Starting phenix.real_space_refine on Fri Mar 6 09:02:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jvc_22506/03_2026/7jvc_22506.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jvc_22506/03_2026/7jvc_22506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jvc_22506/03_2026/7jvc_22506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jvc_22506/03_2026/7jvc_22506.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jvc_22506/03_2026/7jvc_22506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jvc_22506/03_2026/7jvc_22506.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.062 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 129 5.16 5 C 18591 2.51 5 N 5092 2.21 5 O 5750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 130 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29562 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7354 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 48, 'TRANS': 941} Chain breaks: 10 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ASN:plan1': 12, 'GLN:plan1': 8, 'GLU:plan': 11, 'TYR:plan': 10, 'ASP:plan': 11, 'ARG:plan': 5, 'PHE:plan': 6} Unresolved non-hydrogen planarities: 276 Chain: "H" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1105 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 596 Unresolved non-hydrogen angles: 775 Unresolved non-hydrogen dihedrals: 513 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 8, 'ARG:plan': 7, 'PHE:plan': 8, 'TYR:plan': 9, 'TRP:plan': 7, 'ASN:plan1': 9, 'ASP:plan': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 327 Chain: "L" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1094 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Unresolved non-hydrogen bonds: 534 Unresolved non-hydrogen angles: 692 Unresolved non-hydrogen dihedrals: 445 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'ASN:plan1': 8, 'PHE:plan': 5, 'GLN:plan1': 10, 'HIS:plan': 4, 'GLU:plan': 10, 'TYR:plan': 10, 'TRP:plan': 3, 'ARG:plan': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 295 Chain: "B" Number of atoms: 7353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7353 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 48, 'TRANS': 941} Chain breaks: 10 Unresolved non-hydrogen bonds: 405 Unresolved non-hydrogen angles: 518 Unresolved non-hydrogen dihedrals: 334 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ASN:plan1': 12, 'GLN:plan1': 8, 'GLU:plan': 11, 'TYR:plan': 10, 'ASP:plan': 11, 'ARG:plan': 5, 'PHE:plan': 6} Unresolved non-hydrogen planarities: 276 Chain: "C" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1105 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 596 Unresolved non-hydrogen angles: 775 Unresolved non-hydrogen dihedrals: 513 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 8, 'ARG:plan': 7, 'PHE:plan': 8, 'TYR:plan': 9, 'TRP:plan': 7, 'ASN:plan1': 9, 'ASP:plan': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 327 Chain: "D" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1088 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 541 Unresolved non-hydrogen angles: 701 Unresolved non-hydrogen dihedrals: 451 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'ASN:plan1': 8, 'PHE:plan': 5, 'GLN:plan1': 11, 'HIS:plan': 4, 'GLU:plan': 10, 'TYR:plan': 10, 'TRP:plan': 3, 'ARG:plan': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 299 Chain: "E" Number of atoms: 7353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7353 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 48, 'TRANS': 941} Chain breaks: 10 Unresolved non-hydrogen bonds: 405 Unresolved non-hydrogen angles: 518 Unresolved non-hydrogen dihedrals: 334 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ASN:plan1': 12, 'GLN:plan1': 8, 'GLU:plan': 11, 'TYR:plan': 10, 'ASP:plan': 11, 'ARG:plan': 5, 'PHE:plan': 6} Unresolved non-hydrogen planarities: 276 Chain: "F" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1105 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 596 Unresolved non-hydrogen angles: 775 Unresolved non-hydrogen dihedrals: 513 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 8, 'ARG:plan': 7, 'PHE:plan': 8, 'TYR:plan': 9, 'TRP:plan': 7, 'ASN:plan1': 9, 'ASP:plan': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 327 Chain: "G" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1090 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Unresolved non-hydrogen bonds: 538 Unresolved non-hydrogen angles: 697 Unresolved non-hydrogen dihedrals: 448 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'ASN:plan1': 8, 'PHE:plan': 5, 'GLN:plan1': 11, 'HIS:plan': 4, 'GLU:plan': 10, 'TYR:plan': 10, 'TRP:plan': 3, 'ARG:plan': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 299 Chain: "I" 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: "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: "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: 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: "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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.42, per 1000 atoms: 0.22 Number of scatterers: 29562 At special positions: 0 Unit cell: (150.15, 157.5, 193.2, 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 129 16.00 O 5750 8.00 N 5092 7.00 C 18591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.04 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.02 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.05 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.01 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 146 " - pdb=" SG CYS F 202 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 91 " distance=2.03 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 198 " 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 122 " " NAG E1303 " - " ASN E 234 " " NAG E1304 " - " ASN E 282 " " NAG E1305 " - " ASN E 331 " " NAG E1306 " - " ASN E 603 " " NAG E1307 " - " ASN E 616 " " NAG E1308 " - " ASN E 657 " " NAG E1309 " - " ASN E 709 " " NAG E1310 " - " ASN E1074 " " NAG E1311 " - " ASN E 165 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A 343 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B 343 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN E 717 " " NAG U 1 " - " ASN E 801 " " NAG V 1 " - " ASN E 343 " " NAG W 1 " - " ASN E1098 " " NAG X 1 " - " ASN E1134 " Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 84 sheets defined 