Starting phenix.real_space_refine on Sat Jun 28 20:27:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y8a_39039/06_2025/8y8a_39039.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y8a_39039/06_2025/8y8a_39039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y8a_39039/06_2025/8y8a_39039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y8a_39039/06_2025/8y8a_39039.map" model { file = "/net/cci-nas-00/data/ceres_data/8y8a_39039/06_2025/8y8a_39039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y8a_39039/06_2025/8y8a_39039.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 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 209 5.16 5 C 21290 2.51 5 N 5451 2.21 5 O 6437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33387 Number of models: 1 Model: "" Number of chains: 22 Chain: "T" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1725 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 14, 'TRANS': 222} Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "H" 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: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "A" Number of atoms: 9191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1185, 9191 Classifications: {'peptide': 1185} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1128} Chain breaks: 4 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 9236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 9236 Classifications: {'peptide': 1194} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1137} Chain breaks: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 9255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 9255 Classifications: {'peptide': 1194} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1137} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "G" 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: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 18.14, per 1000 atoms: 0.54 Number of scatterers: 33387 At special positions: 0 Unit cell: (144.32, 146.78, 239.44, 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 209 16.00 O 6437 8.00 N 5451 7.00 C 21290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=74, symmetry=0 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 H 410 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 437 " - pdb=" SG CYS H 465 " distance=2.03 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 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " 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 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 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 C 20 " - pdb=" SG CYS C 156 " 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 382 " - pdb=" SG CYS C 603 " 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 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 Simple disulfide: pdb=" SG CYS G 410 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 437 " - pdb=" SG CYS G 465 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 19 " " NAG A1302 " - " ASN A 192 " " NAG A1303 " - " ASN A 703 " " NAG A1304 " - " ASN A 793 " " NAG B1301 " - " ASN B 192 " " NAG B1302 " - " ASN B1211 " " NAG B1303 " - " ASN B 355 " " NAG C1301 " - " ASN C 703 " " NAG C1302 " - " ASN C 771 " " NAG C1303 " - " ASN C 192 " " NAG D 1 " - " ASN A 188 " " NAG E 1 " - " ASN A 725 " " NAG F 1 " - " ASN A1211 " " NAG I 1 " - " ASN A 132 " " NAG J 1 " - " ASN A 664 " " NAG K 1 " - " ASN C 664 " " NAG L 1 " - " ASN C 793 " " NAG M 1 " - " ASN C 188 " " NAG N 1 " - " ASN C 58 " " NAG O 1 " - " ASN B 58 " " NAG P 1 " - " ASN B 188 " " NAG Q 1 " - " ASN B 725 " " NAG R 1 " - " ASN B 664 " Time building additional restraints: 8.11 Conformation dependent library (CDL) restraints added in 4.3 seconds 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8026 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 78 sheets defined 21.9% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.18 Creating SS restraints... Processing helix chain 'T' and resid 299 through 303 Processing helix chain 'T' and resid 406 through 411 Processing helix chain 'T' and resid 480 through 492 removed outlier: 3.505A pdb=" N TYR T 485 " --> pdb=" O THR T 481 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY T 492 " --> pdb=" O MET T 488 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 303 Processing helix chain 'H' and resid 406 through 411 Processing helix chain 'H' and resid 480 through 492 removed outlier: 3.627A pdb=" N TYR H 485 " --> pdb=" O THR H 481 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY H 492 " --> pdb=" O MET H 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 91 Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.690A pdb=" N GLU A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.894A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.607A pdb=" N LEU A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN A 402 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 445 through 449 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 553 through 556 removed outlier: 3.773A pdb=" N CYS A 556 " --> pdb=" O GLU A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 696 through 704 removed outlier: 3.915A pdb=" N ASN A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 819 removed outlier: 3.618A pdb=" N PHE A 817 " --> pdb=" O ASP A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.713A pdb=" N LEU A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 862 removed outlier: 3.575A pdb=" N ASP A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN A 838 " --> pdb=" O THR A 834 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN A 840 " --> pdb=" O CYS A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 removed outlier: 3.768A pdb=" N LEU A 906 " --> pdb=" O PRO A 902 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 924 removed outlier: 3.554A pdb=" N ASN A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 removed outlier: 3.627A pdb=" N VAL A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 941 " --> pdb=" O VAL A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 965 removed outlier: 3.534A pdb=" N ILE A 955 " --> pdb=" O SER A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 993 through 1000 removed outlier: 3.769A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 999 " --> pdb=" O ASP A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1018 Processing helix chain 'A' and resid 1023 through 1045 Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 3.617A 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 1057 through 1063 removed outlier: 3.526A pdb=" N ILE A1061 " --> pdb=" O SER A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1069 Processing helix chain 'A' and resid 1070 through 1114 removed outlier: 3.718A pdb=" N ARG A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.912A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.850A pdb=" N ILE C 378 " --> pdb=" O ASP C 374 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 374 through 379' Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.961A pdb=" N LEU C 401 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN C 402 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 443 through 448 removed outlier: 3.911A pdb=" N TYR C 448 " --> pdb=" O TRP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.656A pdb=" N ASN C 483 " --> pdb=" O PRO C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 696 through 704 removed outlier: 4.666A pdb=" N ASN C 702 " --> pdb=" O SER C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 818 removed outlier: 3.629A pdb=" N PHE C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 818 " --> pdb=" O CYS C 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 813 through 818' Processing helix chain 'C' and resid 822 through 830 removed outlier: 3.680A pdb=" N HIS C 826 " --> pdb=" O TYR C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 833 No H-bonds generated for 'chain 'C' and resid 831 through 833' Processing helix chain 'C' and resid 838 through 862 removed outlier: 3.651A pdb=" N LEU C 843 " --> pdb=" O ILE C 839 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN C 844 " --> pdb=" O ASN C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 909 Processing helix chain 'C' and resid 914 through 924 removed outlier: 3.978A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN C 924 " --> pdb=" O GLU C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 removed outlier: 3.951A pdb=" N VAL C 937 " --> pdb=" O ASP C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 965 removed outlier: 3.604A pdb=" N ILE C 955 " --> pdb=" O SER C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 989 removed outlier: 3.523A pdb=" N GLY C 989 " --> pdb=" O TYR C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.751A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1018 removed outlier: 3.642A 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: 3.658A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1049 removed outlier: 3.959A 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 1058 through 1063 removed outlier: 3.823A pdb=" N LEU C1062 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER C1063 " --> pdb=" O GLN C1059 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1058 through 1063' Processing helix chain 'C' and resid 1064 through 1065 No H-bonds generated for 'chain 'C' and resid 1064 through 1065' Processing helix chain 'C' and resid 1066 through 1069 Processing helix chain 'C' and resid 1070 through 1114 removed outlier: 3.779A pdb=" N ARG C1076 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY C1080 " --> pdb=" O ARG C1076 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C1081 " --> pdb=" O LEU C1077 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing helix chain 'C' and resid 1198 through 1200 No H-bonds generated for 'chain 'C' and resid 1198 through 1200' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 328 through 333 removed outlier: 3.755A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 328 through 333' Processing helix chain 'B' and resid 355 through 363 removed outlier: 3.524A pdb=" N VAL B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 402 removed outlier: 3.523A pdb=" N LEU B 401 " --> pdb=" O ARG B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 413 removed outlier: 3.570A pdb=" N SER B 411 " --> pdb=" O GLY B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 449 removed outlier: 3.537A pdb=" N TYR B 448 " --> pdb=" O ASN B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 485 removed outlier: 3.546A pdb=" N SER B 484 " --> pdb=" O VAL B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 556 removed outlier: 3.569A 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 814 through 819 removed outlier: 3.936A pdb=" N VAL B 818 " --> pdb=" O CYS B 814 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS B 819 " --> pdb=" O SER B 815 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 814 through 819' 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 834 through 862 removed outlier: 3.775A pdb=" N ASN B 838 " --> pdb=" O THR B 834 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE B 839 " --> pdb=" O PHE B 835 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE B 842 " --> pdb=" O ASN B 838 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B 843 " --> pdb=" O ILE B 839 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN B 844 " --> pdb=" O ASN B 840 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLU B 845 " --> pdb=" O SER B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 901 through 909 removed outlier: 3.705A pdb=" N LEU B 906 " --> pdb=" O PRO B 902 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 923 removed outlier: 3.924A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN B 923 " --> pdb=" O VAL B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 928 removed outlier: 4.317A pdb=" N GLY B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 928 " --> pdb=" O ASN B 924 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 923 through 928' Processing helix chain 'B' and resid 933 through 940 removed outlier: 3.515A pdb=" N VAL B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 964 removed outlier: 3.684A pdb=" N VAL B 964 " --> pdb=" O THR B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 967 No H-bonds generated for 'chain 'B' and resid 965 through 967' Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 993 through 998 removed outlier: 3.819A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 998 " --> pdb=" O MET B 994 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 993 through 998' Processing helix chain 'B' and resid 1000 through 1018 Processing helix chain 'B' and resid 1023 through 1045 Processing helix chain 'B' and resid 1046 through 1049 removed outlier: 3.738A pdb=" N ASN B1049 " --> pdb=" O GLN B1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1046 through 1049' Processing helix chain 'B' and resid 1057 through 1065 removed outlier: 3.871A pdb=" N ILE B1061 " --> pdb=" O SER B1057 