 " --> pdb=" O LEU A 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 112 Processing sheet with id=AA6, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.756A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.518A pdb=" N PHE A 713 " --> pdb=" O VAL A 720 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 316 through 319 removed outlier: 6.729A pdb=" N VAL A 317 " --> pdb=" O ASP A 623 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL A 620 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY A 631 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 337 through 338 removed outlier: 6.301A pdb=" N THR A 435 " --> pdb=" O VAL A 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.983A pdb=" N GLU A 345 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 390 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.983A pdb=" N GLU A 345 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 390 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 353 through 354 removed outlier: 3.710A pdb=" N PHE A 354 " --> pdb=" O CYS A 603 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 460 through 463 Processing sheet with id=AB5, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.684A pdb=" N CYS A 466 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 538 " --> pdb=" O CYS A 466 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 536 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 550 through 551 removed outlier: 3.774A pdb=" N GLY A 550 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 724 through 725 removed outlier: 6.482A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 773 through 775 removed outlier: 6.056A pdb=" N SER A 773 " --> pdb=" O LEU C 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 786 through 791 Processing sheet with id=AC1, first strand: chain 'A' and resid 794 through 803 removed outlier: 3.744A pdb=" N LEU A1131 " --> pdb=" O PHE A1146 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.127A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 866 through 868 removed outlier: 6.882A pdb=" N LEU A 867 " --> pdb=" O VAL B 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 1162 through 1163 removed outlier: 3.699A pdb=" N CYS A1163 " --> pdb=" O THR A1213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 1170 through 1172 Processing sheet with id=AC6, first strand: chain 'A' and resid 1175 through 1179 Processing sheet with id=AC7, first strand: chain 'T' and resid 260 through 261 removed outlier: 4.525A pdb=" N ASN T 398 " --> pdb=" O GLY T 383 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY T 383 " --> pdb=" O ASN T 398 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU T 378 " --> pdb=" O SER T 448 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER T 448 " --> pdb=" O LEU T 378 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL T 446 " --> pdb=" O TRP T 380 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS T 449 " --> pdb=" O ILE T 452 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 260 through 261 removed outlier: 4.617A pdb=" N CYS T 426 " --> pdb=" O ILE T 405 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N VAL T 473 " --> pdb=" O SER T 460 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER T 460 " --> pdb=" O VAL T 473 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'T' and resid 278 through 283 removed outlier: 5.301A pdb=" N HIS T 279 " --> pdb=" O VAL T 275 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL T 275 " --> pdb=" O HIS T 279 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS T 281 " --> pdb=" O LEU T 273 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS T 350 " --> pdb=" O GLU T 329 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL T 331 " --> pdb=" O LEU T 348 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU T 348 " --> pdb=" O VAL T 331 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 35 through 36 removed outlier: 4.258A pdb=" N ILE C 35 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C 75 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TRP C 257 " --> pdb=" O LYS C 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 105 " --> pdb=" O TRP C 257 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLY C 101 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 61 through 68 removed outlier: 3.955A pdb=" N ASN C 278 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 80 through 81 removed outlier: 3.658A pdb=" N GLY C 81 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.710A pdb=" N SER C 96 " --> pdb=" O TYR C 235 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 235 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 125 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 109 through 113 removed outlier: 3.896A pdb=" N THR C 109 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU C 120 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 302 through 305 Processing sheet with id=AD7, first strand: chain 'C' and resid 309 through 310 Processing sheet with id=AD8, first strand: chain 'C' and resid 316 through 319 removed outlier: 4.121A pdb=" N ARG C 319 " --> pdb=" O ASP C 623 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 629 " --> pdb=" O TYR C 622 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 55 " --> pdb=" O LEU C 647 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 345 through 349 removed outlier: 4.510A pdb=" N GLU C 345 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS C 390 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C 386 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER C 385 " --> pdb=" O ASN C 595 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN C 595 " --> pdb=" O SER C 385 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 368 through 371 Processing sheet with id=AE2, first strand: chain 'C' and resid 460 through 463 Processing sheet with id=AE3, first strand: chain 'C' and resid 724 through 731 removed outlier: 6.676A pdb=" N VAL C 724 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N THR C 766 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N LEU C 726 " --> pdb=" O THR C 766 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE C 742 " --> pdb=" O MET C 738 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 773 through 775 removed outlier: 5.852A pdb=" N SER C 773 " --> pdb=" O LEU B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 786 through 791 Processing sheet with id=AE6, first strand: chain 'C' and resid 794 through 804 removed outlier: 3.644A pdb=" N LEU C1131 " --> pdb=" O PHE C1146 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR C1148 " --> pdb=" O HIS C1129 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N HIS C1129 " --> pdb=" O TYR C1148 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 809 through 811 removed outlier: 4.238A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 878 through 879 removed outlier: 3.642A pdb=" N VAL C 879 " --> pdb=" O ILE C 882 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 3.501A pdb=" N ILE C1170 " --> pdb=" O LEU C1162 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1175 through 1179 Processing sheet with id=AF2, first strand: chain 'B' and resid 25 through 26 removed outlier: 3.814A pdb=" N ASN B 26 " --> pdb=" O LEU B 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'B' and resid 35 through 39 removed outlier: 5.375A pdb=" N ASP B 38 " --> pdb=" O PHE B 74 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 62 through 68 removed outlier: 4.033A pdb=" N GLY B 101 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B 199 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 214 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR B 203 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 62 through 68 removed outlier: 4.031A pdb=" N ASN B 278 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 110 through 113 Processing sheet with id=AF7, first strand: chain 'B' and resid 183 through 187 removed outlier: 3.682A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS B 187 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE B 148 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR B 123 " --> pdb=" O MET B 238 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 161 through 162 removed outlier: 6.452A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'B' and resid 302 through 305 Processing sheet with id=AG1, first strand: chain 'B' and resid 317 through 319 removed outlier: 3.665A pdb=" N LYS B 665 " --> pdb=" O ASP B 660 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 648 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AG3, first strand: chain 'B' and resid 346 through 349 removed outlier: 6.706A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 459 through 462 Processing sheet with id=AG5, first strand: chain 'B' and resid 467 through 468 removed outlier: 3.627A pdb=" N LYS B 536 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 504 through 506 Processing sheet with id=AG7, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AG8, first strand: chain 'B' and resid 724 through 731 removed outlier: 6.047A pdb=" N ASN B 725 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE B 764 " --> pdb=" O ASN B 725 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR B 766 " --> pdb=" O THR B 727 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TYR B 729 " --> pdb=" O THR B 766 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.776A pdb=" N SER B1152 " --> pdb=" O THR B 792 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE B 794 " --> pdb=" O PRO B1150 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE B 796 " --> pdb=" O TYR B1148 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR B1148 " --> pdb=" O ILE B 796 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY B 798 " --> pdb=" O PHE B1146 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE B1146 " --> pdb=" O GLY B 798 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU B 800 " --> pdb=" O ILE B1144 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE B1144 " --> pdb=" O GLU B 800 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE B 802 " --> pdb=" O LEU B1142 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B1142 " --> pdb=" O PHE B 802 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN B 804 " --> pdb=" O GLY B1140 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLY B1140 " --> pdb=" O GLN B 804 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B1131 " --> pdb=" O PHE B1146 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYR B1148 " --> pdb=" O HIS B1129 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N HIS B1129 " --> pdb=" O TYR B1148 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.093A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 3.657A pdb=" N ILE B1170 " --> pdb=" O LEU B1162 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B1162 " --> pdb=" O ILE B1170 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 1175 through 1179 975 hydrogen bonds defined for protein. 