20.9% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.529A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.721A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.757A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.816A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.733A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 947 through 965 removed outlier: 5.316A pdb=" N ASN A 953 " --> pdb=" O GLN A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.648A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 133 through 138 Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 207 through 210 Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.572A pdb=" N ASN L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.783A pdb=" N GLU L 86 " --> pdb=" O THR L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 131 Processing helix chain 'L' and resid 186 through 191 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.529A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.721A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.758A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.817A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.733A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 947 through 965 removed outlier: 5.316A pdb=" N ASN B 953 " --> pdb=" O GLN B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.647A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 207 through 210 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.572A pdb=" N ASN D 32 " --> pdb=" O ILE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 71 No H-bonds generated for 'chain 'D' and resid 69 through 71' Processing helix chain 'D' and resid 82 through 86 removed outlier: 3.783A pdb=" N GLU D 86 " --> pdb=" O THR D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 131 Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.529A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 388 removed outlier: 3.721A pdb=" N ASN E 388 " --> pdb=" O PRO E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.757A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 removed outlier: 3.816A pdb=" N LEU E 752 " --> pdb=" O GLU E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.734A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 824 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 891 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 913 through 919 Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 947 through 965 removed outlier: 5.317A pdb=" N ASN E 953 " --> pdb=" O GLN E 949 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 983 removed outlier: 3.648A pdb=" N ARG E 983 " --> pdb=" O ASP E 979 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 133 through 138 Processing helix chain 'F' and resid 162 through 164 No H-bonds generated for 'chain 'F' and resid 162 through 164' Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 207 through 210 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.572A pdb=" N ASN G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 71 No H-bonds generated for 'chain 'G' and resid 69 through 71' Processing helix chain 'G' and resid 82 through 86 removed outlier: 3.783A pdb=" N GLU G 86 " --> pdb=" O THR G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 131 Processing helix chain 'G' and resid 186 through 191 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.172A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.543A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.614A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.466A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.343A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.470A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.195A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.526A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.533A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.570A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.570A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.095A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.061A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.328A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.944A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.781A pdb=" N CYS H 96 " --> pdb=" O TRP H 109 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TRP H 109 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG H 98 " --> pdb=" O ASP H 107 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 126 through 130 removed outlier: 4.947A pdb=" N ALA H 143 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL H 190 " --> pdb=" O ALA H 143 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 126 through 130 removed outlier: 4.947A pdb=" N ALA H 143 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL H 190 " --> pdb=" O ALA H 143 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 157 through 160 Processing sheet with id=AC7, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AC8, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.755A pdb=" N VAL L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLN L 38 " --> pdb=" O THR L 47 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.755A pdb=" N VAL L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.633A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.633A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 158 through 159 removed outlier: 3.581A pdb=" N SER L 205 " --> pdb=" O HIS L 202 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.171A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.614A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.465A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.344A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.470A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.194A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE B 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.527A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.533A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AE7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.570A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.570A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.094A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.328A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.944A pdb=" N MET C 34 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.781A pdb=" N CYS C 96 " --> pdb=" O TRP C 109 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TRP C 109 