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1114 removed outlier: 3.713A pdb=" N ALA B1070 " --> pdb=" O ASP B1066 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL B1114 " --> pdb=" O VAL B1110 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 303 Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 480 through 492 removed outlier: 3.530A pdb=" N TYR G 485 " --> pdb=" O THR G 481 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY G 492 " --> pdb=" O MET G 488 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'T' and resid 260 through 261 removed outlier: 4.212A pdb=" N ASN T 398 " --> pdb=" O GLY T 383 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY T 383 " --> pdb=" O ASN T 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'T' and resid 278 through 283 removed outlier: 5.077A pdb=" N HIS T 279 " --> pdb=" O VAL T 275 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL T 275 " --> pdb=" O HIS T 279 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS T 281 " --> pdb=" O LEU T 273 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER T 272 " --> pdb=" O PHE T 311 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS T 330 " --> pdb=" O LYS T 350 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'T' and resid 424 through 427 removed outlier: 7.773A pdb=" N VAL T 473 " --> pdb=" O SER T 460 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TRP T 453 " --> pdb=" O SER T 448 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER T 448 " --> pdb=" O TRP T 453 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU T 455 " --> pdb=" O VAL T 446 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL T 446 " --> pdb=" O LEU T 455 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLY T 457 " --> pdb=" O PRO T 444 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY T 442 " --> pdb=" O THR T 459 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 260 through 261 removed outlier: 4.258A pdb=" N ASN H 398 " --> pdb=" O GLY H 383 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY H 383 " --> pdb=" O ASN H 398 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU H 378 " --> pdb=" O SER H 448 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER H 448 " --> pdb=" O LEU H 378 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL H 446 " --> pdb=" O TRP H 380 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER H 382 " --> pdb=" O PRO H 444 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY H 442 " --> pdb=" O THR H 459 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLY H 457 " --> pdb=" O PRO H 444 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL H 446 " --> pdb=" O LEU H 455 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU H 455 " --> pdb=" O VAL H 446 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER H 448 " --> pdb=" O TRP H 453 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TRP H 453 " --> pdb=" O SER H 448 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER H 460 " --> pdb=" O VAL H 473 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N VAL H 473 " --> pdb=" O SER H 460 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 278 through 283 removed outlier: 5.080A pdb=" N HIS H 279 " --> pdb=" O VAL H 275 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL H 275 " --> pdb=" O HIS H 279 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS H 281 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER H 272 " --> pdb=" O PHE H 311 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS H 330 " --> pdb=" O LYS H 350 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA7, first strand: chain 'A' and resid 60 through 67 removed outlier: 4.216A pdb=" N ASN A 278 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.996A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.716A pdb=" N SER A 96 " --> pdb=" O TYR A 235 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 235 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR A 123 " --> pdb=" O MET A 238 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 148 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 101 through 107 removed outlier: 3.642A pdb=" N SER A 104 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR A 203 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 211 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE A 224 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 109 through 112 removed outlier: 3.748A pdb=" N THR A 109 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 120 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 302 through 305 Processing sheet with id=AB4, first strand: chain 'A' and resid 316 through 319 removed outlier: 6.192A pdb=" N VAL A 317 " --> pdb=" O ASP A 623 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A 620 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 631 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AB6, first strand: chain 'A' and resid 346 through 350 removed outlier: 3.524A pdb=" N ARG A 347 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 385 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 427 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 346 through 350 removed outlier: 3.524A pdb=" N ARG A 347 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 385 " --> pdb=" O ASN A 595 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AB9, first strand: chain 'A' and resid 467 through 468 removed outlier: 3.722A pdb=" N LYS A 536 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 504 through 506 Processing sheet with id=AC2, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AC3, first strand: chain 'A' and resid 635 through 636 removed outlier: 3.710A pdb=" N VAL A 636 " --> pdb=" O THR A 666 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR A 666 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 657 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 724 through 725 removed outlier: 6.540A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE A 742 " --> pdb=" O MET A 738 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 773 through 775 removed outlier: 5.965A pdb=" N SER A 773 " --> pdb=" O LEU C 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 786 through 791 Processing sheet with id=AC7, first strand: chain 'A' and resid 794 through 804 removed outlier: 3.788A pdb=" N LEU A1131 " --> pdb=" O PHE A1146 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.445A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 944 " --> pdb=" O THR A 811 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 866 through 868 removed outlier: 6.810A pdb=" N LEU A 867 " --> pdb=" O VAL B 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 1162 through 1163 Processing sheet with id=AD2, first strand: chain 'A' and resid 1169 through 1172 removed outlier: 3.826A pdb=" N GLY A1169 " --> pdb=" O MET A1205 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 1175 through 1179 Processing sheet with id=AD4, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AD5, first strand: chain 'C' and resid 60 through 67 removed outlier: 3.504A pdb=" N SER C 262 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N GLN C 265 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASP C 281 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU C 267 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA C 279 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ASN C 269 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.882A pdb=" N PHE C 209 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER C 225 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA C 211 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 80 through 81 removed outlier: 6.158A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.667A pdb=" N SER C 96 " --> pdb=" O TYR C 235 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 124 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU C 146 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN C 188 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE C 148 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS C 186 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA C 150 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 109 through 111 removed outlier: 3.741A pdb=" N THR C 109 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 302 through 307 Processing sheet with id=AE2, first strand: chain 'C' and resid 316 through 319 removed outlier: 3.586A pdb=" N VAL C 317 " --> pdb=" O ASN C 621 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG C 319 " --> pdb=" O ASP C 623 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY C 631 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY C 629 " --> pdb=" O TYR C 622 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 337 through 339 Processing sheet with id=AE4, first strand: chain 'C' and resid 346 through 349 removed outlier: 3.760A pdb=" N SER C 385 " --> pdb=" O ASN C 595 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 346 through 349 removed outlier: 3.760A pdb=" N SER C 385 " --> pdb=" O ASN C 595 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 382 through 383 Processing sheet with id=AE7, first strand: chain 'C' and resid 459 through 463 removed outlier: 3.502A pdb=" N VAL C 460 " --> pdb=" O ASP C 578 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 467 through 468 removed outlier: 3.698A pdb=" N LYS C 536 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 504 through 506 Processing sheet with id=AF1, first strand: chain 'C' and resid 550 through 551 Processing sheet with id=AF2, first strand: chain 'C' and resid 666 through 667 removed outlier: 3.534A pdb=" N LEU C 648 " --> pdb=" O GLY C 657 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU C 647 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.654A pdb=" N PHE C 713 " --> pdb=" O VAL C 720 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 724 through 731 removed outlier: 6.483A pdb=" N ASN C 725 " --> pdb=" O TYR C 762 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE C 764 " --> pdb=" O ASN C 725 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR C 766 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR C 729 " --> pdb=" O THR C 766 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE C 742 " --> pdb=" O MET C 738 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 773 through 775 removed outlier: 5.956A pdb=" N SER C 773 " --> pdb=" O LEU B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'C' and resid 788 through 791 Processing sheet with id=AF7, first strand: chain 'C' and resid 794 through 804 removed outlier: 3.590A pdb=" N ALA C 797 " --> pdb=" O SER C1147 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 803 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C1137 " --> pdb=" O GLY C1140 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU C1131 " --> pdb=" O PHE C1146 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR C1148 " --> pdb=" O HIS C1129 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS C1129 " --> pdb=" O TYR C1148 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 809 through 811 removed outlier: 4.382A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS C 944 " --> pdb=" O THR C 811 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 3.882A pdb=" N ARG C1168 " --> pdb=" O LEU C1164 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1175 through 1179 Processing sheet with id=AG2, first strand: chain 'B' and resid 59 through 67 removed outlier: 3.548A pdb=" N THR B 59 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 262 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN B 278 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.527A pdb=" N TRP B 257 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR B 203 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 211 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE B 224 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 109 through 112 Processing sheet with id=AG5, first strand: chain 'B' and resid 183 through 190 removed outlier: 4.066A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 187 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 148 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 140 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 124 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR B 123 " --> pdb=" O MET B 238 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 161 through 162 removed outlier: 6.496A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'B' and resid 302 through 305 removed outlier: 3.516A pdb=" N SER B 678 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE B 713 " --> pdb=" O VAL B 720 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 317 through 319 removed outlier: 6.692A pdb=" N VAL B 317 " --> pdb=" O ASP B 623 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY B 631 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 337 through 339 removed outlier: 6.480A pdb=" N VAL B 338 " --> pdb=" O ASN B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'B' and resid 346 through 349 