2683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.44 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9392 1.34 - 1.46: 7458 1.46 - 1.58: 13188 1.58 - 1.70: 0 1.70 - 1.81: 211 Bond restraints: 30249 Sorted by residual: bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C1 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 ... (remaining 30244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 40757 1.71 - 3.41: 465 3.41 - 5.12: 21 5.12 - 6.83: 8 6.83 - 8.54: 2 Bond angle restraints: 41253 Sorted by residual: angle pdb=" CA LEU C 521 " pdb=" CB LEU C 521 " pdb=" CG LEU C 521 " ideal model delta sigma weight residual 116.30 124.84 -8.54 3.50e+00 8.16e-02 5.95e+00 angle pdb=" C SER C 519 " pdb=" N CYS C 520 " pdb=" CA CYS C 520 " ideal model delta sigma weight residual 122.07 125.31 -3.24 1.43e+00 4.89e-01 5.15e+00 angle pdb=" C3 BMA D 3 " pdb=" C2 BMA D 3 " pdb=" O2 BMA D 3 " ideal model delta sigma weight residual 112.95 106.77 6.18 3.00e+00 1.11e-01 4.24e+00 angle pdb=" C ASN C 53 " pdb=" N ARG C 54 " pdb=" CA ARG C 54 " ideal model delta sigma weight residual 121.87 126.26 -4.39 2.24e+00 1.99e-01 3.84e+00 angle pdb=" CA PRO A1067 " pdb=" C PRO A1067 " pdb=" N PRO A1068 " ideal model delta sigma weight residual 117.93 120.28 -2.35 1.20e+00 6.94e-01 3.82e+00 ... (remaining 41248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.79: 17979 21.79 - 43.58: 322 43.58 - 65.38: 32 65.38 - 87.17: 6 87.17 - 108.96: 4 Dihedral angle restraints: 18343 sinusoidal: 7287 harmonic: 11056 Sorted by residual: dihedral pdb=" CB CYS A 925 " pdb=" SG CYS A 925 " pdb=" SG CYS A 936 " pdb=" CB CYS A 936 " ideal model delta sinusoidal sigma weight residual 93.00 138.96 -45.96 1 1.00e+01 1.00e-02 2.93e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.75 108.96 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C3 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.26 106.88 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 18340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3987 0.054 - 0.108: 665 0.108 - 0.161: 102 0.161 - 0.215: 0 0.215 - 0.269: 1 Chirality restraints: 4755 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CG LEU C 521 " pdb=" CB LEU C 521 " pdb=" CD1 LEU C 521 " pdb=" CD2 LEU C 521 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A1211 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 4752 not shown) Planarity restraints: 5311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 91 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO B 92 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 92 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 92 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1066 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A1067 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A1067 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1067 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B1066 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO B1067 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B1067 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B1067 " -0.019 5.00e-02 4.00e+02 ... (remaining 5308 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 5345 2.78 - 3.31: 26799 3.31 - 3.84: 46158 3.84 - 4.37: 52054 4.37 - 4.90: 93700 Nonbonded interactions: 224056 Sorted by model distance: nonbonded pdb=" OD1 ASN C 355 " pdb=" OG1 THR C 358 " model vdw 2.244 3.040 nonbonded pdb=" O GLN B1180 " pdb=" OG SER B1183 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR C 832 " pdb=" OD1 ASP C1075 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR A 448 " pdb=" O PHE A 473 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THR A 123 " pdb=" O VAL A 139 " model vdw 2.274 3.040 ... (remaining 224051 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 14 through 19 or resid 21 through 24 or (resid 25 and (nam \ e N or name CA or name C or name O or name CB )) or resid 26 or (resid 34 and (n \ ame N or name CA or name C or name O or name CB )) or resid 35 through 79 or (re \ sid 80 and (name N or name CA or name C or name O or name CB )) or resid 81 thro \ ugh 83 or (resid 84 and (name N or name CA or name C or name O or name CB )) or \ resid 85 through 90 or (resid 91 and (name N or name CA or name C or name O or n \ ame CB )) or resid 92 through 109 or (resid 110 and (name N or name CA or name C \ or name O or name CB )) or resid 111 or (resid 112 and (name N or name CA or na \ me C or name O or name CB )) or resid 113 or (resid 114 through 115 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 117 or (resid \ 118 and (name N or name CA or name C or name O or name CB )) or resid 119 throug \ h 139 or (resid 140 and (name N or name CA or name C or name O or name CB )) or \ resid 141 through 156 or (resid 157 and (name N or name CA or name C or name O o \ r name CB )) or resid 158 through 163 or (resid 164 and (name N or name CA or na \ me C or name O or name CB )) or resid 165 or (resid 166 and (name N or name CA o \ r name C or name O or name CB )) or resid 167 through 173 or (resid 174 and (nam \ e N or name CA or name C or name O or name CB )) or resid 175 through 179 or (re \ sid 180 and (name N or name CA or name C or name O or name CB )) or resid 181 th \ rough 185 or (resid 186 and (name N or name CA or name C or name O or name CB )) \ or resid 187 through 205 or (resid 206 and (name N or name CA or name C or name \ O or name CB )) or resid 207 through 244 or resid 254 through 416 or (resid 417 \ and (name N or name CA or name C or name O or name CB )) or resid 418 through 4 \ 91 or (resid 492 through 493 and (name N or name CA or name C or name O or name \ CB )) or resid 494 through 522 or (resid 523 and (name N or name CA or name C or \ name O or name CB )) or resid 524 through 551 or (resid 552 and (name N or name \ CA or name C or name O or name CB )) or resid 553 or (resid 554 and (name N or \ name CA or name C or name O or name CB )) or resid 555 through 557 or resid 563 \ through 572 or (resid 573 and (name N or name CA or name C or name O or name CB \ )) or resid 574 through 615 or (resid 616 and (name N or name CA or name C or na \ me O or name CB )) or resid 617 through 619 or (resid 620 and (name N or name CA \ or name C or name O or name CB )) or resid 621 through 629 or (resid 630 and (n \ ame N or name CA or name C or name O or name CB )) or resid 631 or (resid 632 an \ d (name N or name CA or name C or name O or name CB )) or (resid 634 and (name N \ or name CA or name C or name O or name CB )) or resid 635 through 651 or (resid \ 652 and (name N or name CA or name C or name O or name CB )) or resid 653 or (r \ esid 654 and (name N or name CA or name C or name O or name CB )) or resid 655 t \ hrough 708 or (resid 709 and (name N or name CA or name C or name O or name CB ) \ ) or resid 710 through 779 or (resid 780 and (name N or name CA or name C or nam \ e O or name CB )) or resid 781 through 875 or (resid 876 and (name N or name CA \ or name C or name O or name CB )) or resid 877 through 929 or (resid 930 through \ 932 and (name N or name CA or name C or name O or name CB )) or resid 933 throu \ gh 998 or (resid 999 and (name N or name CA or name C or name O or name CB )) or \ resid 1000 through 1148 or (resid 1149 and (name N or name CA or name C or name \ O or name CB )) or resid 1150 through 1199 or (resid 1200 and (name N or name C \ A or name C or name O or name CB )) or resid 1201 through 1306)) selection = (chain 'B' and (resid 14 through 19 or resid 21 through 26 or resid 34 through 1 \ 09 or (resid 110 and (name N or name CA or name C or name O or name CB )) or res \ id 111 through 117 or (resid 118 and (name N or name CA or name C or name O or n \ ame CB )) or resid 119 through 139 or (resid 140 and (name N or name CA or name \ C or name O or name CB )) or resid 141 through 156 or (resid 157 and (name N or \ name CA or name C or name O or name CB )) or resid 158 through 173 or (resid 174 \ and (name N or name CA or name C or name O or name CB )) or resid 175 through 1 \ 85 or (resid 186 and (name N or name CA or name C or name O or name CB )) or res \ id 187 through 235 or resid 237 through 416 or (resid 417 and (name N or name CA \ or name C or name O or name CB )) or resid 418 through 483 or resid 490 through \ 501 or (resid 502 and (name N or name CA or name C or name O or name CB )) or r \ esid 519 through 520 or (resid 521 and (name N or name CA or name C or name O or \ name CB )) or resid 522 or (resid 523 and (name N or name CA or name C or name \ O or name CB )) or resid 524 through 551 or (resid 552 and (name N or name CA or \ name C or name O or name CB )) or resid 553 through 572 or (resid 573 and (name \ N or name CA or name C or name O or name CB )) or resid 574 through 632 or resi \ d 634 through 705 or (resid 706 and (name N or name CA or name C or name O or na \ me CB )) or resid 707 through 708 or (resid 709 and (name N or name CA or name C \ or name O or name CB )) or resid 710 through 779 or (resid 780 and (name N or n \ ame CA or name C or name O or name CB )) or resid 781 through 929 or (resid 930 \ through 932 and (name N or name CA or name C or name O or name CB )) or resid 93 \ 3 through 998 or (resid 999 and (name N or name CA or name C or name O or name C \ B )) or resid 1000 through 1199 or (resid 1200 and (name N or name CA or name C \ or name O or name CB )) or resid 1201 through 1306)) selection = (chain 'C' and (resid 14 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 79 or (resid 80 and (name N or nam \ e CA or name C or name O or name CB )) or resid 81 through 111 or (resid 112 and \ (name N or name CA or name C or name O or name CB )) or resid 113 or (resid 114 \ through 115 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 16 through 163 or (resid 164 and (name N or name CA or name C or name O or name \ CB )) or resid 165 through 179 or (resid 180 and (name N or name CA or name C or \ name O or name CB )) or resid 181 through 205 or (resid 206 and (name N or name \ CA or name C or name O or name CB )) or resid 207 through 235 or resid 237 thro \ ugh 244 or resid 254 through 311 or (resid 312 and (name N or name CA or name C \ or name O or name CB )) or resid 313 through 483 or resid 490 through 491 or (re \ sid 492 through 493 and (name N or name CA or name C or name O or name CB )) or \ resid 494 through 501 or (resid 502 and (name N or name CA or name C or name O o \ r name CB )) or resid 519 through 520 or (resid 521 and (name N or name CA or na \ me C or name O or name CB )) or resid 522 through 553 or (resid 554 and (name N \ or name CA or name C or name O or name CB )) or resid 555 through 557 or resid 5 \ 63 through 569 or (resid 570 through 571 and (name N or