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG C 98 " --> pdb=" O ASP C 107 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 126 through 130 removed outlier: 4.947A pdb=" N ALA C 143 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL C 190 " --> pdb=" O ALA C 143 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLY C 145 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL C 188 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU C 147 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER C 186 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS C 149 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU C 184 " --> pdb=" O LYS C 149 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 126 through 130 removed outlier: 4.947A pdb=" N ALA C 143 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL C 190 " --> pdb=" O ALA C 143 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLY C 145 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL C 188 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU C 147 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER C 186 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS C 149 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU C 184 " --> pdb=" O LYS C 149 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 157 through 160 Processing sheet with id=AF8, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AF9, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.755A pdb=" N VAL D 10 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLN D 38 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR D 47 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.755A pdb=" N VAL D 10 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 119 through 123 removed outlier: 5.633A pdb=" N TYR D 177 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 119 through 123 removed outlier: 5.633A pdb=" N TYR D 177 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 158 through 159 removed outlier: 3.581A pdb=" N SER D 205 " --> pdb=" O HIS D 202 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 28 through 30 removed outlier: 8.172A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU E 224 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N HIS E 207 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N ALA E 222 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 47 through 55 removed outlier: 7.614A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.465A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.344A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.470A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AH2, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.526A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AH4, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AH5, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.534A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.570A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR E 724 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU E1063 " --> pdb=" O THR E 724 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE E 726 " --> pdb=" O VAL E1061 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL E1061 " --> pdb=" O ILE E 726 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY E1059 " --> pdb=" O PRO E 728 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.570A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR E 724 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU E1063 " --> pdb=" O THR E 724 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE E 726 " --> pdb=" O VAL E1061 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL E1061 " --> pdb=" O ILE E 726 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY E1059 " --> pdb=" O PRO E 728 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.094A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.328A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AI2, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.944A pdb=" N MET F 34 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.781A pdb=" N CYS F 96 " --> pdb=" O TRP F 109 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TRP F 109 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG F 98 " --> pdb=" O ASP F 107 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'F' and resid 126 through 130 removed outlier: 4.947A pdb=" N ALA F 143 " --> pdb=" O VAL F 190 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL F 190 " --> pdb=" O ALA F 143 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLY F 145 " --> pdb=" O VAL F 188 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL F 188 " --> pdb=" O GLY F 145 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU F 147 " --> pdb=" O SER F 186 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER F 186 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS F 149 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU F 184 " --> pdb=" O LYS F 149 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 126 through 130 removed outlier: 4.947A pdb=" N ALA F 143 " --> pdb=" O VAL F 190 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL F 190 " --> pdb=" O ALA F 143 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLY F 145 " --> pdb=" O VAL F 188 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL F 188 " --> pdb=" O GLY F 145 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU F 147 " --> pdb=" O SER F 186 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER F 186 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS F 149 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU F 184 " --> pdb=" O LYS F 149 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 157 through 160 Processing sheet with id=AI7, first strand: chain 'G' and resid 3 through 5 Processing sheet with id=AI8, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.755A pdb=" N VAL G 10 " --> pdb=" O THR G 109 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLN G 38 " --> pdb=" O THR G 47 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.755A pdb=" N VAL G 10 " --> pdb=" O THR G 109 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'G' and resid 119 through 123 removed outlier: 5.633A pdb=" N TYR G 177 " --> pdb=" O ASP G 143 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'G' and resid 119 through 123 removed outlier: 5.633A pdb=" N TYR G 177 " --> pdb=" O ASP G 143 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'G' and resid 158 through 159 removed outlier: 3.581A pdb=" N SER G 205 " --> pdb=" O HIS G 202 " (cutoff:3.500A) 1530 hydrogen bonds defined for protein. 