removed outlier: 3.717A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP B 389 " --> pdb=" O ASN B 591 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR B 427 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 346 through 349 removed outlier: 3.717A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP B 389 " --> pdb=" O ASN B 591 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 353 through 354 removed outlier: 3.745A pdb=" N PHE B 354 " --> pdb=" O CYS B 603 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AH5, first strand: chain 'B' and resid 467 through 468 Processing sheet with id=AH6, first strand: chain 'B' and resid 504 through 506 Processing sheet with id=AH7, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AH8, first strand: chain 'B' and resid 635 through 636 removed outlier: 4.327A pdb=" N THR B 666 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS B 665 " --> pdb=" O ASP B 660 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE B 658 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU B 648 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'B' and resid 724 through 731 removed outlier: 6.671A pdb=" N VAL B 724 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N THR B 766 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N LEU B 726 " --> pdb=" O THR B 766 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.364A pdb=" N SER B1152 " --> pdb=" O THR B 792 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE B 794 " --> pdb=" O PRO B1150 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE B 796 " --> pdb=" O TYR B1148 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR B1148 " --> pdb=" O ILE B 796 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY B 798 " --> pdb=" O PHE B1146 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE B1146 " --> pdb=" O GLY B 798 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLU B 800 " --> pdb=" O ILE B1144 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE B1144 " --> pdb=" O GLU B 800 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N PHE B 802 " --> pdb=" O LEU B1142 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU B1142 " --> pdb=" O PHE B 802 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLN B 804 " --> pdb=" O GLY B1140 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY B1140 " --> pdb=" O GLN B 804 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B1146 " --> pdb=" O LEU B1131 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU B1131 " --> pdb=" O PHE B1146 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR B1148 " --> pdb=" O HIS B1129 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N HIS B1129 " --> pdb=" O TYR B1148 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'B' and resid 809 through 811 removed outlier: 4.348A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 944 " --> pdb=" O THR B 811 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 3.648A pdb=" N ILE B1170 " --> pdb=" O LEU B1162 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B1162 " --> pdb=" O ILE B1170 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'B' and resid 1175 through 1179 Processing sheet with id=AI5, first strand: chain 'G' and resid 260 through 261 removed outlier: 4.623A pdb=" N CYS G 426 " --> pdb=" O ILE G 405 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL G 473 " --> pdb=" O SER G 460 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER G 460 " --> pdb=" O VAL G 473 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TRP G 453 " --> pdb=" O SER G 448 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N SER G 448 " --> pdb=" O TRP G 453 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU G 455 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL G 446 " --> pdb=" O LEU G 455 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLY G 457 " --> pdb=" O PRO G 444 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY G 442 " --> pdb=" O THR G 459 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER G 382 " --> pdb=" O PRO G 444 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL G 446 " --> pdb=" O TRP G 380 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER G 448 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU G 378 " --> pdb=" O SER G 448 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY G 383 " --> pdb=" O ASN G 398 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASN G 398 " --> pdb=" O GLY G 383 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'G' and resid 278 through 283 removed outlier: 5.187A pdb=" N HIS G 279 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL G 275 " --> pdb=" O HIS G 279 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS G 281 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS G 330 " --> pdb=" O LYS G 350 " (cutoff:3.500A) 1032 hydrogen bonds defined for protein. 2823 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.74 Time building geometry restraints manager: 9.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10593 1.34 - 1.46: 8078 1.46 - 1.58: 15290 1.58 - 1.70: 0 1.70 - 1.81: 251 Bond restraints: 34212 Sorted by residual: bond pdb=" N VAL B 113 " pdb=" CA VAL B 113 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.28e-02 6.10e+03 9.04e+00 bond pdb=" C TYR B 112 " pdb=" N VAL B 113 " ideal model delta sigma weight residual 1.331 1.352 -0.021 1.24e-02 6.50e+03 2.99e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.33e+00 ... (remaining 34207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 45639 1.24 - 2.49: 820 2.49 - 3.73: 203 3.73 - 4.97: 19 4.97 - 6.21: 10 Bond angle restraints: 46691 Sorted by residual: angle pdb=" N VAL A 129 " pdb=" CA VAL A 129 " pdb=" C VAL A 129 " ideal model delta sigma weight residual 113.47 109.62 3.85 1.01e+00 9.80e-01 1.45e+01 angle pdb=" CA GLY A 718 " pdb=" C GLY A 718 " pdb=" O GLY A 718 " ideal model delta sigma weight residual 122.22 120.15 2.07 6.50e-01 2.37e+00 1.02e+01 angle pdb=" N VAL B 482 " pdb=" CA VAL B 482 " pdb=" C VAL B 482 " ideal model delta sigma weight residual 112.98 109.88 3.10 1.25e+00 6.40e-01 6.17e+00 angle pdb=" CA VAL B 113 " pdb=" C VAL B 113 " pdb=" N ASN B 114 " ideal model delta sigma weight residual 116.51 119.15 -2.64 1.07e+00 8.73e-01 6.10e+00 angle pdb=" N GLY C 653 " pdb=" CA GLY C 653 " pdb=" C GLY C 653 " ideal model delta sigma weight residual 113.18 118.90 -5.72 2.37e+00 1.78e-01 5.82e+00 ... (remaining 46686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.86: 20385 21.86 - 43.71: 329 43.71 - 65.57: 26 65.57 - 87.43: 12 87.43 - 109.29: 8 Dihedral angle restraints: 20760 sinusoidal: 8256 harmonic: 12504 Sorted by residual: dihedral pdb=" O4 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C5 BMA I 3 " pdb=" O5 BMA I 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.42 109.29 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" O4 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C5 BMA K 3 " pdb=" O5 BMA K 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.81 108.90 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" CA SER B 820 " pdb=" C SER B 820 " pdb=" N ASN B 821 " pdb=" CA ASN B 821 " ideal model delta harmonic sigma weight residual 180.00 161.24 18.76 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 20757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4550 0.055 - 0.110: 738 0.110 - 0.164: 96 0.164 - 0.219: 2 0.219 - 0.274: 2 Chirality restraints: 5388 Sorted by residual: chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB VAL B 113 " pdb=" CA VAL B 113 " pdb=" CG1 VAL B 113 " pdb=" CG2 VAL B 113 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 5385 not shown) Planarity restraints: 5987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B1066 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO B1067 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B1067 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B1067 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1066 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO A1067 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A1067 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1067 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C1066 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO C1067 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C1067 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C1067 " 0.019 5.00e-02 4.00e+02 ... (remaining 5984 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2738 2.75 - 3.29: 31568 3.29 - 3.82: 52022 3.82 - 4.36: 59183 4.36 - 4.90: 106309 Nonbonded interactions: 251820 Sorted by model distance: nonbonded pdb=" O VAL B 113 " pdb=" OG1 THR B 116 " model vdw 2.209 3.040 nonbonded pdb=" OH TYR C 832 " pdb=" OD1 ASP C1075 " model vdw 2.225 3.040 nonbonded pdb=" O VAL A 113 " pdb=" OG1 THR A 116 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR B 832 " pdb=" OD1 ASP B1075 " model vdw 2.242 3.040 nonbonded pdb=" OG SER A1055 " pdb=" OE2 GLU A1060 " model vdw 2.256 3.040 ... (remaining 251815 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 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 90 or (resid 91 and (name N or nam \ e CA or name C or name O or name CB )) or resid 92 through 344 or (resid 345 thr \ ough 346 and (name N or name CA or name C or name O or name CB )) or resid 347 t \ hrough 360 or (resid 361 and (name N or name CA or name C or name O or name CB ) \ ) or resid 362 through 378 or (resid 379 and (name N or name CA or name C or nam \ e O or name CB )) or resid 380 through 389 or (resid 390 and (name N or name CA \ or name C or name O or name CB )) or resid 391 through 520 or (resid 521 through \ 525 and (name N or name CA or name C or name O or name CB )) or resid 526 throu \ gh 606 or (resid 607 through 609 and (name N or name CA or name C or name O or n \ ame CB )) or resid 610 through 626 or (resid 627 and (name N or name CA or name \ C or name O or name CB )) or resid 628 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 name CA or name C or name O or name CB )) or resid 781 through 8 \ 36 or (resid 837 and (name N or name CA or name C or name O or name CB )) or res \ id 838 through 875 or (resid 876 and (name N or name CA or name C or name O or n \ ame 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 through 998 or (resid 999 and \ (name N or name CA or name C or name O or name CB )) or resid 1000 through 1065 \ or (resid 1066 and (name N or name CA or name C or name O or name CB )) or resi \ d 1067 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 CA or \ name C or name O or name CB )) or resid 1201 through 1221 or resid 1301 through \ 1303)) selection = (chain 'B' and (resid 14 through 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 68 or (resid 69 and (name N or nam \ e CA or name C or name O or name CB )) or resid 70 through 232 or (resid 233 and \ (name N or name CA or name C or name O or name CB )) or resid 234 through 246 o \ r (resid 247 through 248 and (name N or name CA or name C or name O or name CB ) \ ) or resid 249 or (resid 250 through 253 and (name N or name CA or name C or nam \ e O or name CB )) or resid 254 through 308 or resid 311 through 344 or (resid 34 \ 5 through 346 and (name N or name CA or name C or name O or name CB )) or resid \ 347 through 360 or (resid 361 and (name N or name CA or name C or name O or name \ CB )) or resid 362 through 378 or (resid 379 and (name N or name CA or name C o \ r name O or name CB )) or resid 380 through 389 or (resid 390 and (name N or nam \ e CA or name C or name O or name CB )) or resid 391 through 606 or (resid 607 th \ rough 609 and (name N or name CA or name C or name O or name CB )) or resid 610 \ through 626 or (resid 627 and (name N or name CA or name C or name O or name CB \ )) or resid 628 through 629 or (resid 630 and (name N or name CA or name C or na \ me O or name CB )) or resid 631 through 705 or (resid 706 and (name N or name CA \ or name C or name O or name CB )) or resid 707 through 708 or (resid 709 and (n \ ame 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 name O or name CB )) or resid 781 \ through 836 or (resid 837 and (name N or name CA or name C or name O or name CB \ )) or resid 838 through 890 or (resid 891 and (name N or name CA or name C or na \ me O or name CB )) or resid 899 through 998 or (resid 999 and (name N or name CA \ or name C or name O or name CB )) 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 1221 \ or resid 1301 through 1303)) selection = (chain 'C' and (resid 14 through 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 40 or (resid 41 and (name N or nam \ e CA or name C or name O or name CB )) or resid 42 through 68 or (resid 69 and ( \ name N or name CA or name C or name O or name CB )) or resid 70 through 90 or (r \ esid 91 and (name N or name CA or name C or name O or name CB )) or resid 92 thr \ ough 232 or (resid 233 and (name N or name CA or name C or name O or name CB )) \ or resid 234 through 246 or (resid 247 through 248 and (name N or name CA or nam \ e C or name O or name CB )) or resid 249 or (resid 250 through 