name CA or name C or nam \ e O or name CB )) or resid 572 through 615 or (resid 616 and (name N or name CA \ or name C or name O or name CB )) or resid 617 through 619 or (resid 620 and (na \ me N or name CA or name C or name O or name CB )) or resid 621 through 629 or (r \ esid 630 and (name N or name CA or name C or name O or name CB )) or resid 631 o \ r (resid 632 and (name N or name CA or name C or name O or name CB )) or (resid \ 634 and (name N or name CA or name C or name O or name CB )) or resid 635 throug \ h 651 or (resid 652 and (name N or name CA or name C or name O or name CB )) or \ resid 653 or (resid 654 and (name N or name CA or name C or name O or name CB )) \ or resid 655 through 705 or (resid 706 and (name N or name CA or name C or name \ O or name CB )) or resid 707 through 875 or (resid 876 and (name N or name CA o \ r name C or name O or name CB )) or resid 877 through 930 or (resid 931 through \ 932 and (name N or name CA or name C or name O or name CB )) or resid 933 throug \ h 1148 or (resid 1149 and (name N or name CA or name C or name O or name CB )) o \ r resid 1150 through 1306)) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.850 Find NCS groups from input model: 0.750 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 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 : 0.002 0.035 30347 Z= 0.106 Angle : 0.432 8.537 41478 Z= 0.222 Chirality : 0.041 0.269 4755 Planarity : 0.003 0.051 5286 Dihedral : 7.819 108.960 11032 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.77 % Allowed : 4.58 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.12), residues: 3749 helix: 0.01 (0.19), residues: 706 sheet: -0.72 (0.17), residues: 732 loop : -2.50 (0.11), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 347 TYR 0.010 0.001 TYR A1148 PHE 0.008 0.001 PHE B 209 TRP 0.011 0.000 TRP B 344 HIS 0.003 0.000 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00208 (30249) covalent geometry : angle 0.43012 (41253) SS BOND : bond 0.00097 ( 69) SS BOND : angle 0.46098 ( 138) hydrogen bonds : bond 0.14182 ( 955) hydrogen bonds : angle 5.15620 ( 2683) link_BETA1-4 : bond 0.00475 ( 4) link_BETA1-4 : angle 1.06993 ( 12) link_NAG-ASN : bond 0.00196 ( 25) link_NAG-ASN : angle 0.90029 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 803 time to evaluate : 1.030 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 62 LEU cc_start: 0.8522 (mt) cc_final: 0.8294 (mt) REVERT: A 106 VAL cc_start: 0.8311 (t) cc_final: 0.8041 (m) REVERT: A 186 LYS cc_start: 0.8198 (tttt) cc_final: 0.7832 (tttt) REVERT: A 238 MET cc_start: 0.6263 (ptp) cc_final: 0.5932 (ptp) REVERT: A 293 LYS cc_start: 0.8627 (ttpp) cc_final: 0.8380 (ttmm) REVERT: A 323 ASN cc_start: 0.6538 (p0) cc_final: 0.6256 (p0) REVERT: A 357 SER cc_start: 0.8422 (t) cc_final: 0.8143 (p) REVERT: A 431 LEU cc_start: 0.8412 (mt) cc_final: 0.8203 (mt) REVERT: A 473 PHE cc_start: 0.7636 (t80) cc_final: 0.7426 (t80) REVERT: A 500 LYS cc_start: 0.8302 (ptpt) cc_final: 0.7879 (ptpt) REVERT: A 577 PHE cc_start: 0.6297 (m-10) cc_final: 0.5863 (m-10) REVERT: A 603 CYS cc_start: 0.4680 (m) cc_final: 0.4369 (m) REVERT: A 610 SER cc_start: 0.8402 (t) cc_final: 0.7901 (m) REVERT: A 635 GLU cc_start: 0.6867 (tm-30) cc_final: 0.6645 (tm-30) REVERT: A 661 PHE cc_start: 0.8073 (m-80) cc_final: 0.7799 (m-10) REVERT: A 673 TYR cc_start: 0.7649 (t80) cc_final: 0.7447 (t80) REVERT: A 720 VAL cc_start: 0.8007 (t) cc_final: 0.7784 (m) REVERT: A 782 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8463 (p) REVERT: A 806 SER cc_start: 0.8594 (m) cc_final: 0.8322 (t) REVERT: A 827 ASP cc_start: 0.7230 (m-30) cc_final: 0.6818 (m-30) REVERT: A 828 LEU cc_start: 0.8463 (mm) cc_final: 0.8157 (mt) REVERT: A 851 ASP cc_start: 0.7044 (m-30) cc_final: 0.6765 (m-30) REVERT: A 1010 LYS cc_start: 0.8207 (tttt) cc_final: 0.7941 (ttmm) REVERT: A 1048 PHE cc_start: 0.8532 (m-10) cc_final: 0.8290 (m-80) REVERT: A 1054 ILE cc_start: 0.8745 (tp) cc_final: 0.8522 (tp) REVERT: A 1095 ASP cc_start: 0.6991 (m-30) cc_final: 0.6573 (m-30) REVERT: A 1116 SER cc_start: 0.8513 (t) cc_final: 0.7977 (p) REVERT: A 1185 MET cc_start: 0.7270 (mtp) cc_final: 0.6119 (mtp) REVERT: C 66 TYR cc_start: 0.8532 (m-80) cc_final: 0.8331 (m-80) REVERT: C 90 TYR cc_start: 0.8150 (m-80) cc_final: 0.7811 (m-10) REVERT: C 107 LYS cc_start: 0.7860 (tttp) cc_final: 0.7604 (tttp) REVERT: C 338 VAL cc_start: 0.4854 (OUTLIER) cc_final: 0.4627 (p) REVERT: C 353 ASN cc_start: 0.7855 (m-40) cc_final: 0.7493 (m-40) REVERT: C 354 PHE cc_start: 0.7861 (p90) cc_final: 0.7594 (p90) REVERT: C 634 LYS cc_start: 0.7552 (ttmm) cc_final: 0.7347 (ttmm) REVERT: C 647 LEU cc_start: 0.8200 (pp) cc_final: 0.7753 (pp) REVERT: C 711 PHE cc_start: 0.7645 (m-80) cc_final: 0.7422 (m-80) REVERT: C 729 TYR cc_start: 0.7312 (t80) cc_final: 0.6981 (t80) REVERT: C 782 VAL cc_start: 0.9126 (t) cc_final: 0.8772 (m) REVERT: C 845 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.6140 (mp0) REVERT: C 848 ASP cc_start: 0.7231 (m-30) cc_final: 0.6845 (m-30) REVERT: C 1056 SER cc_start: 0.8121 (p) cc_final: 0.7868 (t) REVERT: C 1095 ASP cc_start: 0.7477 (t0) cc_final: 0.7148 (t0) REVERT: C 1109 LYS cc_start: 0.8363 (ttmt) cc_final: 0.8081 (tttt) REVERT: C 1112 GLU cc_start: 0.6441 (mt-10) cc_final: 0.6183 (mt-10) REVERT: C 1173 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7867 (mtpp) REVERT: B 124 ILE cc_start: 0.7431 (tt) cc_final: 0.7021 (pt) REVERT: B 133 THR cc_start: 0.7497 (p) cc_final: 0.7293 (p) REVERT: B 147 GLU cc_start: 0.6116 (tm-30) cc_final: 0.5678 (tm-30) REVERT: B 148 ILE cc_start: 0.8013 (mp) cc_final: 0.7770 (tt) REVERT: B 266 TYR cc_start: 0.6997 (m-80) cc_final: 0.6751 (m-80) REVERT: B 324 LEU cc_start: 0.7684 (mt) cc_final: 0.7483 (mp) REVERT: B 651 SER cc_start: 0.8252 (m) cc_final: 0.8037 (m) REVERT: B 702 ASN cc_start: 0.7770 (t0) cc_final: 0.7412 (t0) REVERT: B 878 ASP cc_start: 0.7142 (p0) cc_final: 0.6773 (p0) REVERT: B 883 ASP cc_start: 0.7767 (t0) cc_final: 0.7537 (t0) REVERT: B 905 ASP cc_start: 0.7696 (m-30) cc_final: 0.7427 (m-30) REVERT: B 985 TYR cc_start: 0.8104 (m-10) cc_final: 0.7769 (m-10) REVERT: B 999 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7869 (mtpt) REVERT: B 1038 GLN cc_start: 0.7502 (tp40) cc_final: 0.7198 (tp40) REVERT: B 1060 GLU cc_start: 0.7319 (tt0) cc_final: 0.7078 (tt0) REVERT: B 1090 SER cc_start: 0.8408 (t) cc_final: 0.8177 (m) REVERT: B 1095 ASP cc_start: 0.7313 (t0) cc_final: 0.6867 (t0) REVERT: B 1156 VAL cc_start: 0.8628 (p) cc_final: 0.8302 (m) outliers start: 58 outliers final: 14 residues processed: 845 average time/residue: 0.1905 time to fit residues: 256.2467 Evaluate side-chains 624 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 607 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1114 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 140 GLN A 248 ASN A 265 GLN A 291 GLN ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 ASN ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 HIS A 531 ASN A 545 HIS A 709 GLN A 847 ASN A1017 ASN A1045 GLN A1046 GLN A1049 ASN A1071 GLN A1181 ASN T 276 GLN C 335 ASN C 353 ASN C 562 HIS C 591 ASN C 789 GLN C 872 ASN C 881 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 998 ASN C1000 ASN C1001 GLN C1038 GLN C1059 GLN C1135 GLN B 108 ASN B 152 GLN B 265 GLN B 355 ASN B 395 ASN B 410 GLN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 GLN B 826 HIS B 870 ASN B1059 GLN B1122 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1145 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.162873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.121193 restraints weight = 46451.493| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.61 r_work: 0.3295 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 30347 Z= 0.328 Angle : 0.710 12.884 41478 Z= 0.364 Chirality : 0.051 0.298 4755 Planarity : 0.005 0.055 5286 Dihedral : 6.003 64.621 4685 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.30 % Allowed : 11.36 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.13), residues: 3749 helix: 0.57 (0.20), residues: 757 sheet: -0.48 (0.17), residues: 740 loop : -2.12 (0.12), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1168 TYR 0.047 0.003 TYR B 203 PHE 0.040 0.003 PHE C 767 TRP 0.016 0.002 TRP C 971 HIS 0.017 0.002 HIS C1145 Details of bonding type rmsd covalent geometry : bond 0.00759 (30249) covalent geometry : angle 0.69317 (41253) SS BOND : bond 0.00375 ( 69) SS BOND : angle 1.66673 ( 138) hydrogen bonds : bond 0.06552 ( 955) hydrogen bonds : angle 4.83145 ( 2683) link_BETA1-4 : bond 0.00328 ( 4) link_BETA1-4 : angle 1.95924 ( 12) link_NAG-ASN : bond 0.01273 ( 25) link_NAG-ASN : angle 3.02468 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 635 time to evaluate : 0.670 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 104 SER cc_start: 0.8650 (p) cc_final: 0.8422 (m) REVERT: A 106 VAL cc_start: 0.8628 (t) cc_final: 0.8235 (m) REVERT: A 160 HIS cc_start: 0.7647 (p-80) cc_final: 0.7053 (p-80) REVERT: A 234 HIS cc_start: 0.7847 (m90) cc_final: 0.7543 (m90) REVERT: A 238 MET cc_start: 0.6943 (ptp) cc_final: 0.6646 (ptp) REVERT: A 323 ASN cc_start: 0.7504 (p0) cc_final: 0.7226 (p0) REVERT: A 357 SER cc_start: 0.8610 (t) cc_final: 0.8403 (p) REVERT: A 396 ARG cc_start: 0.8316 (mtp180) cc_final: 0.8051 (mtp180) REVERT: A 467 PHE cc_start: 0.8939 (m-80) cc_final: 0.8708 (m-80) REVERT: A 473 PHE cc_start: 0.8323 (t80) cc_final: 0.7740 (t80) REVERT: A 500 LYS cc_start: 0.8565 (ptpt) cc_final: 0.8105 (ptpt) REVERT: A 535 GLN cc_start: 0.8483 (mt0) cc_final: 0.8188 (mt0) REVERT: A 538 VAL cc_start: 0.8840 (p) cc_final: 0.8588 (m) REVERT: A 610 SER cc_start: 0.8924 (t) cc_final: 0.8382 (m) REVERT: A 632 ILE cc_start: 0.8664 (mt) cc_final: 0.8346 (mp) REVERT: A 635 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7656 (tm-30) REVERT: A 667 TYR cc_start: 0.8510 (m-80) cc_final: 0.8045 (m-80) REVERT: A 806 SER cc_start: 0.8931 (m) cc_final: 0.8699 (t) REVERT: A 827 ASP cc_start: 0.8290 (m-30) cc_final: 0.8008 (m-30) REVERT: A 863 GLN cc_start: 0.8420 (tp40) cc_final: 0.8107 (tt0) REVERT: A 916 VAL cc_start: 0.8816 (p) cc_final: 0.8515 (t) REVERT: A 1010 LYS cc_start: 0.8448 (tttt) cc_final: 0.8078 (ttmm) REVERT: A 1028 LYS cc_start: 0.8549 (mttt) cc_final: 0.8187 (mtmm) REVERT: A 1091 GLN cc_start: 0.8040 (mt0) cc_final: 0.7608 (mt0) REVERT: A 1095 ASP cc_start: 0.7729 (m-30) cc_final: 0.7271 (m-30) REVERT: A 1116 SER cc_start: 0.8772 (t) cc_final: 0.8203 (p) REVERT: A 1179 LYS cc_start: 0.8639 (ttpt) cc_final: 0.8308 (ttmm) REVERT: C 74 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7947 (t80) REVERT: C 86 SER cc_start: 0.8583 (t) cc_final: 0.8277 (p) REVERT: C 128 SER cc_start: 0.8950 (p) cc_final: 0.8708 (m) REVERT: C 261 LEU cc_start: 0.8753 (mt) cc_final: 0.8543 (mp) REVERT: C 275 VAL cc_start: 0.8537 (t) cc_final: 0.8314 (p) REVERT: C 595 ASN cc_start: 0.7758 (m110) cc_final: 0.7523 (p0) REVERT: C 649 TYR cc_start: 0.8741 (m-80) cc_final: 0.8521 (m-10) REVERT: C 711 PHE cc_start: 0.8401 (m-80) cc_final: 0.8006 (m-80) REVERT: C 954 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7838 (mt0) REVERT: C 977 VAL cc_start: 0.8100 (t) cc_final: 0.7837 (m) REVERT: C 1001 GLN cc_start: 0.8869 (mt0) cc_final: 0.8654 (mt0) REVERT: C 1013 LEU cc_start: 0.8546 (mp) cc_final: 0.8332 (mm) REVERT: C 1095 ASP cc_start: 0.8298 (t0) cc_final: 0.7862 (t0) REVERT: C 1183 SER cc_start: 0.8435 (t) cc_final: 0.7762 (p) REVERT: C 1214 LYS cc_start: 0.8923 (mtpp) cc_final: 0.8667 (mtpp) REVERT: B 41 ASP cc_start: 0.8165 (t0) cc_final: 0.7757 (t70) REVERT: B 105 LYS cc_start: 0.8180 (tttm) cc_final: 0.7834 (tttm) REVERT: B 147 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6743 (tm-30) REVERT: B 148 ILE cc_start: 0.8265 (mp) cc_final: 0.7890 (tt) REVERT: B 320 ARG cc_start: 0.8106 (ttm170) cc_final: 0.7704 (mtt-85) REVERT: B 467 PHE cc_start: 0.8524 (m-80) cc_final: 0.8230 (m-10) REVERT: B 702 ASN cc_start: 0.8254 (t0) cc_final: 0.7756 (t0) REVERT: B 745 ASP cc_start: 0.8017 (t0) cc_final: 0.7510 (t70) REVERT: B 746 TYR cc_start: 0.8376 (t80) cc_final: 0.8052 (t80) REVERT: B 883 ASP cc_start: 0.8474 (t0) cc_final: 0.8209 (t0) REVERT: B 888 LEU cc_start: 0.8458 (mt) cc_final: 0.8240 (mp) REVERT: B 904 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7572 (mt-10) REVERT: B 912 LYS cc_start: 0.8609 (ptmt) cc_final: 0.8226 (ptmt) REVERT: B 1038 GLN cc_start: 0.8468 (tp40) cc_final: 0.7723 (tp40) REVERT: B 1060 GLU cc_start: 0.8505 (tt0) cc_final: 0.8150 (tt0) REVERT: B 1064 ARG cc_start: 0.8983 (mtp180) cc_final: 0.8664 (mtp-110) REVERT: B 1090 SER cc_start: 0.8885 (t) cc_final: 0.8600 (m) REVERT: B 1095 ASP cc_start: 0.8047 (t0) cc_final: 0.7663 (t0) REVERT: B 1212 PHE cc_start: 0.7422 (m-10) cc_final: 0.6569 (m-80) outliers start: 108 outliers final: 70 residues processed: 695 average time/residue: 0.1804 time to fit residues: 202.0285 Evaluate side-chains 636 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 564 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 793 ASN Chi-restraints excluded: chain A residue 881 ASN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 998 ASN Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1065 LEU Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1187 THR Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1200 LYS Chi-restraints excluded: chain B residue 1205 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 120 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 359 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 310 optimal weight: 20.0000 chunk 97 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 292 optimal weight: 20.0000 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 909 ASN A 941 ASN C 353 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 998 ASN C1000 ASN B 152 GLN ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1117 GLN B1135 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.163535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121644 restraints weight = 46799.256| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.74 r_work: 0.3329 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30347 Z= 0.151 Angle : 0.580 12.162 41478 Z= 0.292 Chirality : 0.045 0.251 4755 Planarity : 0.004 0.047 5286 Dihedral : 5.266 57.262 4680 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.11 % Allowed : 13.37 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: -1.33 (0.13), residues: 3749 helix: 1.15 (0.21), residues: 750 sheet: -0.24 (0.18), residues: 751 loop : -1.93 (0.12), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1076 TYR 0.018 0.002 TYR C 49 PHE 0.025 0.001 PHE B 658 TRP 0.028 0.001 TRP B 197 HIS 0.007 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00348 (30249) covalent geometry : angle 0.55964 (41253) SS BOND : bond 0.00334 ( 69) SS BOND : angle 1.89967 ( 138) hydrogen bonds : bond 0.05039 ( 955) hydrogen bonds : angle 4.58775 ( 2683) link_BETA1-4 : bond 0.00323 ( 4) link_BETA1-4 : angle 1.70439 ( 12) link_NAG-ASN : bond 0.00353 ( 25) link_NAG-ASN : angle 2.59135 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 570 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 SER cc_start: 0.8676 (p) cc_final: 0.8439 (m) REVERT: A 155 MET cc_start: 0.7063 (mmm) cc_final: 0.6729 (mmm) REVERT: A 160 HIS cc_start: 0.7606 (p-80) cc_final: 0.7095 (p-80) REVERT: A 234 HIS cc_start: 0.7929 (m90) cc_final: 0.7623 (m90) REVERT: A 238 MET cc_start: 0.6966 (ptp) cc_final: 0.6661 (ptp) REVERT: A 323 ASN cc_start: 0.7553 (p0) cc_final: 0.7274 (p0) REVERT: A 366 ASP cc_start: 0.7738 (t0) cc_final: 0.7407 (t0) REVERT: A 464 ASP cc_start: 0.8349 (t0) cc_final: 0.8121 (t0) REVERT: A 473 PHE cc_start: 0.8340 (t80) cc_final: 0.7800 (t80) REVERT: A 500 LYS cc_start: 0.8549 (ptpt) cc_final: 0.8093 (ptpt) REVERT: A 530 PRO cc_start: 0.9287 (Cg_endo) cc_final: 0.9071 (Cg_exo) REVERT: A 535 GLN cc_start: 0.8411 (mt0) cc_final: 0.8176 (mt0) REVERT: A 538 VAL cc_start: 0.8880 (p) cc_final: 0.8635 (m) REVERT: A 555 LYS cc_start: 0.8376 (tppp) cc_final: 0.7942 (tppp) REVERT: A 610 SER cc_start: 0.8920 (t) cc_final: 0.8349 (m) REVERT: A 632 ILE cc_start: 0.8672 (mt) cc_final: 0.8400 (mp) REVERT: A 635 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7704 (tm-30) REVERT: A 667 TYR cc_start: 0.8442 (m-80) cc_final: 0.8241 (m-80) REVERT: A 768 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8330 (mm-30) REVERT: A 806 SER cc_start: 0.8967 (m) cc_final: 0.8712 (t) REVERT: A 827 ASP cc_start: 0.8303 (m-30) cc_final: 0.8001 (m-30) REVERT: A 828 LEU cc_start: 0.8725 (mm) cc_final: 0.8509 (mt) REVERT: A 985 TYR cc_start: 0.8797 (m-80) cc_final: 0.8508 (m-80) REVERT: A 1010 LYS cc_start: 0.8428 (tttt) cc_final: 0.8047 (ttmm) REVERT: A 1028 LYS cc_start: 0.8377 (mttt) cc_final: 0.8083 (mtmm) REVERT: A 1091 GLN cc_start: 0.7971 (mt0) cc_final: 0.7529 (mt0) REVERT: A 1095 ASP cc_start: 0.7782 (m-30) cc_final: 0.7310 (m-30) REVERT: A 1116 SER cc_start: 0.8759 (t) cc_final: 0.8202 (p) REVERT: A 1179 LYS cc_start: 0.8627 (ttpt) cc_final: 0.8311 (ttmm) REVERT: C 53 ASN cc_start: 0.8335 (p0) cc_final: 0.7976 (p0) REVERT: C 74 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.8028 (t80) REVERT: C 86 SER cc_start: 0.8512 (t) cc_final: 0.8264 (p) REVERT: C 120 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7891 (mt-10) REVERT: C 128 SER cc_start: 0.8943 (p) cc_final: 0.8694 (m) REVERT: C 155 MET cc_start: 0.8772 (mmt) cc_final: 0.8378 (mmp) REVERT: C 264 ARG cc_start: 0.8519 (mtp85) cc_final: 0.8205 (mtp85) REVERT: C 275 VAL cc_start: 0.8517 (t) cc_final: 0.8295 (p) REVERT: C 595 ASN cc_start: 0.7701 (m110) cc_final: 0.7455 (p0) REVERT: C 624 LEU cc_start: 0.8783 (mp) cc_final: 0.8562 (mm) REVERT: C 649 TYR cc_start: 0.8748 (m-80) cc_final: 0.8515 (m-10) REVERT: C 711 PHE cc_start: 0.8322 (m-80) cc_final: 0.7949 (m-80) REVERT: C 845 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: C 862 MET cc_start: 0.7778 (mtt) cc_final: 0.7563 (mtp) REVERT: C 981 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8120 (mp) REVERT: C 1001 GLN cc_start: 0.8812 (mt0) cc_final: 0.8556 (mt0) REVERT: C 1095 ASP cc_start: 0.8371 (t0) cc_final: 0.7958 (t0) REVERT: C 1173 LYS cc_start: 0.8382 (mtpp) cc_final: 0.8056 (mtpp) REVERT: C 1183 SER cc_start: 0.8391 (t) cc_final: 0.7698 (p) REVERT: C 1214 LYS cc_start: 0.8939 (mtpp) cc_final: 0.8690 (mtpp) REVERT: B 41 ASP cc_start: 0.8276 (t0) cc_final: 0.7834 (t70) REVERT: B 105 LYS cc_start: 0.7978 (tttm) cc_final: 0.7662 (tmtt) REVERT: B 147 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6779 (tm-30) REVERT: B 148 ILE cc_start: 0.8219 (mp) cc_final: 0.7882 (tt) REVERT: B 237 VAL cc_start: 0.7413 (OUTLIER) cc_final: 0.7195 (p) REVERT: B 320 ARG cc_start: 0.8161 (ttm170) cc_final: 0.7733 (mtt-85) REVERT: B 348 ILE cc_start: 0.8912 (mp) cc_final: 0.8432 (tp) REVERT: B 398 ARG cc_start: 0.8351 (ptp-110) cc_final: 0.7697 (mtt180) REVERT: B 467 PHE cc_start: 0.8495 (m-80) cc_final: 0.8229 (m-10) REVERT: B 702 ASN cc_start: 0.8192 (t0) cc_final: 0.7690 (t0) REVERT: B 745 ASP cc_start: 0.7944 (t0) cc_final: 0.7563 (t0) REVERT: B 746 TYR cc_start: 0.8338 (t80) cc_final: 0.8069 (t80) REVERT: B 883 ASP cc_start: 0.8468 (t0) cc_final: 0.8238 (t0) REVERT: B 912 LYS cc_start: 0.8560 (ptmt) cc_final: 0.8196 (ptmt) REVERT: B 999 LYS cc_start: 0.8558 (mtpt) cc_final: 0.8308 (mtpt) REVERT: B 1038 GLN cc_start: 0.8495 (tp40) cc_final: 0.7730 (tp40) REVERT: B 1060 GLU cc_start: 0.8520 (tt0) cc_final: 0.8260 (tt0) REVERT: B 1090 SER cc_start: 0.8895 (t) cc_final: 0.8598 (m) REVERT: B 1095 ASP cc_start: 0.8097 (t0) cc_final: 0.7728 (t0) REVERT: B 1212 PHE cc_start: 0.7557 (m-10) cc_final: 0.6668 (m-80) outliers start: 102 outliers final: 69 residues processed: 628 average time/residue: 0.1774 time to fit residues: 181.5175 Evaluate side-chains 619 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 546 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 881 ASN Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain T residue 478 MET Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 869 SER Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 959 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1200 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 238 optimal weight: 0.5980 chunk 232 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 354 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 303 optimal weight: 10.0000 chunk 339 optimal weight: 1.9990 chunk 122 optimal weight: 30.0000 chunk 96 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN B 152 GLN B 269 ASN B 413 ASN B 998 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.163897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.122359 restraints weight = 46467.540| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.74 r_work: 0.3324 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30347 Z= 0.132 Angle : 0.541 9.776 41478 Z= 0.274 Chirality : 0.044 0.259 4755 Planarity : 0.004 0.045 5286 Dihedral : 4.767 57.534 4676 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.42 % Allowed : 13.58 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.13), residues: 3749 helix: 1.43 (0.21), residues: 751 sheet: -0.13 (0.18), residues: 751 loop : -1.81 (0.12), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 398 TYR 0.016 0.001 TYR C 49 PHE 0.023 0.001 PHE A 566 TRP 0.018 0.001 TRP B 174 HIS 0.009 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00307 (30249) covalent geometry : angle 0.52576 (41253) SS BOND : bond 0.00278 ( 69) SS BOND : angle 1.52576 ( 138) hydrogen bonds : bond 0.04634 ( 955) hydrogen bonds : angle 4.52380 ( 2683) link_BETA1-4 : bond 0.00465 ( 4) link_BETA1-4 : angle 1.64551 ( 12) link_NAG-ASN : bond 0.00359 ( 25) link_NAG-ASN : angle 2.31664 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 562 