3987 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: 8.16 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6015 1.32 - 1.45: 8475 1.45 - 1.58: 15440 1.58 - 1.72: 15 1.72 - 1.85: 153 Bond restraints: 30098 Sorted by residual: bond pdb=" CD GLN B 607 " pdb=" NE2 GLN B 607 " ideal model delta sigma weight residual 1.328 1.201 0.127 2.10e-02 2.27e+03 3.66e+01 bond pdb=" CD GLN A 607 " pdb=" NE2 GLN A 607 " ideal model delta sigma weight residual 1.328 1.201 0.127 2.10e-02 2.27e+03 3.66e+01 bond pdb=" CD GLN E 607 " pdb=" NE2 GLN E 607 " ideal model delta sigma weight residual 1.328 1.201 0.127 2.10e-02 2.27e+03 3.64e+01 bond pdb=" C5 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.413 1.484 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C5 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.413 1.484 -0.071 2.00e-02 2.50e+03 1.25e+01 ... (remaining 30093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 33202 1.60 - 3.20: 6508 3.20 - 4.80: 1081 4.80 - 6.41: 426 6.41 - 8.01: 61 Bond angle restraints: 41278 Sorted by residual: angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 125.14 -5.48 7.20e-01 1.93e+00 5.78e+01 angle pdb=" C LEU E 861 " pdb=" N PRO E 862 " pdb=" CA PRO E 862 " ideal model delta sigma weight residual 119.66 125.11 -5.45 7.20e-01 1.93e+00 5.73e+01 angle pdb=" C LEU B 861 " pdb=" N PRO B 862 " pdb=" CA PRO B 862 " ideal model delta sigma weight residual 119.66 125.11 -5.45 7.20e-01 1.93e+00 5.72e+01 angle pdb=" C PRO B 862 " pdb=" N PRO B 863 " pdb=" CA PRO B 863 " ideal model delta sigma weight residual 120.03 127.49 -7.46 9.90e-01 1.02e+00 5.67e+01 angle pdb=" C ASP A1139 " pdb=" N PRO A1140 " pdb=" CA PRO A1140 " ideal model delta sigma weight residual 119.56 127.23 -7.67 1.02e+00 9.61e-01 5.65e+01 ... (remaining 41273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.30: 18242 21.30 - 42.60: 376 42.60 - 63.90: 91 63.90 - 85.20: 33 85.20 - 106.50: 18 Dihedral angle restraints: 18760 sinusoidal: 6460 harmonic: 12300 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 91 " pdb=" CB CYS D 91 " ideal model delta sinusoidal sigma weight residual 93.00 50.58 42.42 1 1.00e+01 1.00e-02 2.51e+01 dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 91 " pdb=" CB CYS G 91 " ideal model delta sinusoidal sigma weight residual 93.00 50.60 42.40 1 1.00e+01 1.00e-02 2.51e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 91 " pdb=" CB CYS L 91 " ideal model delta sinusoidal sigma weight residual 93.00 50.63 42.37 1 1.00e+01 1.00e-02 2.51e+01 ... (remaining 18757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3857 0.084 - 0.168: 966 0.168 - 0.252: 180 0.252 - 0.336: 91 0.336 - 0.420: 54 Chirality restraints: 5148 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.79e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.74e+01 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.60e+01 ... (remaining 5145 not shown) Planarity restraints: 5475 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " -0.045 2.00e-02 2.50e+03 4.66e-02 2.71e+01 pdb=" CG ASN B 709 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " 0.072 2.00e-02 2.50e+03 pdb=" C1 NAG B1309 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 709 " -0.045 2.00e-02 2.50e+03 4.65e-02 2.71e+01 pdb=" CG ASN E 709 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN E 709 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN E 709 " 0.072 2.00e-02 2.50e+03 pdb=" C1 NAG E1309 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " 0.045 2.00e-02 2.50e+03 4.65e-02 2.70e+01 pdb=" CG ASN A 709 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " -0.072 2.00e-02 2.50e+03 pdb=" C1 NAG A1309 " 0.057 2.00e-02 2.50e+03 ... (remaining 5472 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 12736 2.92 - 3.42: 25830 3.42 - 3.91: 46762 3.91 - 4.41: 51599 4.41 - 4.90: 86934 Nonbonded interactions: 223861 Sorted by model distance: nonbonded pdb=" NZ LYS E 811 " pdb=" OD2 ASP E 820 " model vdw 2.428 3.120 nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.428 3.120 nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 2.428 3.120 nonbonded pdb=" NZ LYS E1028 " pdb=" O PHE E1042 " model vdw 2.444 3.120 nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.444 3.120 ... (remaining 223856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 513 or (resid 514 and (name N or name CA or nam \ e C or name O or name CB )) or resid 515 through 1311)) selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = (chain 'G' and (resid 1 through 55 or (resid 56 through 57 and (name N or name C \ A or name C or name O or name CB )) or resid 58 through 214)) selection = (chain 'L' and (resid 1 through 55 or (resid 56 through 57 and (name N or name C \ A or name C or name O or name CB )) or resid 58 through 91 or (resid 92 through \ 102 and (name N or name CA or name C or name O or name CB )) or resid 103 throug \ h 214)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Q' selection = chain 'V' } 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: 6.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.420 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.090 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 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 : 0.014 0.127 30215 Z= 0.744 Angle : 1.436 9.756 41578 Z= 0.964 Chirality : 0.091 0.420 5148 Planarity : 0.005 0.024 5427 Dihedral : 10.638 106.500 10639 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.29 % Favored : 97.57 % Rotamer: Outliers : 0.13 % Allowed : 0.38 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.12), residues: 4194 helix: -0.40 (0.17), residues: 753 sheet: 1.28 (0.14), residues: 1245 loop : 0.46 (0.12), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 273 TYR 0.025 0.004 TYR E 674 PHE 0.021 0.003 PHE B 347 TRP 0.017 0.005 TRP E1102 HIS 0.009 0.002 HIS E1083 Details of bonding type rmsd covalent geometry : bond 0.01318 (30098) covalent geometry : angle 1.41829 (41278) SS BOND : bond 0.00757 ( 51) SS BOND : angle 3.09303 ( 102) hydrogen bonds : bond 0.16748 ( 1407) hydrogen bonds : angle 8.30025 ( 3987) link_BETA1-4 : bond 0.06789 ( 18) link_BETA1-4 : angle 4.08518 ( 54) link_NAG-ASN : bond 0.06906 ( 48) link_NAG-ASN : angle 2.38572 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 453 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.6443 (p-90) cc_final: 0.5815 (p-90) REVERT: A 377 PHE cc_start: 0.7073 (t80) cc_final: 0.6872 (t80) REVERT: E 271 GLN cc_start: 0.7134 (mt0) cc_final: 0.6911 (tt0) REVERT: E 317 ASN cc_start: 0.7846 (m-40) cc_final: 0.7110 (m-40) REVERT: E 353 TRP cc_start: 0.6269 (p-90) cc_final: 0.5611 (p-90) outliers start: 3 outliers final: 0 residues processed: 454 average time/residue: 0.1803 time to fit residues: 132.1241 Evaluate side-chains 168 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.0060 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 30.0000 chunk 424 optimal weight: 50.0000 chunk 155 optimal weight: 0.