253 and (name N o \ r name CA or name C or name O or name CB )) or resid 254 through 308 or resid 31 \ 1 or (resid 312 and (name N or name CA or name C or name O or name CB )) or resi \ d 313 through 520 or (resid 521 through 525 and (name N or name CA or name C or \ name O or name CB )) or resid 526 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 \ (name N or name CA or name C or name O or name CB )) or resid 621 through 629 or \ (resid 630 and (name N or name CA or name C or name O or name CB )) or resid 63 \ 1 or (resid 632 and (name N or name CA or name C or name O or name CB )) or resi \ d 633 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 o \ r 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 875 or (resid 876 and (name N or name CA o \ r name C or name O or name CB )) or resid 877 through 890 or (resid 891 and (nam \ e N or name CA or name C or name O or name CB )) or resid 899 through 930 or (re \ sid 931 through 932 and (name N or name CA or name C or name O or name CB )) or \ resid 933 through 1065 or (resid 1066 and (name N or name CA or name C or name O \ or name CB )) or resid 1067 through 1148 or (resid 1149 and (name N or name CA \ or name C or name O or name CB )) or resid 1150 through 1221 or resid 1301 throu \ gh 1303)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = (chain 'G' and (resid 256 through 472 or (resid 473 and (name N or name CA or na \ me C or name O or name CB )) or resid 474 through 492)) selection = (chain 'H' and (resid 256 through 472 or (resid 473 and (name N or name CA or na \ me C or name O or name CB )) or resid 474 through 492)) selection = chain 'T' } ncs_group { reference = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.700 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: 0.030 Extract box with map and model: 1.490 Check model and map are aligned: 0.250 Set scattering table: 0.330 Process input model: 77.280 Find NCS groups from input model: 2.480 Set up NCS constraints: 0.190 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 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 0.044 34324 Z= 0.114 Angle : 0.431 6.214 46953 Z= 0.225 Chirality : 0.041 0.274 5388 Planarity : 0.003 0.043 5964 Dihedral : 7.892 109.285 12512 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.45 % Allowed : 3.62 % Favored : 94.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.11), residues: 4256 helix: -0.68 (0.18), residues: 748 sheet: -0.44 (0.16), residues: 859 loop : -2.27 (0.10), residues: 2649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.002 0.000 HIS C 826 PHE 0.006 0.001 PHE A 121 TYR 0.006 0.001 TYR C 50 ARG 0.002 0.000 ARG B 676 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 23) link_NAG-ASN : angle 1.03720 ( 69) link_BETA1-4 : bond 0.00383 ( 15) link_BETA1-4 : angle 0.90900 ( 45) hydrogen bonds : bond 0.25337 ( 1001) hydrogen bonds : angle 8.10718 ( 2823) SS BOND : bond 0.00082 ( 74) SS BOND : angle 0.44200 ( 148) covalent geometry : bond 0.00225 (34212) covalent geometry : angle 0.42919 (46691) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 780 time to evaluate : 3.492 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 147 GLU cc_start: 0.6196 (tp30) cc_final: 0.5963 (tp30) REVERT: A 149 THR cc_start: 0.7868 (p) cc_final: 0.7552 (p) REVERT: A 158 TYR cc_start: 0.7781 (m-80) cc_final: 0.7543 (m-10) REVERT: A 166 LYS cc_start: 0.7572 (mmtp) cc_final: 0.7366 (mmtt) REVERT: A 262 SER cc_start: 0.7635 (p) cc_final: 0.7186 (p) REVERT: A 608 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6399 (pp) REVERT: A 687 SER cc_start: 0.8483 (m) cc_final: 0.8005 (p) REVERT: A 738 MET cc_start: 0.7725 (mmm) cc_final: 0.7385 (mmm) REVERT: A 746 TYR cc_start: 0.8179 (t80) cc_final: 0.7690 (t80) REVERT: A 780 GLU cc_start: 0.6978 (tp30) cc_final: 0.6766 (tp30) REVERT: A 851 ASP cc_start: 0.6885 (m-30) cc_final: 0.6679 (m-30) REVERT: A 884 PHE cc_start: 0.7480 (m-10) cc_final: 0.7230 (m-10) REVERT: A 912 LYS cc_start: 0.7777 (ptpp) cc_final: 0.7531 (ptpp) REVERT: A 1045 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7877 (mm110) REVERT: A 1135 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7582 (mm110) REVERT: C 66 TYR cc_start: 0.7841 (m-80) cc_final: 0.7333 (m-80) REVERT: C 238 MET cc_start: 0.6242 (ptp) cc_final: 0.5834 (ptp) REVERT: C 305 ASP cc_start: 0.7111 (t0) cc_final: 0.6568 (t0) REVERT: C 659 LYS cc_start: 0.8018 (tttt) cc_final: 0.7783 (tttt) REVERT: C 676 ARG cc_start: 0.8116 (mtm180) cc_final: 0.7619 (mtm180) REVERT: C 727 THR cc_start: 0.8441 (p) cc_final: 0.8091 (m) REVERT: C 878 ASP cc_start: 0.7848 (p0) cc_final: 0.7619 (p0) REVERT: C 880 ASP cc_start: 0.7095 (t0) cc_final: 0.6838 (t0) REVERT: C 885 LYS cc_start: 0.8020 (pttp) cc_final: 0.7680 (pttp) REVERT: C 934 LEU cc_start: 0.7997 (mt) cc_final: 0.7746 (mt) REVERT: C 939 SER cc_start: 0.8423 (t) cc_final: 0.8196 (p) REVERT: C 944 LYS cc_start: 0.8697 (tttt) cc_final: 0.8212 (tptm) REVERT: C 996 VAL cc_start: 0.8068 (p) cc_final: 0.7636 (t) REVERT: C 1095 ASP cc_start: 0.7272 (t0) cc_final: 0.7036 (t0) REVERT: C 1115 LYS cc_start: 0.8671 (mtpp) cc_final: 0.8153 (mmmm) REVERT: C 1156 VAL cc_start: 0.8022 (p) cc_final: 0.7093 (t) REVERT: C 1214 LYS cc_start: 0.7887 (mmmm) cc_final: 0.7181 (mmmm) REVERT: B 99 ASN cc_start: 0.7671 (m-40) cc_final: 0.6958 (m110) REVERT: B 120 GLU cc_start: 0.7162 (mp0) cc_final: 0.6825 (mp0) REVERT: B 138 VAL cc_start: 0.8386 (p) cc_final: 0.8181 (m) REVERT: B 145 ILE cc_start: 0.8161 (mm) cc_final: 0.7791 (mt) REVERT: B 266 TYR cc_start: 0.7600 (m-80) cc_final: 0.7136 (m-80) REVERT: B 398 ARG cc_start: 0.7492 (tmt-80) cc_final: 0.7009 (tmt-80) REVERT: B 415 LYS cc_start: 0.8154 (ttmt) cc_final: 0.7751 (ttmt) REVERT: B 594 PHE cc_start: 0.8599 (m-80) cc_final: 0.8345 (m-10) REVERT: B 595 ASN cc_start: 0.8094 (m110) cc_final: 0.7744 (m-40) REVERT: B 601 THR cc_start: 0.7966 (p) cc_final: 0.7682 (p) REVERT: B 623 ASP cc_start: 0.7681 (t0) cc_final: 0.7351 (t70) REVERT: B 745 ASP cc_start: 0.7250 (t70) cc_final: 0.6992 (t70) REVERT: B 746 TYR cc_start: 0.8551 (t80) cc_final: 0.8305 (t80) REVERT: B 841 SER cc_start: 0.7862 (m) cc_final: 0.7644 (m) REVERT: B 885 LYS cc_start: 0.8473 (ttpp) cc_final: 0.8220 (ttpp) REVERT: B 934 LEU cc_start: 0.7565 (mt) cc_final: 0.7122 (mt) REVERT: B 940 PHE cc_start: 0.8249 (m-10) cc_final: 0.8011 (m-10) REVERT: B 985 TYR cc_start: 0.8172 (m-10) cc_final: 0.7952 (m-80) REVERT: B 1014 SER cc_start: 0.8813 (t) cc_final: 0.8532 (m) REVERT: B 1036 ASN cc_start: 0.7909 (t0) cc_final: 0.7639 (t0) outliers start: 53 outliers final: 20 residues processed: 822 average time/residue: 0.4429 time to fit residues: 600.5611 Evaluate side-chains 629 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 608 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 298 VAL Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 476 CYS Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 836 CYS Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain G residue 387 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 358 optimal weight: 4.9990 chunk 322 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 217 optimal weight: 0.6980 chunk 172 optimal weight: 0.0670 chunk 333 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 202 optimal weight: 0.0770 chunk 247 optimal weight: 2.9990 chunk 385 optimal weight: 2.9990 overall best weight: 1.1680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 276 GLN H 276 GLN H 408 GLN A 26 ASN A 278 ASN A 291 GLN A 433 ASN A 445 ASN A 605 ASN A 646 ASN A 702 ASN A 709 GLN A 799 HIS A 847 ASN A 876 HIS A1016 GLN A1041 ASN A1046 GLN A1059 GLN A1071 GLN A1206 ASN C 160 HIS C 243 ASN C 269 ASN C 645 GLN C 683 GLN C 789 GLN C 804 GLN C 854 GLN C1038 GLN C1045 GLN B 160 HIS B 265 GLN B 278 ASN B 291 GLN B 323 ASN B 402 GLN B 410 GLN B 445 ASN B 645 GLN B 863 GLN B 941 ASN B1041 ASN B1091 GLN G 276 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.191479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.139363 restraints weight = 55817.053| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.26 r_work: 0.3438 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 34324 Z= 0.173 Angle : 0.577 12.171 46953 Z= 0.297 Chirality : 0.045 0.490 5388 Planarity : 0.004 0.046 5964 Dihedral : 5.506 68.657 5406 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.47 % Allowed : 9.22 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.12), residues: 4256 helix: 0.74 (0.20), residues: 760 sheet: -0.00 (0.16), residues: 902 loop : -1.99 (0.11), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 575 HIS 0.007 0.001 HIS C1145 PHE 0.024 0.002 PHE C 681 TYR 0.020 0.002 TYR B 622 ARG 0.004 0.001 ARG C 347 Details of bonding type rmsd link_NAG-ASN : bond 0.01120 ( 23) link_NAG-ASN : angle 2.98373 ( 69) link_BETA1-4 : bond 0.00495 ( 15) link_BETA1-4 : angle 1.53371 ( 45) hydrogen bonds : bond 0.04923 ( 1001) hydrogen bonds : angle 5.64941 ( 2823) SS BOND : bond 0.00296 ( 74) SS BOND : angle 1.83218 ( 148) covalent geometry : bond 0.00397 (34212) covalent geometry : angle 0.55523 (46691) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 644 time to evaluate : 3.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 424 MET cc_start: 0.5712 (tpt) cc_final: 0.5497 (tpt) REVERT: A 26 ASN cc_start: 0.6754 (OUTLIER) cc_final: 0.5758 (p0) REVERT: A 147 GLU cc_start: 0.6925 (tp30) cc_final: 0.6437 (tp30) REVERT: A 264 ARG cc_start: 0.8003 (ptp90) cc_final: 0.7801 (ptp-170) REVERT: A 349 PHE cc_start: 0.6661 (m-80) cc_final: 0.5911 (m-80) REVERT: A 633 PHE cc_start: 0.8668 (m-80) cc_final: 0.8160 (m-80) REVERT: A 644 TRP cc_start: 0.8530 (p90) cc_final: 0.8240 (p90) REVERT: A 646 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7368 (t0) REVERT: A 659 LYS cc_start: 0.8351 (ttpp) cc_final: 0.7961 (ttpp) REVERT: A 669 ILE cc_start: 0.8498 (mt) cc_final: 0.8286 (tp) REVERT: A 687 SER cc_start: 0.8693 (m) cc_final: 0.8282 (p) REVERT: A 746 TYR cc_start: 0.8481 (t80) cc_final: 0.8047 (t80) REVERT: A 780 GLU cc_start: 0.7908 (tp30) cc_final: 0.7577 (tp30) REVERT: A 845 GLU cc_start: 0.7512 (tt0) cc_final: 0.7204 (tt0) REVERT: A 884 PHE cc_start: 0.7680 (m-10) cc_final: 0.7310 (m-10) REVERT: A 908 PHE cc_start: 0.8666 (m-80) cc_final: 0.8405 (m-80) REVERT: A 912 LYS cc_start: 0.8261 (ptpp) cc_final: 0.8027 (ptpp) REVERT: A 1041 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8248 (m-40) REVERT: A 1064 ARG cc_start: 0.8275 (mtp-110) cc_final: 0.8044 (mtp85) REVERT: A 1149 LYS cc_start: 0.8372 (tttp) cc_final: 0.7978 (ttpp) REVERT: C 66 TYR cc_start: 0.8529 (m-80) cc_final: 0.8309 (m-80) REVERT: C 155 MET cc_start: 0.5042 (mmm) cc_final: 0.4825 (mmm) REVERT: C 157 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7909 (tm-30) REVERT: C 160 HIS cc_start: 0.6764 (p90) cc_final: 0.6361 (p90) REVERT: C 189 PHE cc_start: 0.8055 (m-80) cc_final: 0.7785 (m-80) REVERT: C 237 VAL cc_start: 0.6854 (t) cc_final: 0.6643 (p) REVERT: C 238 MET cc_start: 0.6687 (ptp) cc_final: 0.6000 (ptp) REVERT: C 296 SER cc_start: 0.8774 (t) cc_final: 0.8572 (m) REVERT: C 305 ASP cc_start: 0.7634 (t0) cc_final: 0.7338 (t0) REVERT: C 348 ILE cc_start: 0.8008 (tp) cc_final: 0.7773 (tt) REVERT: C 357 SER cc_start: 0.8229 (t) cc_final: 0.7981 (p) REVERT: C 575 TRP cc_start: 0.8857 (p-90) cc_final: 0.8424 (p-90) REVERT: C 613 GLU cc_start: 0.6605 (pp20) cc_final: 0.6219 (pp20) REVERT: C 628 THR cc_start: 0.7711 (p) cc_final: 0.7484 (p) REVERT: C 630 GLN cc_start: 0.8129 (mp10) cc_final: 0.7831 (mt0) REVERT: C 633 PHE cc_start: 0.8187 (m-10) cc_final: 0.7977 (m-80) REVERT: C 685 SER cc_start: 0.8803 (t) cc_final: 0.8562 (p) REVERT: C 880 ASP cc_start: 0.7778 (t0) cc_final: 0.7377 (t0) REVERT: C 885 LYS cc_start: 0.8313 (pttp) cc_final: 0.7997 (pttp) REVERT: C 939 SER cc_start: 0.8621 (t) cc_final: 0.8338 (p) REVERT: C 1064 ARG cc_start: 0.8073 (mmm-85) cc_final: 0.7585 (mtp180) REVERT: C 1095 ASP cc_start: 0.8004 (t0) cc_final: 0.7783 (t0) REVERT: C 1100 LYS cc_start: 0.8623 (ttmm) cc_final: 0.8402 (tttm) REVERT: C 1107 ILE cc_start: 0.8351 (tt) cc_final: 0.8069 (tt) REVERT: C 1112 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7141 (mt-10) REVERT: C 1126 ASN cc_start: 0.8612 (p0) cc_final: 0.8376 (p0) REVERT: C 1214 LYS cc_start: 0.8076 (mmmm) cc_final: 0.7811 (mmmm) REVERT: B 104 SER cc_start: 0.8768 (m) cc_final: 0.8257 (p) REVERT: B 105 LYS cc_start: 0.8254 (ttmm) cc_final: 0.7984 (tttp) REVERT: B 120 GLU cc_start: 0.7522 (mp0) cc_final: 0.7119 (mp0) REVERT: B 138 VAL cc_start: 0.8765 (p) cc_final: 0.8549 (m) REVERT: B 145 ILE cc_start: 0.8547 (mm) cc_final: 0.8315 (mt) REVERT: B 398 ARG cc_start: 0.7674 (tmt-80) cc_final: 0.6973 (tmt-80) REVERT: B 415 LYS cc_start: 0.8443 (ttmt) cc_final: 0.7993 (ttmt) REVERT: B 544 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: B 595 ASN cc_start: 0.8255 (m110) cc_final: 0.7922 (m110) REVERT: B 623 ASP cc_start: 0.8097 (t0) cc_final: 0.7801 (t70) REVERT: B 745 ASP cc_start: 0.8010 (t70) cc_final: 0.7676 (t70) REVERT: B 777 ASP cc_start: 0.7882 (m-30) cc_final: 0.7618 (p0) REVERT: B 841 SER cc_start: 0.8233 (m) cc_final: 0.7938 (m) REVERT: B 885 LYS cc_start: 