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 THR cc_start: 0.8696 (m) cc_final: 0.8457 (p) REVERT: A 94 PHE cc_start: 0.6934 (m-10) cc_final: 0.6716 (m-10) REVERT: A 160 HIS cc_start: 0.7612 (p-80) cc_final: 0.7136 (p-80) REVERT: A 234 HIS cc_start: 0.7929 (m90) cc_final: 0.7631 (m90) REVERT: A 238 MET cc_start: 0.7006 (ptp) cc_final: 0.6649 (ptp) REVERT: A 323 ASN cc_start: 0.7570 (p0) cc_final: 0.7283 (p0) REVERT: A 366 ASP cc_start: 0.7704 (t0) cc_final: 0.7330 (t0) REVERT: A 439 PHE cc_start: 0.8740 (t80) cc_final: 0.8535 (t80) REVERT: A 473 PHE cc_start: 0.8341 (t80) cc_final: 0.7814 (t80) REVERT: A 500 LYS cc_start: 0.8534 (ptpt) cc_final: 0.8080 (ptpt) REVERT: A 530 PRO cc_start: 0.9265 (Cg_endo) cc_final: 0.9059 (Cg_exo) REVERT: A 538 VAL cc_start: 0.8884 (p) cc_final: 0.8627 (m) REVERT: A 555 LYS cc_start: 0.8360 (tppp) cc_final: 0.7914 (tppp) REVERT: A 632 ILE cc_start: 0.8665 (mt) cc_final: 0.8346 (mp) REVERT: A 635 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7712 (tm-30) REVERT: A 673 TYR cc_start: 0.8405 (t80) cc_final: 0.8176 (t80) REVERT: A 768 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8298 (mm-30) REVERT: A 806 SER cc_start: 0.8948 (m) cc_final: 0.8685 (t) REVERT: A 827 ASP cc_start: 0.8303 (m-30) cc_final: 0.7997 (m-30) REVERT: A 828 LEU cc_start: 0.8725 (mm) cc_final: 0.8516 (mt) REVERT: A 985 TYR cc_start: 0.8799 (m-80) cc_final: 0.8483 (m-80) REVERT: A 1010 LYS cc_start: 0.8438 (tttt) cc_final: 0.8060 (ttmm) REVERT: A 1028 LYS cc_start: 0.8325 (mttt) cc_final: 0.8024 (mtmm) REVERT: A 1091 GLN cc_start: 0.7957 (mt0) cc_final: 0.7524 (mt0) REVERT: A 1095 ASP cc_start: 0.7769 (m-30) cc_final: 0.7279 (m-30) REVERT: A 1116 SER cc_start: 0.8766 (t) cc_final: 0.8208 (p) REVERT: A 1179 LYS cc_start: 0.8629 (ttpt) cc_final: 0.8331 (ttmm) REVERT: C 53 ASN cc_start: 0.8338 (p0) cc_final: 0.7943 (p0) REVERT: C 74 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.8022 (t80) REVERT: C 86 SER cc_start: 0.8483 (t) cc_final: 0.8210 (p) REVERT: C 128 SER cc_start: 0.8923 (p) cc_final: 0.8706 (m) REVERT: C 155 MET cc_start: 0.8760 (mmt) cc_final: 0.8397 (mmp) REVERT: C 264 ARG cc_start: 0.8482 (mtp85) cc_final: 0.8270 (mtp85) REVERT: C 275 VAL cc_start: 0.8488 (t) cc_final: 0.8280 (p) REVERT: C 374 ASP cc_start: 0.7662 (t0) cc_final: 0.7444 (t0) REVERT: C 595 ASN cc_start: 0.7681 (m110) cc_final: 0.7407 (p0) REVERT: C 624 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8524 (mm) REVERT: C 649 TYR cc_start: 0.8725 (m-80) cc_final: 0.8453 (m-10) REVERT: C 711 PHE cc_start: 0.8327 (m-80) cc_final: 0.7946 (m-80) REVERT: C 845 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: C 981 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8118 (mp) REVERT: C 1064 ARG cc_start: 0.8416 (ttm110) cc_final: 0.8189 (mmm-85) REVERT: C 1095 ASP cc_start: 0.8361 (t0) cc_final: 0.7956 (t0) REVERT: C 1183 SER cc_start: 0.8345 (t) cc_final: 0.7635 (p) REVERT: C 1214 LYS cc_start: 0.8935 (mtpp) cc_final: 0.8688 (mtpp) REVERT: B 41 ASP cc_start: 0.8295 (t0) cc_final: 0.7852 (t70) REVERT: B 105 LYS cc_start: 0.7951 (tttm) cc_final: 0.7610 (tmtt) REVERT: B 147 GLU cc_start: 0.7367 (tm-30) cc_final: 0.6884 (tm-30) REVERT: B 148 ILE cc_start: 0.8233 (mp) cc_final: 0.7873 (tt) REVERT: B 289 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7890 (mm-30) REVERT: B 320 ARG cc_start: 0.8190 (ttm170) cc_final: 0.7730 (mtt-85) REVERT: B 348 ILE cc_start: 0.8905 (mp) cc_final: 0.8406 (tp) REVERT: B 398 ARG cc_start: 0.8343 (ptp-110) cc_final: 0.7784 (mtt180) REVERT: B 467 PHE cc_start: 0.8512 (m-80) cc_final: 0.8258 (m-10) REVERT: B 702 ASN cc_start: 0.8086 (t0) cc_final: 0.7602 (t0) REVERT: B 745 ASP cc_start: 0.7921 (t0) cc_final: 0.7455 (t70) REVERT: B 746 TYR cc_start: 0.8327 (t80) cc_final: 0.8088 (t80) REVERT: B 883 ASP cc_start: 0.8462 (t0) cc_final: 0.8217 (t0) REVERT: B 912 LYS cc_start: 0.8560 (ptmt) cc_final: 0.8183 (ptmt) REVERT: B 999 LYS cc_start: 0.8532 (mtpt) cc_final: 0.8282 (mtpt) REVERT: B 1038 GLN cc_start: 0.8479 (tp40) cc_final: 0.7718 (tp40) REVERT: B 1060 GLU cc_start: 0.8500 (tt0) cc_final: 0.8228 (tt0) REVERT: B 1069 GLU cc_start: 0.7314 (pm20) cc_final: 0.7110 (pm20) REVERT: B 1095 ASP cc_start: 0.8079 (t0) cc_final: 0.7714 (t0) REVERT: B 1212 PHE cc_start: 0.7633 (m-10) cc_final: 0.6720 (m-80) outliers start: 112 outliers final: 79 residues processed: 627 average time/residue: 0.1710 time to fit residues: 173.5736 Evaluate side-chains 626 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 543 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 881 ASN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 869 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1200 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 58 optimal weight: 2.9990 chunk 361 optimal weight: 0.0770 chunk 129 optimal weight: 50.0000 chunk 99 optimal weight: 2.9990 chunk 273 optimal weight: 0.9980 chunk 359 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 291 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1001 GLN B 152 GLN B 351 ASN B1122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.161882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.120264 restraints weight = 46767.903| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.72 r_work: 0.3308 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30347 Z= 0.202 Angle : 0.578 10.134 41478 Z= 0.295 Chirality : 0.045 0.265 4755 Planarity : 0.004 0.048 5286 Dihedral : 4.809 57.177 4676 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.79 % Allowed : 13.34 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.13), residues: 3749 helix: 1.54 (0.21), residues: 738 sheet: -0.15 (0.18), residues: 773 loop : -1.78 (0.12), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 398 TYR 0.024 0.002 TYR C 49 PHE 0.025 0.002 PHE B 658 TRP 0.018 0.001 TRP B 174 HIS 0.009 0.001 HIS C1145 Details of bonding type rmsd covalent geometry : bond 0.00473 (30249) covalent geometry : angle 0.56089 (41253) SS BOND : bond 0.00359 ( 69) SS BOND : angle 1.73626 ( 138) hydrogen bonds : bond 0.05323 ( 955) hydrogen bonds : angle 4.59283 ( 2683) link_BETA1-4 : bond 0.00366 ( 4) link_BETA1-4 : angle 1.45861 ( 12) link_NAG-ASN : bond 0.00365 ( 25) link_NAG-ASN : angle 2.36390 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 564 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 THR cc_start: 0.8711 (m) cc_final: 0.8474 (p) REVERT: A 147 GLU cc_start: 0.8087 (tt0) cc_final: 0.7477 (tt0) REVERT: A 155 MET cc_start: 0.7194 (mmm) cc_final: 0.6771 (mmm) REVERT: A 160 HIS cc_start: 0.7619 (p-80) cc_final: 0.7221 (p-80) REVERT: A 234 HIS cc_start: 0.7985 (m90) cc_final: 0.7739 (m90) REVERT: A 238 MET cc_start: 0.7009 (ptp) cc_final: 0.6675 (ptp) REVERT: A 323 ASN cc_start: 0.7695 (p0) cc_final: 0.7390 (p0) REVERT: A 366 ASP cc_start: 0.7735 (t0) cc_final: 0.7354 (t0) REVERT: A 408 PHE cc_start: 0.8411 (m-10) cc_final: 0.7958 (m-80) REVERT: A 439 PHE cc_start: 0.8751 (t80) cc_final: 0.8522 (t80) REVERT: A 448 TYR cc_start: 0.8628 (m-10) cc_final: 0.8344 (m-80) REVERT: A 473 PHE cc_start: 0.8386 (t80) cc_final: 0.7920 (t80) REVERT: A 500 LYS cc_start: 0.8582 (ptpt) cc_final: 0.8126 (ptpt) REVERT: A 538 VAL cc_start: 0.8890 (p) cc_final: 0.8650 (m) REVERT: A 555 LYS cc_start: 0.8404 (tppp) cc_final: 0.7919 (tppp) REVERT: A 632 ILE cc_start: 0.8680 (mt) cc_final: 0.8419 (mp) REVERT: A 635 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7745 (tm-30) REVERT: A 673 TYR cc_start: 0.8403 (t80) cc_final: 0.8135 (t80) REVERT: A 806 SER cc_start: 0.8969 (m) cc_final: 0.8736 (t) REVERT: A 827 ASP cc_start: 0.8317 (m-30) cc_final: 0.8020 (m-30) REVERT: A 985 TYR cc_start: 0.8807 (m-80) cc_final: 0.8461 (m-80) REVERT: A 1028 LYS cc_start: 0.8389 (mttt) cc_final: 0.8062 (mtpp) REVERT: A 1091 GLN cc_start: 0.8000 (mt0) cc_final: 0.7605 (mt0) REVERT: A 1095 ASP cc_start: 0.7772 (m-30) cc_final: 0.7314 (m-30) REVERT: A 1116 SER cc_start: 0.8773 (t) cc_final: 0.8216 (p) REVERT: A 1179 LYS cc_start: 0.8646 (ttpt) cc_final: 0.8337 (ttmm) REVERT: A 1185 MET cc_start: 0.8577 (mtp) cc_final: 0.8194 (mtp) REVERT: C 86 SER cc_start: 0.8496 (t) cc_final: 0.8172 (p) REVERT: C 128 SER cc_start: 0.8931 (p) cc_final: 0.8688 (m) REVERT: C 275 VAL cc_start: 0.8518 (t) cc_final: 0.8287 (p) REVERT: C 381 SER cc_start: 0.8851 (m) cc_final: 0.8340 (p) REVERT: C 437 ASN cc_start: 0.7807 (p0) cc_final: 0.7362 (p0) REVERT: C 595 ASN cc_start: 0.7728 (m110) cc_final: 0.7406 (p0) REVERT: C 649 TYR cc_start: 0.8754 (m-80) cc_final: 0.8518 (m-10) REVERT: C 711 PHE cc_start: 0.8367 (m-80) cc_final: 0.8022 (m-80) REVERT: C 845 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: C 981 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8170 (mp) REVERT: C 1001 GLN cc_start: 0.8848 (mt0) cc_final: 0.8642 (mt0) REVERT: C 1095 ASP cc_start: 0.8364 (t0) cc_final: 0.7960 (t0) REVERT: C 1183 SER cc_start: 0.8422 (t) cc_final: 0.7739 (p) REVERT: C 1214 LYS cc_start: 0.8941 (mtpp) cc_final: 0.8690 (mtpp) REVERT: B 41 ASP cc_start: 0.8321 (t0) cc_final: 0.7897 (t70) REVERT: B 147 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7077 (tm-30) REVERT: B 148 ILE cc_start: 0.8280 (mp) cc_final: 0.7890 (tt) REVERT: B 320 ARG cc_start: 0.8264 (ttm170) cc_final: 0.7810 (mtt-85) REVERT: B 348 ILE cc_start: 0.8919 (mp) cc_final: 0.8431 (tp) REVERT: B 398 ARG cc_start: 0.8373 (ptp-110) cc_final: 0.7842 (mtt180) REVERT: B 467 PHE cc_start: 0.8509 (m-80) cc_final: 0.8257 (m-10) REVERT: B 702 ASN cc_start: 0.8170 (t0) cc_final: 0.7713 (t0) REVERT: B 745 ASP cc_start: 0.8001 (t0) cc_final: 0.7587 (t70) REVERT: B 746 TYR cc_start: 0.8367 (t80) cc_final: 0.8130 (t80) REVERT: B 862 MET cc_start: 0.8167 (tpt) cc_final: 0.7823 (mmm) REVERT: B 887 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8215 (pp) REVERT: B 912 LYS cc_start: 0.8626 (ptmt) cc_final: 0.8264 (ptmt) REVERT: B 999 LYS cc_start: 0.8555 (mtpt) cc_final: 0.8299 (mtpt) REVERT: B 1038 GLN cc_start: 0.8500 (tp40) cc_final: 0.7745 (tp40) REVERT: B 1060 GLU cc_start: 0.8515 (tt0) cc_final: 0.8216 (tt0) REVERT: B 1069 GLU cc_start: 0.7432 (pm20) cc_final: 0.7190 (pm20) REVERT: B 1095 ASP cc_start: 0.8088 (t0) cc_final: 0.7730 (t0) REVERT: B 1212 PHE cc_start: 0.7790 (m-10) cc_final: 0.6785 (m-80) outliers start: 124 outliers final: 91 residues processed: 632 average time/residue: 0.1917 time to fit residues: 195.2938 Evaluate side-chains 641 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 547 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 793 ASN Chi-restraints excluded: chain A residue 881 ASN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain T residue 478 MET Chi-restraints excluded: chain T residue 488 MET Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 869 SER Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1030 GLN Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 959 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1200 