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 321 GLN A 388 ASN A 607 GLN A 965 GLN B 207 HIS B 321 GLN B 607 GLN B 954 GLN E 207 HIS E 321 GLN E 388 ASN E 607 GLN E 703 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.170255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.113837 restraints weight = 51713.339| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.17 r_work: 0.3221 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 30215 Z= 0.145 Angle : 0.651 12.968 41578 Z= 0.328 Chirality : 0.047 0.428 5148 Planarity : 0.004 0.031 5427 Dihedral : 6.598 68.912 5793 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.57 % Favored : 98.35 % Rotamer: Outliers : 1.27 % Allowed : 7.95 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.13), residues: 4194 helix: 0.85 (0.19), residues: 741 sheet: 1.41 (0.14), residues: 1320 loop : 0.42 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 237 TYR 0.025 0.002 TYR E1138 PHE 0.017 0.002 PHE B 65 TRP 0.006 0.001 TRP E 104 HIS 0.003 0.001 HIS E 655 Details of bonding type rmsd covalent geometry : bond 0.00319 (30098) covalent geometry : angle 0.60948 (41278) SS BOND : bond 0.00624 ( 51) SS BOND : angle 2.06786 ( 102) hydrogen bonds : bond 0.04414 ( 1407) hydrogen bonds : angle 5.93275 ( 3987) link_BETA1-4 : bond 0.00794 ( 18) link_BETA1-4 : angle 3.07187 ( 54) link_NAG-ASN : bond 0.00694 ( 48) link_NAG-ASN : angle 3.08169 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8745 (p) cc_final: 0.8527 (t) REVERT: A 353 TRP cc_start: 0.5979 (p-90) cc_final: 0.5120 (p-90) REVERT: A 365 TYR cc_start: 0.7801 (m-80) cc_final: 0.7579 (m-80) REVERT: A 377 PHE cc_start: 0.7093 (t80) cc_final: 0.6848 (t80) REVERT: A 751 ASN cc_start: 0.8160 (m-40) cc_final: 0.7953 (m-40) REVERT: A 796 ASP cc_start: 0.8237 (t0) cc_final: 0.7934 (p0) REVERT: A 1019 ARG cc_start: 0.8706 (tpt170) cc_final: 0.8183 (ttp-170) REVERT: B 190 ARG cc_start: 0.7688 (mtt-85) cc_final: 0.7297 (mtt180) REVERT: B 231 ILE cc_start: 0.9071 (mm) cc_final: 0.8866 (mm) REVERT: B 725 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: B 1019 ARG cc_start: 0.8558 (tpt170) cc_final: 0.8097 (ttm-80) REVERT: E 271 GLN cc_start: 0.7798 (mt0) cc_final: 0.7082 (tt0) REVERT: E 353 TRP cc_start: 0.5705 (p-90) cc_final: 0.4840 (p-90) REVERT: E 377 PHE cc_start: 0.6926 (t80) cc_final: 0.4864 (p90) REVERT: E 796 ASP cc_start: 0.8261 (t0) cc_final: 0.8012 (p0) REVERT: E 1019 ARG cc_start: 0.8571 (tpt170) cc_final: 0.8071 (ttp80) outliers start: 30 outliers final: 15 residues processed: 242 average time/residue: 0.1581 time to fit residues: 65.0189 Evaluate side-chains 179 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 773 GLU Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 1130 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 118 optimal weight: 50.0000 chunk 270 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 307 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 405 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 251 optimal weight: 20.0000 chunk 170 optimal weight: 9.9990 chunk 138 optimal weight: 50.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 914 ASN A 926 GLN A 965 GLN A1048 HIS A1071 GLN B 388 ASN B 804 GLN B 914 ASN B1048 HIS B1071 GLN E 804 GLN E1048 HIS E1071 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.163649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.105843 restraints weight = 51954.530| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.26 r_work: 0.3072 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.120 30215 Z= 0.448 Angle : 0.817 14.650 41578 Z= 0.412 Chirality : 0.054 0.446 5148 Planarity : 0.005 0.057 5427 Dihedral : 6.166 41.639 5793 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.03 % Allowed : 9.60 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.13), residues: 4194 helix: 0.38 (0.19), residues: 738 sheet: 0.91 (0.13), residues: 1410 loop : -0.02 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 983 TYR 0.027 0.003 TYR B1067 PHE 0.033 0.003 PHE B1103 TRP 0.021 0.002 TRP B 886 HIS 0.013 0.004 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.01074 (30098) covalent geometry : angle 0.78641 (41278) SS BOND : bond 0.00735 ( 51) SS BOND : angle 2.23041 ( 102) hydrogen bonds : bond 0.04991 ( 1407) hydrogen bonds : angle 5.87274 ( 3987) link_BETA1-4 : bond 0.00672 ( 18) link_BETA1-4 : angle 2.75727 ( 54) link_NAG-ASN : bond 0.00932 ( 48) link_NAG-ASN : angle 3.00240 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 158 time to evaluate : 0.784 Fit side-chains REVERT: A 133 PHE cc_start: 0.6990 (m-80) cc_final: 0.5972 (t80) REVERT: A 316 SER cc_start: 0.8910 (p) cc_final: 0.8650 (t) REVERT: A 353 TRP cc_start: 0.6027 (p-90) cc_final: 0.5202 (p-90) REVERT: A 365 TYR cc_start: 0.7884 (m-80) cc_final: 0.7630 (m-80) REVERT: A 377 PHE cc_start: 0.7140 (t80) cc_final: 0.5647 (p90) REVERT: A 646 ARG cc_start: 0.8159 (ttm-80) cc_final: 0.7953 (ttt-90) REVERT: A 1004 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9263 (tt) REVERT: A 1019 ARG cc_start: 0.8906 (tpt170) cc_final: 0.8338 (ttp-170) REVERT: B 377 PHE cc_start: 0.7249 (t80) cc_final: 0.5860 (p90) REVERT: B 554 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: B 674 TYR cc_start: 0.9079 (t80) cc_final: 0.8869 (t80) REVERT: B 957 GLN cc_start: 0.8528 (tt0) cc_final: 0.8307 (tp-100) REVERT: B 1019 ARG cc_start: 0.8648 (tpt170) cc_final: 0.8173 (ttm-80) REVERT: E 271 GLN cc_start: 0.8118 (mt0) cc_final: 0.7468 (tt0) REVERT: E 377 PHE cc_start: 0.7054 (t80) cc_final: 0.5568 (p90) REVERT: E 1019 ARG cc_start: 0.8727 (tpt170) cc_final: 0.8166 (ttp80) outliers start: 48 outliers final: 32 residues processed: 202 average time/residue: 0.1585 time to fit residues: 54.7411 Evaluate side-chains 174 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 997 ILE Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 