0.8630 (ttpp) cc_final: 0.8411 (ttpp) REVERT: B 934 LEU cc_start: 0.7824 (mt) cc_final: 0.7584 (mm) REVERT: B 940 PHE cc_start: 0.8574 (m-10) cc_final: 0.8236 (m-80) outliers start: 90 outliers final: 47 residues processed: 701 average time/residue: 0.4237 time to fit residues: 489.5183 Evaluate side-chains 636 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 585 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 298 VAL Chi-restraints excluded: chain T residue 478 MET Chi-restraints excluded: chain H residue 405 ILE Chi-restraints excluded: chain H residue 412 SER Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 619 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain G residue 387 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 35 optimal weight: 9.9990 chunk 235 optimal weight: 0.8980 chunk 352 optimal weight: 1.9990 chunk 297 optimal weight: 0.8980 chunk 300 optimal weight: 2.9990 chunk 412 optimal weight: 50.0000 chunk 384 optimal weight: 3.9990 chunk 346 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 646 ASN A 863 GLN C 142 HIS C 175 HIS C 323 ASN C 876 HIS C1135 GLN C1221 ASN B 204 GLN B 278 ASN B 371 ASN B 702 ASN G 274 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.187105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.135036 restraints weight = 55474.753| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 3.24 r_work: 0.3394 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 34324 Z= 0.229 Angle : 0.613 14.800 46953 Z= 0.313 Chirality : 0.047 0.536 5388 Planarity : 0.004 0.055 5964 Dihedral : 4.981 61.673 5395 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.88 % Allowed : 10.75 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.12), residues: 4256 helix: 1.15 (0.20), residues: 758 sheet: 0.12 (0.16), residues: 898 loop : -1.91 (0.11), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 575 HIS 0.009 0.001 HIS C 503 PHE 0.027 0.002 PHE A 222 TYR 0.026 0.002 TYR B 153 ARG 0.005 0.000 ARG B 986 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 23) link_NAG-ASN : angle 3.75359 ( 69) link_BETA1-4 : bond 0.00406 ( 15) link_BETA1-4 : angle 1.41773 ( 45) hydrogen bonds : bond 0.05679 ( 1001) hydrogen bonds : angle 5.27017 ( 2823) SS BOND : bond 0.00412 ( 74) SS BOND : angle 2.07174 ( 148) covalent geometry : bond 0.00537 (34212) covalent geometry : angle 0.58448 (46691) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 610 time to evaluate : 3.755 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: T 424 MET cc_start: 0.5696 (tpt) cc_final: 0.5381 (tpt) REVERT: H 377 GLN cc_start: 0.7833 (tp-100) cc_final: 0.7553 (tp40) REVERT: A 147 GLU cc_start: 0.7035 (tp30) cc_final: 0.6460 (tp30) REVERT: A 161 THR cc_start: 0.8719 (t) cc_final: 0.8338 (p) REVERT: A 349 PHE cc_start: 0.6845 (m-80) cc_final: 0.5990 (m-80) REVERT: A 633 PHE cc_start: 0.8720 (m-80) cc_final: 0.8125 (m-80) REVERT: A 646 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7639 (t0) REVERT: A 659 LYS cc_start: 0.8301 (ttpp) cc_final: 0.7942 (ttpp) REVERT: A 669 ILE cc_start: 0.8628 (mt) cc_final: 0.8308 (tp) REVERT: A 687 SER cc_start: 0.8753 (m) cc_final: 0.8416 (p) REVERT: A 746 TYR cc_start: 0.8547 (t80) cc_final: 0.8215 (t80) REVERT: A 780 GLU cc_start: 0.7964 (tp30) cc_final: 0.7693 (tp30) REVERT: A 845 GLU cc_start: 0.7561 (tt0) cc_final: 0.7255 (tt0) REVERT: A 912 LYS cc_start: 0.8314 (ptpp) cc_final: 0.8073 (ptpp) REVERT: A 1031 SER cc_start: 0.8132 (t) cc_final: 0.7853 (p) REVERT: A 1064 ARG cc_start: 0.8251 (mtp-110) cc_final: 0.8010 (mtp85) REVERT: A 1066 ASP cc_start: 0.7317 (m-30) cc_final: 0.6673 (p0) REVERT: A 1149 LYS cc_start: 0.8391 (tttp) cc_final: 0.8095 (ttpp) REVERT: A 1185 MET cc_start: 0.8706 (mtp) cc_final: 0.8443 (mtt) REVERT: A 1204 PHE cc_start: 0.7946 (m-80) cc_final: 0.7596 (m-80) REVERT: A 1218 ILE cc_start: 0.8597 (mt) cc_final: 0.8383 (mm) REVERT: C 66 TYR cc_start: 0.8611 (m-80) cc_final: 0.8049 (m-80) REVERT: C 155 MET cc_start: 0.5055 (mmm) cc_final: 0.4775 (mmm) REVERT: C 157 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7519 (tm-30) REVERT: C 160 HIS cc_start: 0.6828 (p90) cc_final: 0.6354 (p90) REVERT: C 189 PHE cc_start: 0.8106 (m-80) cc_final: 0.7823 (m-80) REVERT: C 238 MET cc_start: 0.6670 (ptp) cc_final: 0.6007 (ptp) REVERT: C 305 ASP cc_start: 0.7638 (t0) cc_final: 0.7340 (t0) REVERT: C 377 LYS cc_start: 0.8927 (mtmm) cc_final: 0.8632 (mmtm) REVERT: C 424 GLN cc_start: 0.8129 (mp10) cc_final: 0.7283 (mp10) REVERT: C 575 TRP cc_start: 0.8928 (p-90) cc_final: 0.8487 (p-90) REVERT: C 613 GLU cc_start: 0.6765 (pp20) cc_final: 0.6383 (pp20) REVERT: C 630 GLN cc_start: 0.8261 (mp10) cc_final: 0.7975 (mt0) REVERT: C 633 PHE cc_start: 0.8397 (m-10) cc_final: 0.8160 (m-80) REVERT: C 663 THR cc_start: 0.9065 (m) cc_final: 0.8801 (p) REVERT: C 684 ASN cc_start: 0.8493 (t0) cc_final: 0.8201 (t0) REVERT: C 685 SER cc_start: 0.8864 (t) cc_final: 0.8634 (p) REVERT: C 939 SER cc_start: 0.8671 (t) cc_final: 0.8408 (p) REVERT: C 1064 ARG cc_start: 0.8122 (mmm-85) cc_final: 0.7758 (mtp180) REVERT: C 1112 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7442 (mt-10) REVERT: C 1126 ASN cc_start: 0.8664 (p0) cc_final: 0.8272 (p0) REVERT: C 1216 PRO cc_start: 0.8883 (Cg_endo) cc_final: 0.7350 (Cg_exo) REVERT: B 90 TYR cc_start: 0.7973 (m-10) cc_final: 0.7769 (m-10) REVERT: B 104 SER cc_start: 0.8772 (m) cc_final: 0.8309 (p) REVERT: B 120 GLU cc_start: 0.7598 (mp0) cc_final: 0.7271 (mp0) REVERT: B 245 ILE cc_start: 0.6987 (OUTLIER) cc_final: 0.6660 (mm) REVERT: B 387 THR cc_start: 0.7713 (OUTLIER) cc_final: 0.7079 (p) REVERT: B 398 ARG cc_start: 0.7802 (tmt-80) cc_final: 0.7038 (tmt-80) REVERT: B 542 ILE cc_start: 0.8875 (mm) cc_final: 0.8621 (mt) REVERT: B 595 ASN cc_start: 0.8311 (m110) cc_final: 0.7950 (m-40) REVERT: B 623 ASP cc_start: 0.8122 (t0) cc_final: 0.7883 (t70) REVERT: B 745 ASP cc_start: 0.7959 (t70) cc_final: 0.7644 (t70) REVERT: B 777 ASP cc_start: 0.7932 (m-30) cc_final: 0.7709 (p0) REVERT: B 800 GLU cc_start: 0.7552 (pm20) cc_final: 0.7284 (pm20) REVERT: B 885 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8339 (ttpp) REVERT: B 910 LYS cc_start: 0.8659 (mttm) cc_final: 0.8312 (mtpp) REVERT: B 912 LYS cc_start: 0.8247 (ptpt) cc_final: 0.7905 (ptpt) REVERT: B 1028 LYS cc_start: 0.8135 (mtpp) cc_final: 0.7769 (mtpp) outliers start: 105 outliers final: 66 residues processed: 685 average time/residue: 0.4567 time to fit residues: 518.8578 Evaluate side-chains 644 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 575 time to evaluate : 4.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 298 VAL Chi-restraints excluded: chain T residue 478 MET Chi-restraints excluded: chain H residue 405 ILE Chi-restraints excluded: chain H residue 412 SER Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 730 SER 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 800 GLU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 997 LEU Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain G residue 387 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 395 optimal weight: 1.9990 chunk 1 optimal weight: 40.0000 chunk 116 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 323 optimal weight: 7.9990 chunk 347 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 chunk 197 optimal weight: 0.0570 chunk 22 optimal weight: 20.0000 chunk 419 optimal weight: 20.0000 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 ASN A 826 HIS A 863 GLN A1041 ASN ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 826 HIS C 863 GLN C 876 HIS ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN B 278 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.186957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134521 restraints weight = 55401.103| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.29 r_work: 0.3371 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 34324 Z= 0.187 Angle : 0.577 15.565 46953 Z= 0.296 Chirality : 0.046 0.410 5388 Planarity : 0.004 0.054 5964 Dihedral : 4.650 55.930 5392 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.04 % Allowed : 11.90 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 4256 helix: 1.35 (0.20), residues: 763 sheet: 0.20 (0.17), residues: 891 loop : -1.83 (0.11), residues: 2602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 575 HIS 0.007 0.001 HIS C1145 PHE 0.020 0.002 PHE C 764 TYR 0.023 0.002 TYR A 649 ARG 0.008 0.000 ARG C 502 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 23) link_NAG-ASN : angle 3.04430 ( 69) link_BETA1-4 : bond 0.00367 ( 15) link_BETA1-4 : angle 1.33813 ( 45) hydrogen bonds : bond 0.05082 ( 1001) hydrogen bonds : angle 5.04027 ( 2823) SS BOND : bond 0.00337 ( 74) SS BOND : angle 2.11281 ( 148) covalent geometry : bond 0.00439 (34212) covalent geometry : angle 0.55243 (46691) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 594 time to evaluate : 3.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 349 MET cc_start: 0.0345 (tpt) cc_final: -0.0253 (tpt) REVERT: T 424 MET cc_start: 0.5768 (tpt) cc_final: 0.5397 (tpt) REVERT: A 110 LYS cc_start: 0.8555 (mttt) cc_final: 0.8154 (mttt) REVERT: A 147 GLU cc_start: 0.7065 (tp30) cc_final: 0.6455 (tp30) REVERT: A 161 THR cc_start: 0.8737 (t) cc_final: 0.8309 (p) REVERT: A 349 PHE cc_start: 0.6827 (m-80) cc_final: 0.6574 (m-80) REVERT: A 646 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.7522 (t0) REVERT: A 659 LYS cc_start: 0.8369 (ttpp) cc_final: 0.8055 (tttm) REVERT: A 669 ILE cc_start: 0.8590 (mt) cc_final: 0.8252 (tp) REVERT: A 687 SER cc_start: 0.8733 (m) cc_final: 0.8441 (p) REVERT: A 746 TYR cc_start: 0.8516 (t80) cc_final: 0.8263 (t80) REVERT: A 780 GLU cc_start: 0.8047 (tp30) cc_final: 0.7765 (tp30) REVERT: A 845 GLU cc_start: 0.7553 (tt0) cc_final: 0.7256 (tt0) REVERT: A 912 LYS cc_start: 0.8315 (ptpp) cc_final: 0.8082 (ptpp) REVERT: A 1028 LYS cc_start: 0.8108 (mtpp) cc_final: 0.7840 (mtpp) REVERT: A 1031 SER cc_start: 0.8169 (t) cc_final: 0.7842 (p) REVERT: A 1064 ARG cc_start: 0.8313 (mtp-110) cc_final: 0.8094 (mtp85) REVERT: A 1069 GLU cc_start: 0.7575 (pm20) cc_final: 0.7222 (pm20) REVERT: A 1149 LYS cc_start: 0.8420 (tttp) cc_final: 0.8123 (ttpp) REVERT: A 1185 MET cc_start: 0.8757 (mtp) cc_final: 0.8487 (mtt) REVERT: A 1198 SER cc_start: 0.8648 (t) cc_final: 0.8440 (p) REVERT: A 1218 ILE cc_start: 0.8599 (mt) cc_final: 0.8396 (mm) REVERT: C 66 TYR cc_start: 0.8646 (m-80) cc_final: 0.8097 (m-80) REVERT: C 94 PHE cc_start: 0.5488 (m-10) cc_final: 0.5011 (m-10) REVERT: C 155 MET cc_start: 0.5172 (mmm) cc_final: 0.4832 (mmm) REVERT: C 157 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7580 (tm-30) REVERT: C 160 HIS cc_start: 0.7054 (p90) cc_final: 0.6496 (p90) REVERT: C 189 PHE cc_start: 0.8134 (m-80) cc_final: 0.7871 (m-80) REVERT: C 238 MET cc_start: 0.6565 (ptp) cc_final: 0.5889 (ptp) REVERT: C 305 ASP cc_start: 0.7542 (t0) cc_final: 0.7152 (t0) REVERT: C 377 LYS cc_start: 0.8916 (mtmm) cc_final: 0.8604 (mmtm) REVERT: C 415 LYS cc_start: 0.7837 (tppt) cc_final: 0.7616 (tptm) REVERT: C 423 CYS cc_start: 0.7004 (m) cc_final: 0.6779 (m) REVERT: C 424 GLN cc_start: 0.8173 (mp10) cc_final: 0.7430 (mp10) REVERT: C 575 TRP cc_start: 0.8944 (p-90) cc_final: 0.8487 (p-90) REVERT: C 612 THR cc_start: 0.5713 (p) cc_final: 0.4915 (t) REVERT: C 613 GLU cc_start: 0.6866 (pp20) cc_final: 0.6522 (pp20) REVERT: C 633 PHE cc_start: 0.8509 (m-10) cc_final: 0.8294 (m-10) REVERT: C 663 THR cc_start: 0.9056 (m) cc_final: 0.8801 (p) REVERT: C 676 ARG cc_start: 0.8461 (mtm180) cc_final: 0.7899 (mtm180) REVERT: C 684 ASN cc_start: 0.8534 (t0) cc_final: 0.8252 (t0) REVERT: C 768 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7816 (mm-30) REVERT: C 939 SER cc_start: 0.8654 (t) cc_final: 0.8401 (p) REVERT: C 1064 ARG cc_start: 0.8101 (mmm-85) cc_final: 0.7735 (mtp180) REVERT: C 1112 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7426 (mt-10) REVERT: C 1126 ASN cc_start: 0.8665 (p0) cc_final: 0.8233 (p0) REVERT: C 1216 PRO cc_start: 0.8991 (Cg_endo) cc_final: 0.8717 (Cg_exo) REVERT: B 90 TYR cc_start: 0.8097 (m-10) cc_final: 0.7865 (m-10) REVERT: B 104 SER cc_start: 0.8763 (m) cc_final: 0.8333 (p) REVERT: B 245 ILE cc_start: 0.7040 (OUTLIER) cc_final: 0.6705 (mm) REVERT: B 283 SER cc_start: 0.9025 (m) cc_final: 0.8652 (p) REVERT: B 320 ARG cc_start: 0.8391 (ttm170) cc_final: 0.8162 (ttm110) REVERT: B 398 ARG cc_start: 0.7841 (tmt-80) cc_final: 0.7051 (tmt-80) REVERT: B 415 LYS cc_start: 0.8528 (ttmt) cc_final: 0.8123 (ttmt) REVERT: B 595 ASN cc_start: 0.8282 (m110) cc_final: 0.7971 (m110) REVERT: B 623 ASP cc_start: 0.8121 (t0) cc_final: 0.7882 (t70) REVERT: B 777 ASP cc_start: 0.7920 (m-30) cc_final: 0.7712 (p0) REVERT: B 800 GLU cc_start: 0.7584 (pm20) cc_final: 0.7327 (pm20) REVERT: B 910 LYS cc_start: 0.8665 (mttm) cc_final: 0.8312 (mtmm) REVERT: B 912 LYS cc_start: 0.8285 (ptpt) cc_final: 0.7932 (ptpt) REVERT: B 1112 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8291 (mt-10) outliers start: 111 outliers final: 72 residues processed: 661 average time/residue: 0.4401 time to fit residues: 478.0867 Evaluate side-chains 653 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 