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 372 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 111 optimal weight: 0.0040 chunk 315 optimal weight: 10.0000 chunk 305 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 329 optimal weight: 1.9990 chunk 279 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 605 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1206 ASN B 152 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.161589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120049 restraints weight = 46687.498| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.75 r_work: 0.3302 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30347 Z= 0.188 Angle : 0.573 10.494 41478 Z= 0.294 Chirality : 0.045 0.290 4755 Planarity : 0.004 0.048 5286 Dihedral : 4.833 56.808 4676 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.00 % Allowed : 13.86 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.13), residues: 3749 helix: 1.62 (0.21), residues: 733 sheet: -0.10 (0.18), residues: 781 loop : -1.73 (0.12), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1064 TYR 0.020 0.002 TYR C 49 PHE 0.026 0.002 PHE C 74 TRP 0.021 0.001 TRP B 174 HIS 0.008 0.001 HIS C1145 Details of bonding type rmsd covalent geometry : bond 0.00438 (30249) covalent geometry : angle 0.55671 (41253) SS BOND : bond 0.00338 ( 69) SS BOND : angle 1.73597 ( 138) hydrogen bonds : bond 0.05272 ( 955) hydrogen bonds : angle 4.62720 ( 2683) link_BETA1-4 : bond 0.00385 ( 4) link_BETA1-4 : angle 1.34678 ( 12) link_NAG-ASN : bond 0.00308 ( 25) link_NAG-ASN : angle 2.26989 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 564 time to evaluate : 0.969 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 64 THR cc_start: 0.8713 (m) cc_final: 0.8476 (p) REVERT: A 147 GLU cc_start: 0.8079 (tt0) cc_final: 0.7475 (tt0) REVERT: A 160 HIS cc_start: 0.7592 (p-80) cc_final: 0.7284 (p-80) REVERT: A 232 LEU cc_start: 0.8775 (mt) cc_final: 0.8413 (mm) REVERT: A 234 HIS cc_start: 0.8021 (m90) cc_final: 0.7779 (m90) REVERT: A 238 MET cc_start: 0.7114 (ptp) cc_final: 0.6809 (ptp) REVERT: A 323 ASN cc_start: 0.7788 (p0) cc_final: 0.7491 (p0) REVERT: A 366 ASP cc_start: 0.7724 (t0) cc_final: 0.7363 (t0) REVERT: A 408 PHE cc_start: 0.8439 (m-10) cc_final: 0.7971 (m-80) REVERT: A 439 PHE cc_start: 0.8734 (t80) cc_final: 0.8522 (t80) REVERT: A 448 TYR cc_start: 0.8707 (m-10) cc_final: 0.8350 (m-80) REVERT: A 473 PHE cc_start: 0.8421 (t80) cc_final: 0.7998 (t80) REVERT: A 500 LYS cc_start: 0.8584 (ptpt) cc_final: 0.8134 (ptpt) REVERT: A 538 VAL cc_start: 0.8928 (p) cc_final: 0.8689 (m) REVERT: A 555 LYS cc_start: 0.8395 (tppp) cc_final: 0.7889 (tppp) REVERT: A 635 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7766 (tm-30) REVERT: A 806 SER cc_start: 0.8975 (m) cc_final: 0.8753 (t) REVERT: A 815 SER cc_start: 0.8740 (p) cc_final: 0.8536 (m) REVERT: A 827 ASP cc_start: 0.8331 (m-30) cc_final: 0.8012 (m-30) REVERT: A 915 ASP cc_start: 0.7214 (t0) cc_final: 0.6989 (t0) REVERT: A 985 TYR cc_start: 0.8796 (m-80) cc_final: 0.8447 (m-80) REVERT: A 1028 LYS cc_start: 0.8420 (mttt) cc_final: 0.8106 (mtpp) REVERT: A 1091 GLN cc_start: 0.8024 (mt0) cc_final: 0.7639 (mt0) REVERT: A 1095 ASP cc_start: 0.7789 (m-30) cc_final: 0.7343 (m-30) REVERT: A 1100 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7857 (tmtt) REVERT: A 1116 SER cc_start: 0.8780 (t) cc_final: 0.8233 (p) REVERT: C 53 ASN cc_start: 0.8326 (p0) cc_final: 0.8053 (p0) REVERT: C 74 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7999 (t80) REVERT: C 86 SER cc_start: 0.8521 (t) cc_final: 0.8184 (p) REVERT: C 128 SER cc_start: 0.8917 (p) cc_final: 0.8659 (m) REVERT: C 275 VAL cc_start: 0.8520 (t) cc_final: 0.8304 (p) REVERT: C 381 SER cc_start: 0.8877 (m) cc_final: 0.8373 (p) REVERT: C 385 SER cc_start: 0.8674 (m) cc_final: 0.8070 (m) REVERT: C 595 ASN cc_start: 0.7745 (m110) cc_final: 0.7395 (p0) REVERT: C 711 PHE cc_start: 0.8366 (m-80) cc_final: 0.8046 (m-80) REVERT: C 845 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: C 981 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8136 (mp) REVERT: C 1001 GLN cc_start: 0.8816 (mt0) cc_final: 0.8584 (mt0) REVERT: C 1010 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8281 (ttmm) REVERT: C 1095 ASP cc_start: 0.8395 (t0) cc_final: 0.7999 (t0) REVERT: C 1183 SER cc_start: 0.8420 (t) cc_final: 0.7745 (p) REVERT: C 1214 LYS cc_start: 0.8929 (mtpp) cc_final: 0.8679 (mtpp) REVERT: B 41 ASP cc_start: 0.8334 (t0) cc_final: 0.7923 (t70) REVERT: B 105 LYS cc_start: 0.8003 (tttm) cc_final: 0.7658 (tmtt) REVERT: B 147 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7143 (tm-30) REVERT: B 148 ILE cc_start: 0.8310 (mp) cc_final: 0.7921 (tt) REVERT: B 152 GLN cc_start: 0.6494 (OUTLIER) cc_final: 0.6247 (pt0) REVERT: B 320 ARG cc_start: 0.8248 (ttm170) cc_final: 0.7760 (mtt-85) REVERT: B 348 ILE cc_start: 0.8914 (mp) cc_final: 0.8417 (tp) REVERT: B 398 ARG cc_start: 0.8348 (ptp-110) cc_final: 0.7843 (mtt180) REVERT: B 467 PHE cc_start: 0.8458 (m-80) cc_final: 0.8211 (m-10) REVERT: B 702 ASN cc_start: 0.8162 (t0) cc_final: 0.7709 (t0) REVERT: B 745 ASP cc_start: 0.8027 (t0) cc_final: 0.7615 (t70) REVERT: B 746 TYR cc_start: 0.8376 (t80) cc_final: 0.7553 (t80) REVERT: B 887 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8288 (pp) REVERT: B 912 LYS cc_start: 0.8658 (ptmt) cc_final: 0.8300 (ptmt) REVERT: B 999 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8298 (mtpt) REVERT: B 1038 GLN cc_start: 0.8510 (tp40) cc_final: 0.7767 (tp40) REVERT: B 1060 GLU cc_start: 0.8528 (tt0) cc_final: 0.8237 (tt0) REVERT: B 1069 GLU cc_start: 0.7445 (pm20) cc_final: 0.7202 (pm20) outliers start: 131 outliers final: 97 residues processed: 636 average time/residue: 0.1701 time to fit residues: 175.0333 Evaluate side-chains 649 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 546 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 793 ASN Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1100 LYS Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain T residue 488 MET Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 869 SER Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1030 GLN Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 959 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1200 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 158 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 349 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 320 optimal weight: 0.2980 chunk 288 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 121 optimal weight: 6.9990 chunk 280 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 HIS A 595 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1206 ASN B 152 GLN B 201 HIS B 643 ASN B1117 GLN B1122 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.162789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121392 restraints weight = 46610.783| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.77 r_work: 0.3318 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30347 Z= 0.127 Angle : 0.546 10.453 41478 Z= 0.278 Chirality : 0.044 0.263 4755 Planarity : 0.004 0.046 5286 Dihedral : 4.668 56.944 4676 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.36 % Allowed : 14.80 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.14), residues: 3749 helix: 1.74 (0.21), residues: 734 sheet: -0.02 (0.18), residues: 778 loop : -1.65 (0.12), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1064 TYR 0.017 0.001 TYR C 649 PHE 0.025 0.001 PHE A 566 TRP 0.020 0.001 TRP B 174 HIS 0.006 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00294 (30249) covalent geometry : angle 0.53219 (41253) SS BOND : bond 0.00300 ( 69) SS BOND : angle 1.58210 ( 138) hydrogen bonds : bond 0.04633 ( 955) hydrogen bonds : angle 4.52596 ( 2683) link_BETA1-4 : bond 0.00374 ( 4) link_BETA1-4 : angle 1.30801 ( 12) link_NAG-ASN : bond 0.00232 ( 25) link_NAG-ASN : angle 2.10465 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 547 time to evaluate : 1.112 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 64 THR cc_start: 0.8710 (m) cc_final: 0.8445 (p) REVERT: A 94 PHE cc_start: 0.6946 (m-10) cc_final: 0.6727 (m-10) REVERT: A 160 HIS cc_start: 0.7637 (p-80) cc_final: 0.7319 (p-80) REVERT: A 232 LEU cc_start: 0.8733 (mt) cc_final: 0.8357 (mm) REVERT: A 234 HIS cc_start: 0.8040 (m90) cc_final: 0.7794 (m90) REVERT: A 238 MET cc_start: 0.7120 (ptp) cc_final: 0.6809 (ptp) REVERT: A 323 ASN cc_start: 0.7795 (p0) cc_final: 0.7513 (p0) REVERT: A 366 ASP cc_start: 0.7700 (t0) cc_final: 0.7331 (t0) REVERT: A 408 PHE cc_start: 0.8460 (m-10) cc_final: 0.8030 (m-80) REVERT: A 439 PHE cc_start: 0.8727 (t80) cc_final: 0.8493 (t80) REVERT: A 448 TYR cc_start: 0.8679 (m-80) cc_final: 0.8349 (m-80) REVERT: A 473 PHE cc_start: 0.8405 (t80) cc_final: 0.7996 (t80) REVERT: A 500 LYS cc_start: 0.8557 (ptpt) cc_final: 0.8107 (ptpt) REVERT: A 538 VAL cc_start: 0.8940 (p) cc_final: 0.8700 (m) REVERT: A 555 LYS cc_start: 0.8385 (tppp) cc_final: 0.7864 (tppp) REVERT: A 632 ILE cc_start: 0.8680 (mt) cc_final: 0.8418 (mp) REVERT: A 635 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7723 (tm-30) REVERT: A 806 SER cc_start: 0.8936 (m) cc_final: 0.8720 (t) REVERT: A 827 ASP cc_start: 0.8311 (m-30) cc_final: 0.7989 (m-30) REVERT: A 915 ASP cc_start: 0.7150 (t0) cc_final: 0.6908 (t0) REVERT: A 985 TYR cc_start: 0.8771 (m-80) cc_final: 0.8434 (m-80) REVERT: A 1028 LYS cc_start: 0.8327 (mttt) cc_final: 0.8037 (mtpp) REVERT: A 1091 GLN cc_start: 0.7986 (mt0) cc_final: 0.7598 (mt0) REVERT: A 1095 ASP cc_start: 0.7786 (m-30) cc_final: 0.7315 (m-30) REVERT: A 1100 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7792 (tmtt) REVERT: A 1116 SER cc_start: 0.8789 (t) cc_final: 0.8227 (p) REVERT: C 53 ASN cc_start: 0.8343 (p0) cc_final: 0.8043 (p0) REVERT: C 86 SER cc_start: 0.8495 (t) cc_final: 0.8146 (p) REVERT: C 128 SER cc_start: 0.8913 (p) cc_final: 0.8654 (m) REVERT: C 275 VAL cc_start: 0.8486 (t) cc_final: 0.8279 (p) REVERT: C 381 SER cc_start: 0.8852 (m) cc_final: 0.8325 (p) REVERT: C 385 SER cc_start: 0.8694 (m) cc_final: 0.8069 (m) REVERT: C 595 ASN cc_start: 0.7706 (m110) cc_final: 0.7360 (p0) REVERT: C 635 GLU cc_start: 0.8092 (tp30) cc_final: 0.7855 (tp30) REVERT: C 700 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8008 (p) REVERT: C 711 PHE cc_start: 0.8341 (m-80) cc_final: 0.8105 (m-10) REVERT: C 763 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8391 (mtm-85) REVERT: C 845 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: C 981 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8122 (mp) REVERT: C 1010 LYS cc_start: 0.8659 (mtpp) cc_final: 0.8258 (ttmm) REVERT: C 1095 ASP cc_start: 0.8380 (t0) cc_final: 0.7980 (t0) REVERT: C 1214 LYS cc_start: 0.8930 (mtpp) cc_final: 0.8676 (mtpp) REVERT: B 41 ASP cc_start: 0.8344 (t0) cc_final: 0.7902 (t0) REVERT: B 105 LYS cc_start: 0.7984 (tttm) cc_final: 