10 optimal weight: 1.9990 chunk 415 optimal weight: 50.0000 chunk 293 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 406 optimal weight: 50.0000 chunk 311 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 118 optimal weight: 50.0000 chunk 342 optimal weight: 0.7980 chunk 239 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 901 GLN E 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.166839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.107281 restraints weight = 51528.077| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.73 r_work: 0.3177 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30215 Z= 0.145 Angle : 0.586 16.250 41578 Z= 0.287 Chirality : 0.046 0.432 5148 Planarity : 0.004 0.038 5427 Dihedral : 5.146 35.105 5793 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.90 % Allowed : 10.82 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.13), residues: 4194 helix: 1.33 (0.20), residues: 708 sheet: 1.04 (0.14), residues: 1320 loop : 0.06 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 983 TYR 0.017 0.001 TYR E1067 PHE 0.021 0.001 PHE E 374 TRP 0.009 0.001 TRP E 436 HIS 0.004 0.001 HIS E1083 Details of bonding type rmsd covalent geometry : bond 0.00334 (30098) covalent geometry : angle 0.55190 (41278) SS BOND : bond 0.00365 ( 51) SS BOND : angle 1.54326 ( 102) hydrogen bonds : bond 0.03563 ( 1407) hydrogen bonds : angle 5.38596 ( 3987) link_BETA1-4 : bond 0.00699 ( 18) link_BETA1-4 : angle 2.45071 ( 54) link_NAG-ASN : bond 0.00438 ( 48) link_NAG-ASN : angle 2.80756 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 1.089 Fit side-chains REVERT: A 133 PHE cc_start: 0.6612 (m-80) cc_final: 0.5529 (t80) REVERT: A 135 PHE cc_start: 0.5347 (OUTLIER) cc_final: 0.4845 (m-80) REVERT: A 190 ARG cc_start: 0.7685 (mtt-85) cc_final: 0.7475 (mtt180) REVERT: A 287 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8515 (m-30) REVERT: A 365 TYR cc_start: 0.7778 (m-80) cc_final: 0.7557 (m-80) REVERT: A 646 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.8005 (ttt-90) REVERT: A 957 GLN cc_start: 0.8802 (tt0) cc_final: 0.8531 (tt0) REVERT: A 1004 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9165 (tt) REVERT: A 1019 ARG cc_start: 0.8964 (tpt170) cc_final: 0.8328 (ttp-170) REVERT: B 394 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7456 (t0) REVERT: B 619 GLU cc_start: 0.7286 (mp0) cc_final: 0.7044 (mp0) REVERT: B 1019 ARG cc_start: 0.8806 (tpt170) cc_final: 0.8199 (ttm-80) REVERT: E 271 GLN cc_start: 0.8184 (mt0) cc_final: 0.7546 (tt0) REVERT: E 619 GLU cc_start: 0.7224 (mp0) cc_final: 0.6991 (mp0) REVERT: E 900 MET cc_start: 0.8982 (mtp) cc_final: 0.8718 (mtp) REVERT: E 1019 ARG cc_start: 0.8754 (tpt170) cc_final: 0.8238 (ttp-170) outliers start: 45 outliers final: 18 residues processed: 200 average time/residue: 0.1636 time to fit residues: 55.4359 Evaluate side-chains 169 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1130 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 348 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 414 optimal weight: 0.8980 chunk 388 optimal weight: 50.0000 chunk 125 optimal weight: 8.9990 chunk 115 optimal weight: 50.0000 chunk 398 optimal weight: 0.0870 chunk 419 optimal weight: 30.0000 chunk 273 optimal weight: 50.0000 chunk 54 optimal weight: 0.9990 chunk 361 optimal weight: 1.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 914 ASN B 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.166228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.108441 restraints weight = 51869.465| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.43 r_work: 0.3112 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 30215 Z= 0.177 Angle : 0.588 16.233 41578 Z= 0.287 Chirality : 0.046 0.491 5148 Planarity : 0.004 0.040 5427 Dihedral : 4.927 40.014 5793 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.20 % Allowed : 10.53 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.13), residues: 4194 helix: 1.45 (0.20), residues: 708 sheet: 0.90 (0.14), residues: 1338 loop : 0.07 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.017 0.001 TYR B1138 PHE 0.017 0.002 PHE A 106 TRP 0.010 0.001 TRP E 436 HIS 0.003 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00418 (30098) covalent geometry : angle 0.55660 (41278) SS BOND : bond 0.00585 ( 51) SS BOND : angle 1.44122 ( 102) hydrogen bonds : bond 0.03528 ( 1407) hydrogen bonds : angle 5.25177 ( 3987) link_BETA1-4 : bond 0.00589 ( 18) link_BETA1-4 : angle 2.23776 ( 54) link_NAG-ASN : bond 0.00550 ( 48) link_NAG-ASN : angle 2.77219 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6819 (m-80) cc_final: 0.5670 (t80) REVERT: A 135 PHE cc_start: 0.5436 (OUTLIER) cc_final: 0.5076 (m-80) REVERT: A 287 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8355 (m-30) REVERT: A 365 TYR cc_start: 0.7802 (m-80) cc_final: 0.7569 (m-80) REVERT: A 957 GLN cc_start: 0.8708 (tt0) cc_final: 0.8436 (tt0) REVERT: A 1004 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9100 (tt) REVERT: A 1019 ARG cc_start: 0.8868 (tpt170) cc_final: 0.8306 (ttp-170) REVERT: B 135 PHE cc_start: 0.5067 (OUTLIER) cc_final: 0.4519 (m-80) REVERT: B 619 GLU cc_start: 0.7196 (mp0) cc_final: 0.6975 (mp0) REVERT: B 1019 ARG cc_start: 0.8586 (tpt170) cc_final: 0.8202 (ttm-80) REVERT: E 133 PHE cc_start: 0.7138 (m-80) cc_final: 0.5409 (t80) REVERT: E 135 PHE cc_start: 0.5356 (OUTLIER) cc_final: 0.4861 (m-80) REVERT: E 271 GLN cc_start: 0.8129 (mt0) cc_final: 0.7560 (tt0) REVERT: E 900 MET cc_start: 0.8877 (mtp) cc_final: 0.8629 (mtp) REVERT: E 1019 ARG cc_start: 0.8666 (tpt170) cc_final: 0.8222 (ttp-170) outliers start: 52 outliers final: 34 residues processed: 194 average time/residue: 0.1618 time to fit residues: 53.9087 Evaluate side-chains 184 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 166 CYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 338 PHE Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 758 SER Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 420 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 296 optimal weight: 2.9990 chunk 242 optimal weight: 0.0470 chunk 240 optimal weight: 0.7980 chunk 257 optimal weight: 50.0000 chunk 361 optimal weight: 0.5980 chunk 21 optimal weight: 0.0570 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 318 optimal weight: 0.7980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.167920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.109225 restraints