579 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 298 VAL Chi-restraints excluded: chain T residue 478 MET Chi-restraints excluded: chain H residue 405 ILE Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 997 LEU Chi-restraints excluded: chain C residue 1060 GLU Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1173 LYS Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain G residue 387 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 409 optimal weight: 50.0000 chunk 246 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 419 optimal weight: 50.0000 chunk 339 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 380 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 ASN A 863 GLN A1071 GLN C 273 HIS C 323 ASN ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN C 804 GLN C 876 HIS ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1086 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN B 278 ASN B 343 ASN B 445 ASN B 702 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.182998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130569 restraints weight = 54834.085| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 3.20 r_work: 0.3323 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 34324 Z= 0.344 Angle : 0.692 16.139 46953 Z= 0.358 Chirality : 0.050 0.388 5388 Planarity : 0.005 0.059 5964 Dihedral : 5.153 57.247 5392 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.25 % Favored : 93.73 % Rotamer: Outliers : 3.68 % Allowed : 12.31 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.12), residues: 4256 helix: 1.18 (0.20), residues: 765 sheet: 0.10 (0.17), residues: 895 loop : -1.98 (0.11), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 575 HIS 0.011 0.002 HIS C1145 PHE 0.035 0.003 PHE A 222 TYR 0.027 0.002 TYR B 236 ARG 0.007 0.001 ARG B1168 Details of bonding type rmsd link_NAG-ASN : bond 0.00740 ( 23) link_NAG-ASN : angle 3.34173 ( 69) link_BETA1-4 : bond 0.00467 ( 15) link_BETA1-4 : angle 1.40906 ( 45) hydrogen bonds : bond 0.06530 ( 1001) hydrogen bonds : angle 5.20881 ( 2823) SS BOND : bond 0.00453 ( 74) SS BOND : angle 2.68212 ( 148) covalent geometry : bond 0.00806 (34212) covalent geometry : angle 0.66399 (46691) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 598 time to evaluate : 3.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 424 MET cc_start: 0.5763 (tpt) cc_final: 0.5303 (tpt) REVERT: H 410 CYS cc_start: 0.6586 (t) cc_final: 0.6273 (t) REVERT: A 147 GLU cc_start: 0.7041 (tp30) cc_final: 0.6593 (tp30) REVERT: A 161 THR cc_start: 0.8773 (t) cc_final: 0.8381 (p) REVERT: A 646 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7703 (t0) REVERT: A 659 LYS cc_start: 0.8315 (ttpp) cc_final: 0.7833 (ttpp) REVERT: A 669 ILE cc_start: 0.8581 (mt) cc_final: 0.8167 (tp) REVERT: A 687 SER cc_start: 0.8767 (m) cc_final: 0.8499 (p) REVERT: A 746 TYR cc_start: 0.8493 (t80) cc_final: 0.8273 (t80) REVERT: A 780 GLU cc_start: 0.8092 (tp30) cc_final: 0.7847 (tp30) REVERT: A 827 ASP cc_start: 0.7899 (m-30) cc_final: 0.7652 (m-30) REVERT: A 845 GLU cc_start: 0.7690 (tt0) cc_final: 0.7422 (tt0) REVERT: A 912 LYS cc_start: 0.8307 (ptpp) cc_final: 0.8067 (ptpp) REVERT: A 1064 ARG cc_start: 0.8340 (mtp-110) cc_final: 0.8107 (mtp85) REVERT: A 1149 LYS cc_start: 0.8437 (tttp) cc_final: 0.8137 (ttpp) REVERT: C 66 TYR cc_start: 0.8695 (m-80) cc_final: 0.8214 (m-80) REVERT: C 155 MET cc_start: 0.5179 (mmm) cc_final: 0.4817 (mmm) REVERT: C 157 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: C 160 HIS cc_start: 0.7328 (OUTLIER) cc_final: 0.6715 (p90) REVERT: C 213 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.8096 (p90) REVERT: C 238 MET cc_start: 0.6679 (ptp) cc_final: 0.6021 (ptp) REVERT: C 421 SER cc_start: 0.7616 (p) cc_final: 0.7381 (t) REVERT: C 424 GLN cc_start: 0.8221 (mp10) cc_final: 0.7536 (mp10) REVERT: C 575 TRP cc_start: 0.9014 (p-90) cc_final: 0.8467 (p-90) REVERT: C 595 ASN cc_start: 0.7477 (m110) cc_final: 0.7203 (m110) REVERT: C 612 THR cc_start: 0.5763 (p) cc_final: 0.4482 (t) REVERT: C 613 GLU cc_start: 0.7007 (pp20) cc_final: 0.6715 (pp20) REVERT: C 663 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8867 (p) REVERT: C 676 ARG cc_start: 0.8526 (mtm180) cc_final: 0.8155 (mtm180) REVERT: C 684 ASN cc_start: 0.8539 (t0) cc_final: 0.8240 (t0) REVERT: C 768 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7809 (mm-30) REVERT: C 994 MET cc_start: 0.8239 (mmt) cc_final: 0.7759 (mmt) REVERT: C 1064 ARG cc_start: 0.8163 (mmm-85) cc_final: 0.7831 (mtp180) REVERT: C 1112 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7549 (mt-10) REVERT: C 1126 ASN cc_start: 0.8661 (p0) cc_final: 0.8247 (p0) REVERT: B 90 TYR cc_start: 0.8381 (m-10) cc_final: 0.8167 (m-10) REVERT: B 104 SER cc_start: 0.8761 (m) cc_final: 0.8431 (t) REVERT: B 157 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7489 (tm-30) REVERT: B 245 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6765 (mm) REVERT: B 283 SER cc_start: 0.9060 (m) cc_final: 0.8534 (t) REVERT: B 398 ARG cc_start: 0.7882 (tmt-80) cc_final: 0.7198 (tmt-80) REVERT: B 415 LYS cc_start: 0.8588 (ttmt) cc_final: 0.8144 (ttmt) REVERT: B 595 ASN cc_start: 0.8330 (m110) cc_final: 0.8035 (m110) REVERT: B 623 ASP cc_start: 0.8097 (t0) cc_final: 0.7843 (t70) REVERT: B 745 ASP cc_start: 0.7994 (t0) cc_final: 0.7746 (t0) REVERT: B 800 GLU cc_start: 0.7716 (pm20) cc_final: 0.7444 (pm20) REVERT: B 841 SER cc_start: 0.8485 (m) cc_final: 0.7893 (p) REVERT: B 910 LYS cc_start: 0.8710 (mttm) cc_final: 0.8294 (mtpp) REVERT: B 912 LYS cc_start: 0.8354 (ptpt) cc_final: 0.8032 (ptpt) REVERT: B 1112 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8360 (mt-10) outliers start: 134 outliers final: 97 residues processed: 676 average time/residue: 0.4501 time to fit residues: 501.1235 Evaluate side-chains 682 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 579 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 298 VAL Chi-restraints excluded: chain T residue 405 ILE Chi-restraints excluded: chain T residue 478 MET Chi-restraints excluded: chain H residue 405 ILE Chi-restraints excluded: chain H residue 412 SER Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 575 TRP Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 730 SER 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 800 GLU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 997 LEU Chi-restraints excluded: chain C residue 1086 ASN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1099 ILE Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1173 LYS Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 814 CYS Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 488 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 80 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 285 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 133 optimal weight: 0.2980 chunk 291 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 77 optimal weight: 0.0670 chunk 314 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 863 GLN A1071 GLN A1122 ASN ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN C 630 GLN C 876 HIS ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1086 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN B 343 ASN B 702 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.185561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.133747 restraints weight = 54847.963| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.44 r_work: 0.3380 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34324 Z= 0.117 Angle : 0.565 15.001 46953 Z= 0.289 Chirality : 0.045 0.358 5388 Planarity : 0.004 0.050 5964 Dihedral : 4.630 58.409 5392 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.85 % Allowed : 13.69 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.13), residues: 4256 helix: 1.50 (0.20), residues: 770 sheet: 0.28 (0.17), residues: 876 loop : -1.83 (0.11), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 575 HIS 0.006 0.001 HIS A 201 PHE 0.027 0.001 PHE A 661 TYR 0.021 0.001 TYR C 191 ARG 0.007 0.000 ARG B1168 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 23) link_NAG-ASN : angle 2.91252 ( 69) link_BETA1-4 : bond 0.00407 ( 15) link_BETA1-4 : angle 1.13417 ( 45) hydrogen bonds : bond 0.04613 ( 1001) hydrogen bonds : angle 4.89058 ( 2823) SS BOND : bond 0.00291 ( 74) SS BOND : angle 2.02974 ( 148) covalent geometry : bond 0.00270 (34212) covalent geometry : angle 0.54192 (46691) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 593 time to evaluate : 3.541 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: T 424 MET cc_start: 0.5817 (tpt) cc_final: 0.5329 (tpt) REVERT: A 110 LYS cc_start: 0.8534 (mttt) cc_final: 0.8132 (mttm) REVERT: A 147 GLU cc_start: 0.6973 (tp30) cc_final: 0.6422 (tp30) REVERT: A 646 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.7594 (t0) REVERT: A 659 LYS cc_start: 0.8337 (ttpp) cc_final: 0.7918 (ttpp) REVERT: A 669 ILE cc_start: 0.8525 (mt) cc_final: 0.8188 (tp) REVERT: A 687 SER cc_start: 0.8737 (m) cc_final: 0.8447 (p) REVERT: A 780 GLU cc_start: 0.7995 (tp30) cc_final: 0.7738 (tp30) REVERT: A 845 GLU cc_start: 0.7561 (tt0) cc_final: 0.7264 (tt0) REVERT: A 884 PHE cc_start: 0.8021 (m-10) cc_final: 0.7581 (m-10) REVERT: A 912 LYS cc_start: 0.8308 (ptpp) cc_final: 0.8082 (ptpp) REVERT: A 936 CYS cc_start: 0.7408 (m) cc_final: 0.7050 (m) REVERT: A 1064 ARG cc_start: 0.8282 (mtp-110) cc_final: 0.8062 (mtp85) REVERT: A 1069 GLU cc_start: 0.7560 (pm20) cc_final: 0.7255 (pm20) REVERT: A 1149 LYS cc_start: 0.8403 (tttp) cc_final: 0.8107 (ttpp) REVERT: C 66 TYR cc_start: 0.8628 (m-80) cc_final: 0.8400 (m-80) REVERT: C 155 MET cc_start: 0.5237 (mmm) cc_final: 0.4877 (mmm) REVERT: C 213 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.8036 (p90) REVERT: C 238 MET cc_start: 0.6639 (ptp) cc_final: 0.6182 (ptp) REVERT: C 288 SER cc_start: 0.8603 (m) cc_final: 0.8353 (p) REVERT: C 305 ASP cc_start: 0.7529 (t0) cc_final: 0.6949 (t0) REVERT: C 421 SER cc_start: 0.7423 (p) cc_final: 0.7189 (t) REVERT: C 424 GLN cc_start: 0.8179 (mp10) cc_final: 0.7471 (mp10) REVERT: C 575 TRP cc_start: 0.8924 (p-90) cc_final: 0.8348 (p-90) REVERT: C 595 ASN cc_start: 0.7365 (m110) cc_final: 0.7090 (m110) REVERT: C 612 THR cc_start: 0.5685 (p) cc_final: 0.4529 (t) REVERT: C 613 GLU cc_start: 0.7031 (pp20) cc_final: 0.6760 (pp20) REVERT: C 663 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8835 (p) REVERT: C 676 ARG cc_start: 0.8325 (mtm180) cc_final: 0.7843 (mtm180) REVERT: C 684 ASN cc_start: 0.8553 (t0) cc_final: 0.8241 (t0) REVERT: C 768 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7792 (mm-30) REVERT: C 939 SER cc_start: 0.8592 (t) cc_final: 0.8376 (p) REVERT: C 994 MET cc_start: 0.8072 (mmt) cc_final: 0.7563 (mmt) REVERT: C 1064 ARG cc_start: 0.8026 (mmm-85) cc_final: 0.7684 (mtp180) REVERT: C 1112 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7460 (mt-10) REVERT: C 1126 ASN cc_start: 0.8599 (p0) cc_final: 0.8148 (p0) REVERT: B 104 SER cc_start: 0.8704 (m) cc_final: 0.8355 (t) REVERT: B 245 ILE cc_start: 0.6979 (OUTLIER) cc_final: 0.6681 (mm) REVERT: B 283 SER cc_start: 0.9022 (m) cc_final: 0.8660 (p) REVERT: B 398 ARG cc_start: 0.7797 (tmt-80) cc_final: 0.7075 (tmt-80) REVERT: B 415 LYS cc_start: 0.8512 (ttmt) cc_final: 0.8067 (ttmt) REVERT: B 595 ASN cc_start: 0.8273 (m110) cc_final: 0.7968 (m110) REVERT: B 623 ASP cc_start: 0.8030 (t0) cc_final: 0.7829 (t70) REVERT: B 745 ASP cc_start: 0.8010 (t0) cc_final: 0.7717 (t0) REVERT: B 779 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8375 (p) REVERT: B 780 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7097 (mm-30) REVERT: B 800 GLU cc_start: 0.7585 (pm20) cc_final: 0.7321 (pm20) REVERT: B 841 SER cc_start: 0.8394 (m) cc_final: 0.7763 (p) REVERT: B 891 LEU cc_start: 0.7890 (tp) cc_final: 0.7615 (tt) REVERT: B 910 LYS cc_start: 0.8667 (mttm) cc_final: 0.8311 (mtmm) REVERT: B 912 LYS cc_start: 0.8282 (ptpt) cc_final: 0.7984 (ptpt) REVERT: B 913 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8456 (mp) outliers start: 104 outliers final: 71 residues processed: 653 average time/residue: 0.4856 time to fit residues: 520.1497 Evaluate side-chains 654 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 577 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 298 VAL Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 405 ILE Chi-restraints excluded: chain H residue 412 SER Chi-restraints excluded: chain H residue 478 MET Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 575 TRP Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 717 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 820 SER Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 997 LEU Chi-restraints excluded: chain C residue 1060 GLU Chi-restraints excluded: chain C residue 1086 ASN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1173 LYS Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 488 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 153 optimal weight: 2.9990 chunk 417 optimal weight: 50.0000 chunk 364 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 chunk 404 