0.7640 (tmtt) REVERT: B 148 ILE cc_start: 0.8285 (mp) cc_final: 0.7893 (tt) REVERT: B 320 ARG cc_start: 0.8230 (ttm170) cc_final: 0.7763 (mtt-85) REVERT: B 348 ILE cc_start: 0.8908 (mp) cc_final: 0.8403 (tp) REVERT: B 398 ARG cc_start: 0.8367 (ptp-110) cc_final: 0.7845 (mtt180) REVERT: B 467 PHE cc_start: 0.8465 (m-80) cc_final: 0.8220 (m-10) REVERT: B 702 ASN cc_start: 0.8141 (t0) cc_final: 0.7748 (t0) REVERT: B 745 ASP cc_start: 0.8026 (t0) cc_final: 0.7588 (t70) REVERT: B 912 LYS cc_start: 0.8598 (ptmt) cc_final: 0.8220 (ptmt) REVERT: B 999 LYS cc_start: 0.8489 (mtpt) cc_final: 0.8231 (mtpt) REVERT: B 1038 GLN cc_start: 0.8494 (tp40) cc_final: 0.7752 (tp40) REVERT: B 1060 GLU cc_start: 0.8519 (tt0) cc_final: 0.8218 (tt0) REVERT: B 1069 GLU cc_start: 0.7331 (pm20) cc_final: 0.7043 (pm20) outliers start: 110 outliers final: 91 residues processed: 602 average time/residue: 0.1845 time to fit residues: 178.9688 Evaluate side-chains 639 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 544 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 793 ASN Chi-restraints excluded: chain A residue 885 LYS Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1100 LYS Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain T residue 478 MET Chi-restraints excluded: chain T residue 488 MET Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 869 SER Chi-restraints excluded: chain C residue 884 PHE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1013 LEU Chi-restraints excluded: chain C residue 1030 GLN Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 THR Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1200 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 292 optimal weight: 2.9990 chunk 354 optimal weight: 1.9990 chunk 375 optimal weight: 0.8980 chunk 361 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 310 optimal weight: 20.0000 chunk 327 optimal weight: 0.5980 chunk 319 optimal weight: 1.9990 chunk 272 optimal weight: 7.9990 chunk 106 optimal weight: 0.0870 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 HIS ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1206 ASN B 152 GLN B 821 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.162856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121494 restraints weight = 46767.898| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.76 r_work: 0.3309 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30347 Z= 0.135 Angle : 0.549 10.300 41478 Z= 0.278 Chirality : 0.044 0.439 4755 Planarity : 0.004 0.045 5286 Dihedral : 4.700 57.360 4676 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.45 % Allowed : 15.20 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.14), residues: 3749 helix: 1.80 (0.21), residues: 733 sheet: -0.02 (0.18), residues: 780 loop : -1.61 (0.12), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1064 TYR 0.018 0.001 TYR C 649 PHE 0.028 0.001 PHE C 74 TRP 0.021 0.001 TRP B 174 HIS 0.014 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00313 (30249) covalent geometry : angle 0.53442 (41253) SS BOND : bond 0.00286 ( 69) SS BOND : angle 1.42613 ( 138) hydrogen bonds : bond 0.04644 ( 955) hydrogen bonds : angle 4.49247 ( 2683) link_BETA1-4 : bond 0.00583 ( 4) link_BETA1-4 : angle 1.34960 ( 12) link_NAG-ASN : bond 0.00610 ( 25) link_NAG-ASN : angle 2.33838 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 542 time to evaluate : 1.125 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 64 THR cc_start: 0.8709 (m) cc_final: 0.8440 (p) REVERT: A 160 HIS cc_start: 0.7638 (p-80) cc_final: 0.7357 (p-80) REVERT: A 232 LEU cc_start: 0.8760 (mt) cc_final: 0.8380 (mm) REVERT: A 238 MET cc_start: 0.7142 (ptp) cc_final: 0.6840 (ptp) REVERT: A 323 ASN cc_start: 0.7819 (p0) cc_final: 0.7534 (p0) REVERT: A 366 ASP cc_start: 0.7710 (t0) cc_final: 0.7343 (t0) REVERT: A 408 PHE cc_start: 0.8481 (m-10) cc_final: 0.8058 (m-80) REVERT: A 439 PHE cc_start: 0.8725 (t80) cc_final: 0.8501 (t80) REVERT: A 448 TYR cc_start: 0.8686 (m-80) cc_final: 0.8364 (m-80) REVERT: A 473 PHE cc_start: 0.8409 (t80) cc_final: 0.8014 (t80) REVERT: A 538 VAL cc_start: 0.8954 (p) cc_final: 0.8718 (m) REVERT: A 555 LYS cc_start: 0.8369 (tppp) cc_final: 0.7851 (tppp) REVERT: A 632 ILE cc_start: 0.8691 (mt) cc_final: 0.8443 (mp) REVERT: A 806 SER cc_start: 0.8951 (m) cc_final: 0.8727 (t) REVERT: A 815 SER cc_start: 0.8681 (p) cc_final: 0.8449 (m) REVERT: A 827 ASP cc_start: 0.8318 (m-30) cc_final: 0.7998 (m-30) REVERT: A 915 ASP cc_start: 0.7155 (t0) cc_final: 0.6916 (t0) REVERT: A 985 TYR cc_start: 0.8782 (m-80) cc_final: 0.8449 (m-80) REVERT: A 1028 LYS cc_start: 0.8338 (mttt) cc_final: 0.8046 (mtpp) REVERT: A 1091 GLN cc_start: 0.7996 (mt0) cc_final: 0.7616 (mt0) REVERT: A 1095 ASP cc_start: 0.7811 (m-30) cc_final: 0.7345 (m-30) REVERT: A 1100 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7788 (tmtt) REVERT: A 1116 SER cc_start: 0.8786 (t) cc_final: 0.8237 (p) REVERT: C 53 ASN cc_start: 0.8373 (p0) cc_final: 0.8043 (p0) REVERT: C 86 SER cc_start: 0.8491 (t) cc_final: 0.8125 (p) REVERT: C 128 SER cc_start: 0.8911 (p) cc_final: 0.8654 (m) REVERT: C 381 SER cc_start: 0.8848 (m) cc_final: 0.8416 (p) REVERT: C 647 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8786 (mt) REVERT: C 700 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.8006 (p) REVERT: C 711 PHE cc_start: 0.8345 (m-80) cc_final: 0.8107 (m-10) REVERT: C 763 ARG cc_start: 0.8662 (mtm-85) cc_final: 0.8330 (mtm110) REVERT: C 845 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: C 981 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8136 (mp) REVERT: C 1095 ASP cc_start: 0.8390 (t0) cc_final: 0.7998 (t0) REVERT: C 1173 LYS cc_start: 0.8325 (mtpp) cc_final: 0.8080 (mtpp) REVERT: C 1214 LYS cc_start: 0.8938 (mtpp) cc_final: 0.8690 (mtpp) REVERT: C 1218 ILE cc_start: 0.8785 (mt) cc_final: 0.8569 (mm) REVERT: B 41 ASP cc_start: 0.8337 (t0) cc_final: 0.7901 (t0) REVERT: B 105 LYS cc_start: 0.8001 (tttm) cc_final: 0.7644 (tmtt) REVERT: B 148 ILE cc_start: 0.8338 (mp) cc_final: 0.7946 (tt) REVERT: B 320 ARG cc_start: 0.8226 (ttm170) cc_final: 0.7758 (mtt-85) REVERT: B 326 ASP cc_start: 0.6736 (t70) cc_final: 0.6244 (t70) REVERT: B 348 ILE cc_start: 0.8908 (mp) cc_final: 0.8404 (tp) REVERT: B 398 ARG cc_start: 0.8368 (ptp-110) cc_final: 0.7867 (mtt180) REVERT: B 467 PHE cc_start: 0.8419 (m-80) cc_final: 0.8174 (m-10) REVERT: B 643 ASN cc_start: 0.8607 (t0) cc_final: 0.8393 (t0) REVERT: B 702 ASN cc_start: 0.8168 (t0) cc_final: 0.7782 (t0) REVERT: B 745 ASP cc_start: 0.8048 (t0) cc_final: 0.7625 (t70) REVERT: B 912 LYS cc_start: 0.8606 (ptmt) cc_final: 0.8231 (ptmt) REVERT: B 999 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8255 (mtpt) REVERT: B 1038 GLN cc_start: 0.8505 (tp40) cc_final: 0.7784 (tp40) REVERT: B 1060 GLU cc_start: 0.8528 (tt0) cc_final: 0.8236 (tt0) REVERT: B 1069 GLU cc_start: 0.7346 (pm20) cc_final: 0.7062 (pm20) outliers start: 113 outliers final: 99 residues processed: 598 average time/residue: 0.1895 time to fit residues: 182.3149 Evaluate side-chains 639 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 535 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 793 ASN Chi-restraints excluded: chain A residue 885 LYS Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1100 LYS Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain T residue 488 MET Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 869 SER Chi-restraints excluded: chain C residue 884 PHE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1013 LEU Chi-restraints excluded: chain C residue 1030 GLN Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 821 ASN Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 THR Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1200 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 203 optimal weight: 1.9990 chunk 104 optimal weight: 0.0770 chunk 71 optimal weight: 0.6980 chunk 301 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 195 optimal weight: 9.9990 chunk 369 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 7 optimal weight: 0.0970 chunk 374 optimal weight: 3.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 HIS ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1206 ASN B 821 ASN B 826 HIS B1122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.163411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123227 restraints weight = 46731.269| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.60 r_work: 0.3349 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 30347 Z= 0.127 Angle : 0.548 11.030 41478 Z= 0.278 Chirality : 0.044 0.401 4755 Planarity : 0.004 0.045 5286 Dihedral : 4.668 57.869 4676 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.33 % Allowed : 15.51 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.14), residues: 3749 helix: 1.82 (0.21), residues: 733 sheet: 0.03 (0.18), residues: 772 loop : -1.58 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 397 TYR 0.020 0.001 TYR B 822 PHE 0.027 0.001 PHE A 566 TRP 0.022 0.001 TRP B 174 HIS 0.012 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00294 (30249) covalent geometry : angle 0.53267 (41253) SS BOND : bond 0.00285 ( 69) SS BOND : angle 1.71633 ( 138) hydrogen bonds : bond 0.04495 ( 955) hydrogen bonds : angle 4.44500 ( 2683) link_BETA1-4 : bond 0.00424 ( 4) link_BETA1-4 : angle 1.27538 ( 12) link_NAG-ASN : bond 0.00488 ( 25) link_NAG-ASN : angle 2.11893 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 535 time to evaluate : 1.199 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 64 THR cc_start: 0.8687 (m) cc_final: 0.8407 (p) REVERT: A 94 PHE cc_start: 0.6923 (m-10) cc_final: 0.6666 (m-10) REVERT: A 160 HIS cc_start: 0.7628 (p-80) cc_final: 0.7300 (p-80) REVERT: A 232 LEU cc_start: 0.8730 (mt) cc_final: 0.8343 (mm) REVERT: A 238 MET cc_start: 0.7119 (ptp) cc_final: 0.6804 (ptp) REVERT: A 323 ASN cc_start: 0.7799 (p0) cc_final: 0.7519 (p0) REVERT: A 366 ASP cc_start: 0.7671 (t0) cc_final: 0.7299 (t0) REVERT: A 408 PHE cc_start: 0.8469 (m-10) cc_final: 0.8104 (m-80) REVERT: A 439 PHE cc_start: 0.8710 (t80) cc_final: 0.8495 (t80) REVERT: A 446 ARG cc_start: 0.8522 (ttm-80) cc_final: 0.7875 (ttm-80) REVERT: A 448 TYR cc_start: 0.8645 (m-80) cc_final: 0.8345 (m-80) REVERT: A 473 PHE cc_start: 0.8412 (t80) cc_final: 0.8024 (t80) REVERT: A 538 VAL cc_start: 0.8946 (p) cc_final: 0.8707 (m) REVERT: A 555 LYS cc_start: 0.8359 (tppp) cc_final: 0.7831 (tppp) REVERT: A 632 ILE cc_start: 0.8628 (mt) cc_final: 0.8358 (mp) REVERT: A 806 SER cc_start: 0.8923 (m) cc_final: 0.8695 (t) REVERT: A 827 ASP cc_start: 0.8299 (m-30) cc_final: 0.7968 (m-30) REVERT: A 915 ASP cc_start: 0.7191 (t0) cc_final: 0.6954 (t0) REVERT: A 985 TYR cc_start: 0.8761 (m-80) cc_final: 0.8486 (m-80) REVERT: A 1028 LYS cc_start: 0.8280 (mttt) cc_final: 0.7990 (mtpp) REVERT: A 1091 GLN cc_start: 0.7959 (mt0) cc_final: 0.7566 (mt0) REVERT: A 1095 ASP cc_start: 0.7707 (m-30) cc_final: 0.7233 (m-30) REVERT: A 1100 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7751 (tmtt) REVERT: A 1116 SER cc_start: 0.8795 (t) cc_final: 0.8230 (p) REVERT: C 53 ASN cc_start: 0.8357 (p0) cc_final: 0.8026 (p0) REVERT: C 86 SER cc_start: 0.8456 (t) cc_final: 0.8079 (p) REVERT: C 128 SER cc_start: 0.8927 (p) cc_final: 0.8676 (m) REVERT: C 595 ASN cc_start: 0.7745 (m110) cc_final: 0.7272 (p0) REVERT: C 635 GLU cc_start: 0.8046 (tp30) cc_final: 0.7833 (tp30) REVERT: C 647 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8751 (mt) REVERT: C 649 TYR cc_start: 0.8463 (m-10) cc_final: 0.8256 (m-10) REVERT: C 700 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.7970 (p) REVERT: C 711 PHE cc_start: 0.8323 (m-80) cc_final: 0.8077 (m-10) REVERT: C 763 ARG cc_start: 0.8621 (mtm-85) cc_final: 0.8306 (mtm110) REVERT: C 845 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: C 981 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8095 (mp) REVERT: C 1095 ASP cc_start: 0.8370 (t0) cc_final: 0.7974 (t0) REVERT: C 1214 LYS cc_start: 0.8930 (mtpp) cc_final: 0.8675 (mtpp) REVERT: C 1218 ILE cc_start: 0.8800 (mt) cc_final: 0.8574 (mm) REVERT: B 41 ASP cc_start: 0.8269 (t0) cc_final: 0.7825 (t0) REVERT: B 105 LYS cc_start: 0.7973 (tttm) cc_final: 0.7601 (tmtt) REVERT: B 148 ILE cc_start: 0.8321 (mp) cc_final: 0.7887 (tt) REVERT: B 174 TRP cc_start: 0.6911 (p-90) cc_final: 0.6079 (p-90) REVERT: B 320 ARG cc_start: 0.8136 (ttm170) cc_final: 0.7656 (mtt-85) REVERT: B 326 ASP cc_start: 0.6747 (t70) cc_final: 0.6261 (t70) REVERT: B 348 ILE cc_start: 0.8884 (mp) cc_final: 0.8382 (tp) REVERT: B 398 ARG cc_start: 0.8340 (ptp-110) cc_final: 0.7850 (mtt180) REVERT: B 467 PHE cc_start: 0.8376 (m-80) cc_final: 0.8129 (m-10) REVERT: B 643 ASN cc_start: 0.8628 (t0) cc_final: 0.8360 (t0) REVERT: B 702 ASN cc_start: 0.8128 (t0) cc_final: 0.7750 (t0) REVERT: B 745 ASP cc_start: 0.8016 (t0) cc_final: 0.7573 (t70) REVERT: B 862 MET cc_start: 0.8081 (tpt) cc_final: 0.7813 (mmm) REVERT: B 912 LYS cc_start: 0.8585 (ptmt) cc_final: 0.8197 (ptmt) REVERT: B 999 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8216 (mtpt) REVERT: B 1038 GLN cc_start: 0.8437 (tp40) cc_final: 0.7704 (tp40) REVERT: B 1060 GLU cc_start: 0.8553 (tt0) cc_final: 0.8258 (tt0) REVERT: B 1069 GLU cc_start: 0.7264 (pm20) cc_final: 0.6953 (pm20) REVERT: B 1185 MET cc_start: 0.8507 (mtt) cc_final: 0.8254 (mtt) outliers start: 109 outliers final: 94 residues processed: 587 average time/residue: 0.1878 time to fit residues: 177.6524 Evaluate side-chains 631 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 532 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 793 ASN Chi-restraints excluded: chain A residue 885 LYS Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1100 LYS Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain T residue 488 MET Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 869 SER Chi-restraints excluded: chain C residue 884 PHE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1013 LEU Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1200 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 87 optimal weight: 0.8980 chunk 46 optimal weight: 0.0870 chunk 314 optimal weight: 4.9990 chunk 275 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 180 optimal weight: 0.0070 chunk 124 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 overall best weight: 1.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1206 ASN B 821 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.161317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119995 restraints weight = 46406.605| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.71 r_work: 0.3300 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 30347 Z= 0.198 Angle : 0.585 10.612 41478 Z= 0.299 Chirality : 0.046 0.380 4755 Planarity : 0.004 0.047 5286 Dihedral : 4.841 59.351 4676 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.30 % Allowed : 15.60 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.14), residues: 3749 helix: 1.70 (0.21), residues: 733 sheet: -0.02 (0.18), residues: 789 loop : -1.62 (0.13), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 397 TYR 0.021 0.002 TYR B 203 PHE 0.028 0.002 PHE C 74 TRP 0.021 0.001 TRP B 174 HIS 0.008 0.001 HIS C1145 Details of bonding type rmsd covalent geometry : bond 0.00462 (30249) covalent geometry : angle 0.56981 (41253) SS BOND : bond 0.00460 ( 69) SS BOND : angle 1.69149 ( 138) hydrogen bonds : bond 0.05293 ( 955) hydrogen bonds : angle 4.56069 ( 2683) link_BETA1-4 : bond 0.00432 ( 4) link_BETA1-4 : angle 1.32478 ( 12) link_NAG-ASN : bond 0.00510 ( 25) link_NAG-ASN : angle 2.21722 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 550 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 THR cc_start: 0.8720 (m) cc_final: 0.8466 (p) REVERT: A 160 HIS cc_start: 0.7612 (p-80) cc_final: 0.7343 (p-80) REVERT: A 232 LEU cc_start: 0.8800 (mt) cc_final: 0.8250 (mm) REVERT: A 233 SER cc_start: 0.8353 (m) cc_final: 0.7861 (p) REVERT: A 238 MET cc_start: 0.7156 (ptp) cc_final: 0.6849 (ptp) REVERT: A 323 ASN cc_start: 0.7910 (p0) cc_final: 0.7620 (p0) REVERT: A 366 ASP cc_start: 0.7687 (t0) cc_final: 0.7316 (t0) REVERT: A 408 PHE cc_start: 0.8514 (m-10) cc_final: 0.8131 (m-80) REVERT: A 439 PHE cc_start: 0.8708 (t80) cc_final: 0.8494 (t80) REVERT: A 473 PHE cc_start: 0.8429 (t80) cc_final: 0.8078 (t80) REVERT: A 500 LYS cc_start: 0.8598 (ptpt) cc_final: 0.8157 (ptpt) REVERT: A 538 VAL cc_start: 0.8957 (p) cc_final: 0.8716 (m) REVERT: A 555 LYS cc_start: 0.8386 (tppp) cc_final: 0.7867 (tppp) REVERT: A 632 ILE cc_start: 0.8698 (mt) cc_final: 0.8448 (mp) REVERT: A 806 SER cc_start: 0.8954 (m) cc_final: 0.8736 (t) REVERT: A 827 ASP cc_start: 0.8315 (m-30) cc_final: 0.7992 (m-30) REVERT: A 884 PHE cc_start: 0.7819 (m-10) cc_final: 0.7612 (m-10) REVERT: A 915 ASP cc_start: 0.7196 (t0) cc_final: 0.6963 (t0) REVERT: A 985 TYR cc_start: 0.8777 (m-80) cc_final: 0.8460 (m-80) REVERT: A 1028 LYS cc_start: 0.8411 (mttt) cc_final: 0.8115 (mtpp) REVERT: A 1091 GLN cc_start: 0.8009 (mt0) cc_final: 0.7630 (mt0) REVERT: A 1095 ASP cc_start: 0.7802 (m-30) cc_final: 0.7349 (m-30) REVERT: A 1100 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7825 (tmtt) REVERT: A 1116 SER cc_start: 0.8785 (t) cc_final: 0.8212 (p) REVERT: C 53 ASN cc_start: 0.8376 (p0) cc_final: 0.8051 (p0) REVERT: C 80 LYS cc_start: 0.7998 (tptp) cc_final: 0.7732 (tptp) REVERT: C 128 SER cc_start: 0.8923 (p) cc_final: 0.8666 (m) REVERT: C 176 ILE cc_start: 0.7774 (tp) cc_final: 0.7561 (tp) REVERT: C 381 SER cc_start: 0.8848 (m) cc_final: 0.8435 (p) REVERT: C 595 ASN cc_start: 0.7817 (m110) cc_final: 0.7332 (p0) REVERT: C 635 GLU cc_start: 0.8058 (tp30) cc_final: 0.7822 (tp30) REVERT: C 647 LEU cc_start: 0.9036 (mp) cc_final: 0.8830 (mt) REVERT: C 649 TYR cc_start: 0.8529 (m-10) cc_final: 0.8319 (m-10) REVERT: C 711 PHE cc_start: 0.8389 (m-80) cc_final: 0.8020 (m-80) REVERT: C 845 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: C 981 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8117 (mp) REVERT: C 1095 ASP cc_start: 0.8369 (t0) cc_final: 0.7970 (t0) REVERT: C 1126 ASN cc_start: 0.8725 (p0) cc_final: 0.8415 (p0) REVERT: C 1214 LYS cc_start: 0.8927 (mtpp) cc_final: 0.8678 (mtpp) REVERT: C 1218 ILE cc_start: 0.8808 (mt) cc_final: 0.8584 (mm) REVERT: B 41 ASP cc_start: 0.8339 (t0) cc_final: 0.7925 (t0) REVERT: B 105 LYS cc_start: 0.8006 (tttm) cc_final: 0.7656 (tmtt) REVERT: B 148 ILE cc_start: 0.8351 (mp) cc_final: 0.7890 (tt) REVERT: B 191 TYR cc_start: 0.7644 (p90) cc_final: 0.7411 (p90) REVERT: B 320 ARG cc_start: 0.8244 (ttm170) cc_final: 0.7564 (mtt-85) REVERT: B 326 ASP cc_start: 0.6792 (t70) cc_final: 0.6324 (t70) REVERT: B 348 ILE cc_start: 0.8910 (mp) cc_final: 0.8407 (tp) REVERT: B 398 ARG cc_start: 0.8373 (ptp-110) cc_final: 0.7818 (mtt180) REVERT: B 467 PHE cc_start: 0.8435 (m-80) cc_final: 0.8178 (m-10) REVERT: B 702 ASN cc_start: 0.8209 (t0) cc_final: 0.7880 (t0) REVERT: B 745 ASP cc_start: 0.8074 (t0) cc_final: 0.7649 (t70) REVERT: B 746 TYR cc_start: 0.8316 (t80) cc_final: 0.7802 (t80) REVERT: B 862 MET cc_start: 0.8318 (tpt) cc_final: 0.7984 (tpt) REVERT: B 912 LYS cc_start: 0.8668 (ptmt) cc_final: 0.8304 (ptmt) REVERT: B 999 LYS cc_start: 0.8521 (mtpt) cc_final: 0.8265 (mtpt) REVERT: B 1038 GLN cc_start: 0.8481 (tp40) cc_final: 0.7767 (tp40) REVERT: B 1060 GLU cc_start: 0.8526 (tt0) cc_final: 0.8215 (tt0) REVERT: B 1069 GLU cc_start: 0.7371 (pm20) cc_final: 0.7088 (pm20) outliers start: 108 outliers final: 98 residues processed: 601 average time/residue: 0.1924 time to fit residues: 186.5792 Evaluate side-chains 655 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 554 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 793 ASN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1100 LYS Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain T residue 488 MET Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 869 SER Chi-restraints excluded: chain C residue 884 PHE Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 821 ASN Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1162 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 294 optimal weight: 7.9990 chunk 305 optimal weight: 5.9990 chunk 351 optimal weight: 0.0670 chunk 47 optimal weight: 0.0970 chunk 156 optimal weight: 2.9990 chunk 283 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 278 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 299 optimal weight: 9.9990 chunk 312 optimal weight: 2.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1206 ASN B1122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.162478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.122253 restraints weight = 46932.487| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.62 r_work: 0.3337 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30347 Z= 0.131 Angle : 0.558 10.712 41478 Z= 0.284 Chirality : 0.044 0.367 4755 Planarity : 0.004 0.046 5286 Dihedral : 4.735 59.163 4676 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.96 % Allowed : 16.03 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.14), residues: 3749 helix: 1.79 (0.21), residues: 733 sheet: 0.04 (0.18), residues: 781 loop : -1.60 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 397 TYR 0.023 0.001 TYR B 822 PHE 0.031 0.001 PHE A 566 TRP 0.022 0.001 TRP B 174 HIS 0.005 0.001 HIS C1145 Details of bonding type rmsd covalent geometry : bond 0.00300 (30249) covalent geometry : angle 0.54419 (41253) SS BOND : bond 0.00325 ( 69) SS BOND : angle 1.62786 ( 138) hydrogen bonds : bond 0.04779 ( 955) hydrogen bonds : angle 4.49462 ( 2683) link_BETA1-4 : bond 0.00399 ( 4) link_BETA1-4 : angle 1.25322 ( 12) link_NAG-ASN : bond 0.00462 ( 25) link_NAG-ASN : angle 2.10571 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11262.85 seconds wall clock time: 192 minutes 7.64 seconds (11527.64 seconds total)