weight = 51509.455| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.98 r_work: 0.3187 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 30215 Z= 0.101 Angle : 0.540 16.354 41578 Z= 0.259 Chirality : 0.045 0.528 5148 Planarity : 0.004 0.042 5427 Dihedral : 4.620 44.517 5793 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.73 % Allowed : 10.70 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.13), residues: 4194 helix: 1.79 (0.20), residues: 705 sheet: 1.04 (0.14), residues: 1341 loop : 0.03 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.013 0.001 TYR A 660 PHE 0.018 0.001 PHE A 106 TRP 0.007 0.001 TRP B 436 HIS 0.002 0.000 HIS E1083 Details of bonding type rmsd covalent geometry : bond 0.00228 (30098) covalent geometry : angle 0.50950 (41278) SS BOND : bond 0.00267 ( 51) SS BOND : angle 1.21315 ( 102) hydrogen bonds : bond 0.02982 ( 1407) hydrogen bonds : angle 5.01985 ( 3987) link_BETA1-4 : bond 0.00660 ( 18) link_BETA1-4 : angle 2.09509 ( 54) link_NAG-ASN : bond 0.00387 ( 48) link_NAG-ASN : angle 2.68350 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6692 (m-80) cc_final: 0.5999 (t80) REVERT: A 287 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8599 (m-30) REVERT: A 365 TYR cc_start: 0.7859 (m-80) cc_final: 0.7589 (m-80) REVERT: A 619 GLU cc_start: 0.7451 (mp0) cc_final: 0.7234 (mp0) REVERT: A 1004 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9068 (tt) REVERT: A 1019 ARG cc_start: 0.9006 (tpt170) cc_final: 0.8316 (ttp-170) REVERT: B 135 PHE cc_start: 0.5058 (OUTLIER) cc_final: 0.4467 (m-80) REVERT: B 190 ARG cc_start: 0.7769 (mtt-85) cc_final: 0.7563 (mtt180) REVERT: B 619 GLU cc_start: 0.7415 (mp0) cc_final: 0.7111 (mp0) REVERT: B 957 GLN cc_start: 0.8582 (tt0) cc_final: 0.8268 (tp-100) REVERT: B 1019 ARG cc_start: 0.8771 (tpt170) cc_final: 0.8222 (ttm-80) REVERT: E 131 CYS cc_start: 0.3538 (OUTLIER) cc_final: 0.3186 (m) REVERT: E 133 PHE cc_start: 0.6944 (m-80) cc_final: 0.5541 (t80) REVERT: E 135 PHE cc_start: 0.5630 (OUTLIER) cc_final: 0.5202 (m-80) REVERT: E 271 GLN cc_start: 0.8313 (mt0) cc_final: 0.7593 (tt0) REVERT: E 900 MET cc_start: 0.9009 (mtp) cc_final: 0.8737 (mtp) REVERT: E 1019 ARG cc_start: 0.8803 (tpt170) cc_final: 0.8218 (ttp-170) outliers start: 41 outliers final: 22 residues processed: 199 average time/residue: 0.1554 time to fit residues: 52.9931 Evaluate side-chains 179 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 658 ASN Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 878 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 371 optimal weight: 1.9990 chunk 324 optimal weight: 20.0000 chunk 313 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 390 optimal weight: 50.0000 chunk 170 optimal weight: 8.9990 chunk 425 optimal weight: 30.0000 chunk 305 optimal weight: 0.1980 chunk 216 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.166761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.107430 restraints weight = 51614.004| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.97 r_work: 0.3161 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 30215 Z= 0.155 Angle : 0.554 16.487 41578 Z= 0.268 Chirality : 0.046 0.528 5148 Planarity : 0.004 0.043 5427 Dihedral : 4.662 45.134 5793 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.73 % Allowed : 10.70 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.13), residues: 4194 helix: 1.63 (0.20), residues: 726 sheet: 1.03 (0.14), residues: 1347 loop : -0.00 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 765 TYR 0.018 0.001 TYR B1138 PHE 0.014 0.001 PHE A 106 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00369 (30098) covalent geometry : angle 0.52567 (41278) SS BOND : bond 0.00321 ( 51) SS BOND : angle 1.27997 ( 102) hydrogen bonds : bond 0.03157 ( 1407) hydrogen bonds : angle 5.00659 ( 3987) link_BETA1-4 : bond 0.00586 ( 18) link_BETA1-4 : angle 2.04249 ( 54) link_NAG-ASN : bond 0.00533 ( 48) link_NAG-ASN : angle 2.60161 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6567 (m-80) cc_final: 0.5647 (t80) REVERT: A 135 PHE cc_start: 0.5548 (OUTLIER) cc_final: 0.4655 (m-80) REVERT: A 287 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8586 (m-30) REVERT: A 365 TYR cc_start: 0.7855 (m-80) cc_final: 0.7562 (m-80) REVERT: A 619 GLU cc_start: 0.7426 (mp0) cc_final: 0.7200 (mp0) REVERT: A 737 ASP cc_start: 0.7655 (m-30) cc_final: 0.7402 (p0) REVERT: A 957 GLN cc_start: 0.8723 (tt0) cc_final: 0.8391 (tt0) REVERT: A 1004 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9112 (tt) REVERT: A 1019 ARG cc_start: 0.9007 (tpt170) cc_final: 0.8336 (ttp-170) REVERT: B 135 PHE cc_start: 0.5078 (OUTLIER) cc_final: 0.4480 (m-80) REVERT: B 619 GLU cc_start: 0.7493 (mp0) cc_final: 0.7134 (mp0) REVERT: B 957 GLN cc_start: 0.8557 (tt0) cc_final: 0.8222 (tp-100) REVERT: B 1019 ARG cc_start: 0.8792 (tpt170) cc_final: 0.8224 (ttm-80) REVERT: E 133 PHE cc_start: 0.7020 (m-80) cc_final: 0.5642 (t80) REVERT: E 135 PHE cc_start: 0.5590 (OUTLIER) cc_final: 0.5135 (m-80) REVERT: E 271 GLN cc_start: 0.8355 (mt0) cc_final: 0.7641 (tt0) REVERT: E 900 MET cc_start: 0.9043 (mtp) cc_final: 0.8775 (mtp) REVERT: E 1019 ARG cc_start: 0.8824 (tpt170) cc_final: 0.8224 (ttp-110) outliers start: 41 outliers final: 29 residues processed: 183 average time/residue: 0.1554 time to fit residues: 48.9910 Evaluate side-chains 184 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 166 CYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 347 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 319 optimal weight: 20.0000 chunk 293 optimal weight: 0.0000 chunk 140 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 236 optimal weight: 0.9990 chunk 420 optimal weight: 40.0000 chunk 356 optimal weight: 1.9990 chunk 222 optimal weight: 0.