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 274 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 863 GLN A1071 GLN ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN B 343 ASN B 702 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.182338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.130925 restraints weight = 54982.721| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.99 r_work: 0.3361 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 34324 Z= 0.302 Angle : 0.656 14.745 46953 Z= 0.338 Chirality : 0.049 0.393 5388 Planarity : 0.005 0.054 5964 Dihedral : 4.924 59.535 5390 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.10 % Allowed : 13.58 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.13), residues: 4256 helix: 1.32 (0.20), residues: 770 sheet: 0.16 (0.17), residues: 859 loop : -1.91 (0.11), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 575 HIS 0.010 0.002 HIS C1145 PHE 0.033 0.002 PHE B 309 TYR 0.032 0.002 TYR B 236 ARG 0.010 0.001 ARG B 986 Details of bonding type rmsd link_NAG-ASN : bond 0.00626 ( 23) link_NAG-ASN : angle 3.36707 ( 69) link_BETA1-4 : bond 0.00394 ( 15) link_BETA1-4 : angle 1.32205 ( 45) hydrogen bonds : bond 0.06107 ( 1001) hydrogen bonds : angle 5.03583 ( 2823) SS BOND : bond 0.00478 ( 74) SS BOND : angle 2.30536 ( 148) covalent geometry : bond 0.00711 (34212) covalent geometry : angle 0.63005 (46691) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 596 time to evaluate : 5.059 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: T 424 MET cc_start: 0.5840 (tpt) cc_final: 0.5313 (tpt) REVERT: H 488 MET cc_start: -0.3484 (tmm) cc_final: -0.4447 (tpp) REVERT: A 110 LYS cc_start: 0.8539 (mttt) cc_final: 0.8176 (mttm) REVERT: A 147 GLU cc_start: 0.6964 (tp30) cc_final: 0.6568 (tp30) REVERT: A 166 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7825 (mttm) REVERT: A 424 GLN cc_start: 0.7551 (mp10) cc_final: 0.7204 (mp10) REVERT: A 669 ILE cc_start: 0.8504 (mt) cc_final: 0.8136 (tp) REVERT: A 687 SER cc_start: 0.8767 (m) cc_final: 0.8495 (p) REVERT: A 780 GLU cc_start: 0.8014 (tp30) cc_final: 0.7777 (tp30) REVERT: A 845 GLU cc_start: 0.7667 (tt0) cc_final: 0.7389 (tt0) REVERT: A 912 LYS cc_start: 0.8257 (ptpp) cc_final: 0.8024 (ptpp) REVERT: A 936 CYS cc_start: 0.7483 (m) cc_final: 0.7209 (m) REVERT: A 1064 ARG cc_start: 0.8287 (mtp-110) cc_final: 0.8028 (mtp85) REVERT: A 1069 GLU cc_start: 0.7577 (pm20) cc_final: 0.7317 (pm20) REVERT: A 1149 LYS cc_start: 0.8436 (tttp) cc_final: 0.8146 (ttpp) REVERT: A 1185 MET cc_start: 0.8711 (mtp) cc_final: 0.8464 (mtt) REVERT: C 66 TYR cc_start: 0.8674 (m-80) cc_final: 0.8157 (m-80) REVERT: C 155 MET cc_start: 0.5248 (mmm) cc_final: 0.4883 (mmm) REVERT: C 157 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: C 238 MET cc_start: 0.6676 (ptp) cc_final: 0.6063 (ptp) REVERT: C 421 SER cc_start: 0.7657 (p) cc_final: 0.7402 (t) REVERT: C 423 CYS cc_start: 0.6802 (m) cc_final: 0.6444 (m) REVERT: C 424 GLN cc_start: 0.8200 (mp10) cc_final: 0.7333 (mp10) REVERT: C 595 ASN cc_start: 0.7478 (m110) cc_final: 0.7149 (m110) REVERT: C 613 GLU cc_start: 0.6997 (pp20) cc_final: 0.6707 (pp20) REVERT: C 676 ARG cc_start: 0.8380 (mtm180) cc_final: 0.7952 (mtm180) REVERT: C 684 ASN cc_start: 0.8509 (t0) cc_final: 0.8166 (t0) REVERT: C 768 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7750 (mm-30) REVERT: C 994 MET cc_start: 0.8174 (mmt) cc_final: 0.7709 (mmt) REVERT: C 1064 ARG cc_start: 0.8078 (mmm-85) cc_final: 0.7745 (mtp180) REVERT: C 1112 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7490 (mt-10) REVERT: C 1126 ASN cc_start: 0.8597 (p0) cc_final: 0.8169 (p0) REVERT: B 104 SER cc_start: 0.8701 (m) cc_final: 0.8357 (t) REVERT: B 157 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7590 (tm-30) REVERT: B 245 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6823 (mm) REVERT: B 283 SER cc_start: 0.9056 (m) cc_final: 0.8693 (p) REVERT: B 289 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8069 (mt-10) REVERT: B 331 ASN cc_start: 0.8607 (t0) cc_final: 0.8260 (t0) REVERT: B 398 ARG cc_start: 0.7790 (tmt-80) cc_final: 0.7140 (tmt-80) REVERT: B 415 LYS cc_start: 0.8584 (ttmt) cc_final: 0.8170 (ttmt) REVERT: B 595 ASN cc_start: 0.8316 (m110) cc_final: 0.8013 (m110) REVERT: B 623 ASP cc_start: 0.8015 (t0) cc_final: 0.7792 (t70) REVERT: B 745 ASP cc_start: 0.7946 (t0) cc_final: 0.7591 (t0) REVERT: B 780 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7272 (mm-30) REVERT: B 800 GLU cc_start: 0.7652 (pm20) cc_final: 0.7382 (pm20) REVERT: B 841 SER cc_start: 0.8523 (m) cc_final: 0.7906 (p) REVERT: B 891 LEU cc_start: 0.7993 (tp) cc_final: 0.7786 (tt) REVERT: B 910 LYS cc_start: 0.8672 (mttm) cc_final: 0.8268 (mtpp) REVERT: B 912 LYS cc_start: 0.8284 (ptpt) cc_final: 0.7980 (ptpt) REVERT: B 1069 GLU cc_start: 0.7823 (pm20) cc_final: 0.7415 (pm20) outliers start: 113 outliers final: 83 residues processed: 658 average time/residue: 0.4630 time to fit residues: 502.4920 Evaluate side-chains 674 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 589 time to evaluate : 3.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 298 VAL Chi-restraints excluded: chain T residue 478 MET Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 405 ILE Chi-restraints excluded: chain H residue 412 SER Chi-restraints excluded: chain H residue 478 MET Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 575 TRP Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 704 ILE 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 810 VAL Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1152 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 997 LEU Chi-restraints excluded: chain C residue 1060 GLU Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1099 ILE Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1173 LYS Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 488 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 212 optimal weight: 6.9990 chunk 304 optimal weight: 0.6980 chunk 266 optimal weight: 0.0770 chunk 345 optimal weight: 0.9980 chunk 371 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 254 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 300 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 863 GLN A1071 GLN C 108 ASN ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 ASN C 630 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN B 343 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.185792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135263 restraints weight = 54865.137| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.18 r_work: 0.3397 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34324 Z= 0.114 Angle : 0.562 15.648 46953 Z= 0.289 Chirality : 0.045 0.550 5388 Planarity : 0.004 0.053 5964 Dihedral : 4.506 57.882 5390 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.39 % Allowed : 14.84 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 4256 helix: 1.49 (0.20), residues: 787 sheet: 0.30 (0.17), residues: 854 loop : -1.77 (0.11), residues: 2615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 575 HIS 0.006 0.001 HIS A 201 PHE 0.027 0.001 PHE A 661 TYR 0.025 0.001 TYR A 699 ARG 0.006 0.000 ARG B1168 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 23) link_NAG-ASN : angle 3.08657 ( 69) link_BETA1-4 : bond 0.00442 ( 15) link_BETA1-4 : angle 1.09217 ( 45) hydrogen bonds : bond 0.04346 ( 1001) hydrogen bonds : angle 4.74278 ( 2823) SS BOND : bond 0.00277 ( 74) SS BOND : angle 1.92790 ( 148) covalent geometry : bond 0.00266 (34212) covalent geometry : angle 0.53934 (46691) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 583 time to evaluate : 3.476 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: T 424 MET cc_start: 0.5807 (tpt) cc_final: 0.5228 (tpt) REVERT: H 410 CYS cc_start: 0.6423 (t) cc_final: 0.6138 (t) REVERT: A 18 PHE cc_start: 0.7550 (t80) cc_final: 0.7291 (t80) REVERT: A 110 LYS cc_start: 0.8516 (mttt) cc_final: 0.8174 (mttm) REVERT: A 147 GLU cc_start: 0.6917 (tp30) cc_final: 0.6470 (tp30) REVERT: A 646 ASN cc_start: 0.8269 (m-40) cc_final: 0.7611 (t0) REVERT: A 659 LYS cc_start: 0.8378 (ttpp) cc_final: 0.7849 (tttm) REVERT: A 669 ILE cc_start: 0.8492 (mt) cc_final: 0.8126 (tp) REVERT: A 687 SER cc_start: 0.8749 (m) cc_final: 0.8455 (p) REVERT: A 780 GLU cc_start: 0.8011 (tp30) cc_final: 0.7738 (tp30) REVERT: A 845 GLU cc_start: 0.7454 (tt0) cc_final: 0.7156 (tt0) REVERT: A 862 MET cc_start: 0.8304 (mmm) cc_final: 0.8055 (mmm) REVERT: A 884 PHE cc_start: 0.7996 (m-10) cc_final: 0.7574 (m-10) REVERT: A 912 LYS cc_start: 0.8214 (ptpp) cc_final: 0.7986 (ptpp) REVERT: A 936 CYS cc_start: 0.7320 (m) cc_final: 0.6985 (m) REVERT: A 1069 GLU cc_start: 0.7542 (pm20) cc_final: 0.7214 (pm20) REVERT: A 1149 LYS cc_start: 0.8381 (tttp) cc_final: 0.8090 (ttpp) REVERT: A 1168 ARG cc_start: 0.8088 (mtm-85) cc_final: 0.7835 (mtm-85) REVERT: C 66 TYR cc_start: 0.8597 (m-80) cc_final: 0.8080 (m-80) REVERT: C 155 MET cc_start: 0.5217 (mmm) cc_final: 0.4854 (mmm) REVERT: C 157 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: C 218 MET cc_start: 0.8005 (ptp) cc_final: 0.7772 (ptp) REVERT: C 238 MET cc_start: 0.6637 (ptp) cc_final: 0.6161 (ptp) REVERT: C 288 SER cc_start: 0.8631 (m) cc_final: 0.8341 (p) REVERT: C 385 SER cc_start: 0.8688 (p) cc_final: 0.8357 (t) REVERT: C 421 SER cc_start: 0.7539 (p) cc_final: 0.7249 (t) REVERT: C 424 GLN cc_start: 0.8110 (mp10) cc_final: 0.7422 (mp10) REVERT: C 502 ARG cc_start: 0.6093 (tpm170) cc_final: 0.5787 (tpm170) REVERT: C 575 TRP cc_start: 0.8871 (p-90) cc_final: 0.8327 (p-90) REVERT: C 595 ASN cc_start: 0.7413 (m110) cc_final: 0.7167 (m110) REVERT: C 612 THR cc_start: 0.5727 (p) cc_final: 0.4487 (t) REVERT: C 613 GLU cc_start: 0.6997 (pp20) cc_final: 0.6772 (pp20) REVERT: C 684 ASN cc_start: 0.8544 (t0) cc_final: 0.8206 (t0) REVERT: C 768 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7697 (mm-30) REVERT: C 939 SER cc_start: 0.8553 (t) cc_final: 0.8342 (p) REVERT: C 994 MET cc_start: 0.8017 (mmt) cc_final: 0.7581 (mmt) REVERT: C 1000 ASN cc_start: 0.8244 (m110) cc_final: 0.7899 (p0) REVERT: C 1064 ARG cc_start: 0.7935 (mmm-85) cc_final: 0.7606 (mtp180) REVERT: C 1112 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7437 (mt-10) REVERT: C 1126 ASN cc_start: 0.8579 (p0) cc_final: 0.8168 (p0) REVERT: B 104 SER cc_start: 0.8657 (m) cc_final: 0.8324 (t) REVERT: B 157 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7433 (tm-30) REVERT: B 245 ILE cc_start: 0.6981 (OUTLIER) cc_final: 0.6714 (mm) REVERT: B 283 SER cc_start: 0.9014 (m) cc_final: 0.8658 (p) REVERT: B 398 ARG cc_start: 0.7758 (tmt-80) cc_final: 0.7056 (tmt-80) REVERT: B 415 LYS cc_start: 0.8527 (ttmt) cc_final: 0.8084 (ttmt) REVERT: B 595 ASN cc_start: 0.8270 (m110) cc_final: 0.7957 (m110) REVERT: B 714 ASP cc_start: 0.8128 (m-30) cc_final: 0.7865 (m-30) REVERT: B 745 ASP cc_start: 0.7968 (t0) cc_final: 0.7665 (t0) REVERT: B 800 GLU cc_start: 0.7598 (pm20) cc_final: 0.7345 (pm20) REVERT: B 910 LYS cc_start: 0.8607 (mttm) cc_final: 0.8305 (mtmm) REVERT: B 912 LYS cc_start: 0.8217 (ptpt) cc_final: 0.7931 (ptpt) outliers start: 87 outliers final: 66 residues processed: 631 average time/residue: 0.4533 time to fit residues: 469.5469 Evaluate side-chains 641 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 573 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 298 VAL Chi-restraints excluded: chain T residue 478 MET Chi-restraints excluded: chain H residue 405 ILE Chi-restraints excluded: chain H residue 412 SER Chi-restraints excluded: chain H residue 452 ILE Chi-restraints excluded: chain H residue 478 MET Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 575 TRP Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 997 LEU Chi-restraints excluded: chain C residue 1060 GLU Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1173 LYS Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 488 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 423 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 9 optimal weight: 30.0000 chunk 415 optimal weight: 3.9990 chunk 424 optimal weight: 50.0000 chunk 78 optimal weight: 9.9990 chunk 31 optimal weight: 40.0000 chunk 245 optimal weight: 2.9990 chunk 375 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 ASN A 863 GLN A 876 HIS A1071 GLN C 108 ASN ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1086 ASN B 278 ASN B 343 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.182696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130467 restraints weight = 55115.647| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.11 r_work: 0.3345 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 34324 Z= 0.284 Angle : 0.657 15.116 46953 Z= 0.338 Chirality : 0.049 0.429 5388 Planarity : 0.005 0.054 5964 Dihedral : 4.786 56.785 5387 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.61 % Allowed : 14.78 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.13), residues: 4256 helix: 1.48 (0.20), residues: 761 sheet: 0.24 (0.17), residues: 843 loop : -1.86 (0.11), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 575 HIS 0.010 0.001 HIS C1145 PHE 0.032 0.002 PHE A 661 TYR 0.034 0.002 TYR B 236 ARG 0.008 0.001 ARG A1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 23) link_NAG-ASN : angle 3.31134 ( 69) link_BETA1-4 : bond 0.00400 ( 15) link_BETA1-4 : angle 1.30850 ( 45) hydrogen bonds : bond 0.05950 ( 1001) hydrogen bonds : angle 4.94928 ( 2823) SS BOND : bond 0.00397 ( 74) SS BOND : angle 2.41823 ( 148) covalent geometry : bond 0.00674 (34212) covalent geometry : angle 0.63027 (46691) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 597 time to evaluate : 3.345 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: T 424 MET cc_start: 0.5804 (tpt) cc_final: 0.5224 (tpt) REVERT: H 410 CYS cc_start: 0.6868 (t) cc_final: 0.6591 (t) REVERT: H 488 MET cc_start: -0.3667 (tmm) cc_final: -0.4604 (tpp) REVERT: A 147 GLU cc_start: 0.7007 (tp30) cc_final: 0.6605 (tp30) REVERT: A 646 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.7635 (t0) REVERT: A 669 ILE cc_start: 0.8520 (mt) cc_final: 0.8116 (tp) REVERT: A 687 SER cc_start: 0.8783 (m) cc_final: 0.8508 (p) REVERT: A 780 GLU cc_start: 0.8042 (tp30) cc_final: 0.7791 (tp30) REVERT: A 845 GLU cc_start: 0.7712 (tt0) cc_final: 0.7426 (tt0) REVERT: A 912 LYS cc_start: 0.8233 (ptpp) cc_final: 0.7987 (ptpp) REVERT: A 936 CYS cc_start: 0.7610 (m) cc_final: 0.7336 (m) REVERT: A 1112 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7953 (mt-10) REVERT: A 1149 LYS cc_start: 0.8438 (tttp) cc_final: 0.8145 (ttpp) REVERT: A 1168 ARG cc_start: 0.8159 (mtm-85) cc_final: 0.7894 (mtm-85) REVERT: A 1185 MET cc_start: 0.8708 (mtp) cc_final: 0.8457 (mtt) REVERT: C 66 TYR cc_start: 0.8682 (m-80) cc_final: 0.8165 (m-80) REVERT: C 155 MET cc_start: 0.5345 (mmm) cc_final: 0.4975 (mmm) REVERT: C 157 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: C 238 MET cc_start: 0.6723 (ptp) cc_final: 0.6068 (ptp) REVERT: C 331 ASN cc_start: 0.8509 (m110) cc_final: 0.8164 (m110) REVERT: C 372 ASN cc_start: 0.8193 (t0) cc_final: 0.7961 (t0) REVERT: C 421 SER cc_start: 0.7750 (p) cc_final: 0.7420 (t) REVERT: C 423 CYS cc_start: 0.6963 (m) cc_final: 0.6587 (m) REVERT: C 424 GLN cc_start: 0.8173 (mp10) cc_final: 0.7315 (mp10) REVERT: C 502 ARG cc_start: 0.6363 (tpm170) cc_final: 0.6066 (tpm170) REVERT: C 595 ASN cc_start: 0.7548 (m110) cc_final: 0.7141 (m110) REVERT: C 613 GLU cc_start: 0.7087 (pp20) cc_final: 0.6821 (pp20) REVERT: C 684 ASN cc_start: 0.8534 (t0) cc_final: 0.8166 (t0) REVERT: C 768 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7720 (mm-30) REVERT: C 994 MET cc_start: 0.8124 (mmt) cc_final: 0.7666 (mmt) REVERT: C 1064 ARG cc_start: 0.8068 (mmm-85) cc_final: 0.7745 (mtp180) REVERT: C 1086 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7859 (m110) REVERT: C 1112 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7520 (mt-10) REVERT: C 1126 ASN cc_start: 0.8612 (p0) cc_final: 0.8179 (p0) REVERT: B 25 ILE cc_start: 0.8341 (mm) cc_final: 0.8124 (tt) REVERT: B 104 SER cc_start: 0.8693 (m) cc_final: 0.8357 (t) REVERT: B 157 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7528 (tm-30) REVERT: B 236 TYR cc_start: 0.8544 (t80) cc_final: 0.8324 (t80) REVERT: B 245 ILE cc_start: 0.7159 (OUTLIER) cc_final: 0.6951 (mm) REVERT: B 263 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8035 (ptm160) REVERT: B 283 SER cc_start: 0.9053 (m) cc_final: 0.8683 (p) REVERT: B 331 ASN cc_start: 0.8622 (t0) cc_final: 0.8405 (t0) REVERT: B 398 ARG cc_start: 0.7772 (tmt-80) cc_final: 0.7103 (tmt-80) REVERT: B 415 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8156 (ttmt) REVERT: B 590 SER cc_start: 0.7651 (t) cc_final: 0.7094 (m) REVERT: B 595 ASN cc_start: 0.8335 (m110) cc_final: 0.8031 (m110) REVERT: B 635 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7721 (tm-30) REVERT: B 745 ASP cc_start: 0.8001 (t0) cc_final: 0.7605 (t0) REVERT: B 800 GLU cc_start: 0.7694 (pm20) cc_final: 0.7422 (pm20) REVERT: B 841 SER cc_start: 0.8469 (m) cc_final: 0.7952 (p) REVERT: B 910 LYS cc_start: 0.8685 (mttm) cc_final: 0.8274 (mtpp) REVERT: B 912 LYS cc_start: 0.8312 (ptpt) cc_final: 0.8031 (ptpt) REVERT: B 913 LEU cc_start: 0.8852 (mm) cc_final: 0.8537 (mt) REVERT: B 1060 GLU cc_start: 0.8180 (tt0) cc_final: 0.7971 (tp30) outliers start: 95 outliers final: 76 residues processed: 647 average time/residue: 0.4372 time to fit residues: 469.4642 Evaluate side-chains 665 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 584 time to evaluate : 3.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 298 VAL Chi-restraints excluded: chain H residue 405 ILE Chi-restraints excluded: chain H residue 412 SER Chi-restraints excluded: chain H residue 452 ILE Chi-restraints excluded: chain H residue 478 MET Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 575 TRP Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 730 SER 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 810 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 719 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 997 LEU Chi-restraints excluded: chain C residue 1060 GLU Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1086 ASN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1173 LYS Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 488 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 27 optimal weight: 30.0000 chunk 390 optimal weight: 0.5980 chunk 195 optimal weight: 0.3980 chunk 83 optimal weight: 9.9990 chunk 106 optimal weight: 0.1980 chunk 347 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 92 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 863 GLN A 876 HIS A1071 GLN C 108 ASN ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 GLN C 876 HIS ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1086 ASN B 278 ASN B 343 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.185343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133524 restraints weight = 54839.398| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.23 r_work: 0.3381 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 34324 Z= 0.116 Angle : 0.575 15.261 46953 Z= 0.294 Chirality : 0.045 0.346 5388 Planarity : 0.004 0.058 5964 Dihedral : 4.450 55.355 5387 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.95 % Allowed : 15.69 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.13), residues: 4256 helix: 1.55 (0.20), residues: 775 sheet: 0.32 (0.17), residues: 848 loop : -1.74 (0.11), residues: 2633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 575 HIS 0.007 0.001 HIS A 201 PHE 0.032 0.001 PHE A 661 TYR 0.030 0.001 TYR B 236 ARG 0.009 0.000 ARG A1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 23) link_NAG-ASN : angle 3.02524 ( 69) link_BETA1-4 : bond 0.00429 ( 15) link_BETA1-4 : angle 1.12116 ( 45) hydrogen bonds : bond 0.04428 ( 1001) hydrogen bonds : angle 4.73446 ( 2823) SS BOND : bond 0.00275 ( 74) SS BOND : angle 1.86198 ( 148) covalent geometry : bond 0.00267 (34212) covalent geometry : angle 0.55433 (46691) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8512 Ramachandran restraints generated. 4256 Oldfield, 0 Emsley, 4256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 586 time to evaluate : 3.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 424 MET cc_start: 0.5747 (tpt) cc_final: 0.5174 (tpt) REVERT: H 377 GLN cc_start: 0.7593 (tp-100) cc_final: 0.7163 (tp-100) REVERT: H 488 MET cc_start: -0.3560 (tmm) cc_final: -0.4529 (tpp) REVERT: A 110 LYS cc_start: 0.8552 (mttt) cc_final: 0.8217 (mttm) REVERT: A 147 GLU cc_start: 0.6965 (tp30) cc_final: 0.6567 (tp30) REVERT: A 166 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7855 (mptt) REVERT: A 646 ASN cc_start: 0.8155 (m-40) cc_final: 0.7465 (t0) REVERT: A 669 ILE cc_start: 0.8494 (mt) cc_final: 0.8140 (tp) REVERT: A 687 SER cc_start: 0.8771 (m) cc_final: 0.8466 (p) REVERT: A 780 GLU cc_start: 0.8033 (tp30) cc_final: 0.7768 (tp30) REVERT: A 845 GLU cc_start: 0.7519 (tt0) cc_final: 0.7241 (tt0) REVERT: A 912 LYS cc_start: 0.8243 (ptpp) cc_final: 0.8011 (ptpp) REVERT: A 936 CYS cc_start: 0.7452 (m) cc_final: 0.7133 (m) REVERT: A 1069 GLU cc_start: 0.7503 (pm20) cc_final: 0.7107 (pm20) REVERT: A 1112 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7939 (mt-10) REVERT: A 1149 LYS cc_start: 0.8401 (tttp) cc_final: 0.8109 (ttpp) REVERT: A 1168 ARG cc_start: 0.8135 (mtm-85) cc_final: 0.7887 (mtm-85) REVERT: C 66 TYR cc_start: 0.8613 (m-80) cc_final: 0.8086 (m-80) REVERT: C 155 MET cc_start: 0.5335 (mmm) cc_final: 0.5040 (mmm) REVERT: C 157 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: C 238 MET cc_start: 0.6612 (ptp) cc_final: 0.5968 (ptp) REVERT: C 288 SER cc_start: 0.8628 (m) cc_final: 0.8340 (p) REVERT: C 372 ASN cc_start: 0.8150 (t0) cc_final: 0.7854 (t0) REVERT: C 385 SER cc_start: 0.8700 (p) cc_final: 0.8293 (t) REVERT: C 421 SER cc_start: 0.7585 (p) cc_final: 0.7230 (t) REVERT: C 424 GLN cc_start: 0.8097 (mp10) cc_final: 0.7446 (mp10) REVERT: C 502 ARG cc_start: 0.6178 (tpm170) cc_final: 0.5895 (tpm170) REVERT: C 595 ASN cc_start: 0.7469 (m110) cc_final: 0.7188 (m110) REVERT: C 613 GLU cc_start: 0.7078 (pp20) cc_final: 0.6860 (pp20) REVERT: C 684 ASN cc_start: 0.8565 (t0) cc_final: 0.8228 (t0) REVERT: C 768 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7711 (mm-30) REVERT: C 939 SER cc_start: 0.8569 (t) cc_final: 0.8355 (p) REVERT: C 1064 ARG cc_start: 0.7905 (mmm-85) cc_final: 0.7595 (mtp180) REVERT: C 1112 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7448 (mt-10) REVERT: C 1126 ASN cc_start: 0.8574 (p0) cc_final: 0.8168 (p0) REVERT: B 25 ILE cc_start: 0.8304 (mm) cc_final: 0.7646 (tt) REVERT: B 104 SER cc_start: 0.8648 (m) cc_final: 0.8334 (t) REVERT: B 157 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7471 (tm-30) REVERT: B 236 TYR cc_start: 0.8520 (t80) cc_final: 0.8290 (t80) REVERT: B 245 ILE cc_start: 0.7067 (OUTLIER) cc_final: 0.6840 (mm) REVERT: B 283 SER cc_start: 0.9024 (m) cc_final: 0.8656 (p) REVERT: B 331 ASN cc_start: 0.8531 (t0) cc_final: 0.8311 (t0) REVERT: B 398 ARG cc_start: 0.7733 (tmt-80) cc_final: 0.6939 (tmt-80) REVERT: B 415 LYS cc_start: 0.8546 (ttmt) cc_final: 0.8100 (ttmt) REVERT: B 595 ASN cc_start: 0.8272 (m110) cc_final: 0.7948 (m110) REVERT: B 635 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7668 (tm-30) REVERT: B 745 ASP cc_start: 0.7979 (t0) cc_final: 0.7586 (t0) REVERT: B 800 GLU cc_start: 0.7642 (pm20) cc_final: 0.7389 (pm20) REVERT: B 910 LYS cc_start: 0.8642 (mttm) cc_final: 0.8246 (mtpp) REVERT: B 912 LYS cc_start: 0.8287 (ptpt) cc_final: 0.7983 (ptpt) outliers start: 71 outliers final: 59 residues processed: 631 average time/residue: 0.4583 time to fit residues: 473.2087 Evaluate side-chains 641 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 580 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 298 VAL Chi-restraints excluded: chain H residue 405 ILE Chi-restraints excluded: chain H residue 452 ILE Chi-restraints excluded: chain H residue 478 MET Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 575 TRP Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 997 LEU Chi-restraints excluded: chain C residue 1060 GLU Chi-restraints excluded: chain C residue 1086 ASN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1173 LYS Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain G residue 387 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 281 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 chunk 177 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 258 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 334 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 374 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 392 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 ASN A 863 GLN A 876 HIS A1071 GLN C 108 ASN ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1086 ASN B 278 ASN B 343 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.183454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.131634 restraints weight = 54795.301| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.21 r_work: 0.3339 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 34324 Z= 0.229 Angle : 0.623 14.796 46953 Z= 0.320 Chirality : 0.047 0.331 5388 Planarity : 0.005 0.058 5964 Dihedral : 4.590 53.902 5386 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.09 % Favored : 93.89 % Rotamer: Outliers : 2.30 % Allowed : 15.44 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.13), residues: 4256 helix: 1.50 (0.20), residues: 776 sheet: 0.29 (0.17), residues: 831 loop : -1.80 (0.11), residues: 2649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 575 HIS 0.008 0.001 HIS C1145 PHE 0.031 0.002 PHE A 661 TYR 0.032 0.002 TYR A 682 ARG 0.009 0.001 ARG B1168 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 23) link_NAG-ASN : angle 3.13809 ( 69) link_BETA1-4 : bond 0.00379 ( 15) link_BETA1-4 : angle 1.23821 ( 45) hydrogen bonds : bond 0.05422 ( 1001) hydrogen bonds : angle 4.81561 ( 2823) SS BOND : bond 0.00378 ( 74) SS BOND : angle 2.20549 ( 148) covalent geometry : bond 0.00542 (34212) covalent geometry : angle 0.59866 (46691) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22387.27 seconds wall clock time: 391 minutes 53.47 seconds (23513.47 seconds total)