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.167587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108436 restraints weight = 51568.197| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.85 r_work: 0.3188 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30215 Z= 0.120 Angle : 0.527 16.322 41578 Z= 0.254 Chirality : 0.045 0.451 5148 Planarity : 0.004 0.038 5427 Dihedral : 4.513 46.689 5793 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.78 % Allowed : 10.66 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.13), residues: 4194 helix: 1.73 (0.20), residues: 720 sheet: 1.08 (0.14), residues: 1335 loop : 0.05 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 646 TYR 0.014 0.001 TYR E1067 PHE 0.014 0.001 PHE A 106 TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00279 (30098) covalent geometry : angle 0.49898 (41278) SS BOND : bond 0.00246 ( 51) SS BOND : angle 1.17479 ( 102) hydrogen bonds : bond 0.02919 ( 1407) hydrogen bonds : angle 4.87691 ( 3987) link_BETA1-4 : bond 0.00635 ( 18) link_BETA1-4 : angle 1.98222 ( 54) link_NAG-ASN : bond 0.00577 ( 48) link_NAG-ASN : angle 2.52560 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6659 (m-80) cc_final: 0.6162 (t80) REVERT: A 287 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8559 (m-30) REVERT: A 365 TYR cc_start: 0.7828 (m-80) cc_final: 0.7626 (m-80) REVERT: A 619 GLU cc_start: 0.7479 (mp0) cc_final: 0.7218 (mp0) REVERT: A 1004 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9141 (tt) REVERT: A 1019 ARG cc_start: 0.8990 (tpt170) cc_final: 0.8367 (ttp-170) REVERT: B 135 PHE cc_start: 0.5092 (OUTLIER) cc_final: 0.4512 (m-80) REVERT: B 326 ILE cc_start: 0.8760 (mm) cc_final: 0.8436 (pt) REVERT: B 619 GLU cc_start: 0.7518 (mp0) cc_final: 0.7188 (mp0) REVERT: B 957 GLN cc_start: 0.8556 (tt0) cc_final: 0.8231 (tp-100) REVERT: B 1019 ARG cc_start: 0.8774 (tpt170) cc_final: 0.8240 (ttm-80) REVERT: E 133 PHE cc_start: 0.6917 (m-80) cc_final: 0.5712 (t80) REVERT: E 135 PHE cc_start: 0.5440 (OUTLIER) cc_final: 0.5050 (m-80) REVERT: E 271 GLN cc_start: 0.8348 (mt0) cc_final: 0.7663 (tt0) REVERT: E 900 MET cc_start: 0.9020 (mtp) cc_final: 0.8749 (mtp) REVERT: E 1019 ARG cc_start: 0.8803 (tpt170) cc_final: 0.8248 (ttp-110) outliers start: 42 outliers final: 34 residues processed: 189 average time/residue: 0.1579 time to fit residues: 51.3417 Evaluate side-chains 190 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 166 CYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 338 PHE Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 338 optimal weight: 0.6980 chunk 191 optimal weight: 1.9990 chunk 129 optimal weight: 50.0000 chunk 92 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 251 optimal weight: 20.0000 chunk 192 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 122 optimal weight: 50.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.167071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.105904 restraints weight = 50802.650| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.87 r_work: 0.3163 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30215 Z= 0.184 Angle : 0.563 16.155 41578 Z= 0.274 Chirality : 0.046 0.449 5148 Planarity : 0.004 0.040 5427 Dihedral : 4.692 41.213 5793 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.03 % Allowed : 10.61 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.13), residues: 4194 helix: 1.42 (0.20), residues: 747 sheet: 0.96 (0.14), residues: 1356 loop : 0.05 (0.14), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.017 0.001 TYR B1138 PHE 0.014 0.001 PHE B 92 TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS E1048 Details of bonding type rmsd covalent geometry : bond 0.00437 (30098) covalent geometry : angle 0.53667 (41278) SS BOND : bond 0.00332 ( 51) SS BOND : angle 1.31075 ( 102) hydrogen bonds : bond 0.03259 ( 1407) hydrogen bonds : angle 4.95265 ( 3987) link_BETA1-4 : bond 0.00580 ( 18) link_BETA1-4 : angle 1.94800 ( 54) link_NAG-ASN : bond 0.00541 ( 48) link_NAG-ASN : angle 2.53636 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6686 (m-80) cc_final: 0.5811 (t80) REVERT: A 135 PHE cc_start: 0.5740 (OUTLIER) cc_final: 0.5345 (m-80) REVERT: A 287 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8528 (m-30) REVERT: A 365 TYR cc_start: 0.7895 (m-80) cc_final: 0.7683 (m-80) REVERT: A 619 GLU cc_start: 0.7464 (mp0) cc_final: 0.7169 (mp0) REVERT: A 1004 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9158 (tt) REVERT: A 1019 ARG cc_start: 0.8990 (tpt170) cc_final: 0.8353 (ttp-170) REVERT: B 135 PHE cc_start: 0.5136 (OUTLIER) cc_final: 0.4557 (m-80) REVERT: B 165 ASN cc_start: 0.5259 (OUTLIER) cc_final: 0.4998 (p0) REVERT: B 619 GLU cc_start: 0.7580 (mp0) cc_final: 0.7212 (mp0) REVERT: B 1019 ARG cc_start: 0.8839 (tpt170) cc_final: 0.8268 (ttm110) REVERT: E 133 PHE cc_start: 0.6938 (m-80) cc_final: 0.5694 (t80) REVERT: E 135 PHE cc_start: 0.5396 (OUTLIER) cc_final: 0.5009 (m-80) REVERT: E 271 GLN cc_start: 0.8365 (mt0) cc_final: 0.7671 (tt0) REVERT: E 900 MET cc_start: 0.9044 (mtp) cc_final: 0.8754 (mtp) REVERT: E 1019 ARG cc_start: 0.8803 (tpt170) cc_final: 0.8231 (ttp-170) outliers start: 48 outliers final: 40 residues processed: 188 average time/residue: 0.1544 time to fit residues: 50.3575 Evaluate side-chains 197 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 166 CYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 338 PHE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 166 optimal weight: 0.8980 chunk 47 optimal weight: 0.0770 chunk 373 optimal weight: 0.5980 chunk 36 optimal weight: 20.0000 chunk 213 optimal weight: 0.9990 chunk 196 optimal weight: 5.9990 chunk 372 optimal weight: 0.4980 chunk 211 optimal weight: 0.7980 chunk 341 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 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 955 ASN B 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.168730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109073 restraints weight = 50954.860| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.69 r_work: 0.3208 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30215 Z= 0.109 Angle : 0.522 16.443 41578 Z= 0.251 Chirality : 0.045 0.418 5148 Planarity : 0.004 0.039 5427 Dihedral : 4.399 35.730 5793 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.86 % Allowed : 10.82 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.13), residues: 4194 helix: 1.80 (0.20), residues: 720 sheet: 1.12 (0.14), residues: 1302 loop : 0.08 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.013 0.001 TYR E1067 PHE 0.014 0.001 PHE A 374 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00251 (30098) covalent geometry : angle 0.49492 (41278) SS BOND : bond 0.00240 ( 51) SS BOND : angle 1.11526 ( 102) hydrogen bonds : bond 0.02868 ( 1407) hydrogen bonds : angle 4.81800 ( 3987) link_BETA1-4 : bond 0.00609 ( 18) link_BETA1-4 : angle 1.91702 ( 54) link_NAG-ASN : bond 0.00535 ( 48) link_NAG-ASN : angle 2.46327 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6633 (m-80) cc_final: 0.5793 (t80) REVERT: A 135 PHE cc_start: 0.5773 (OUTLIER) cc_final: 0.5119 (m-80) REVERT: A 287 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8511 (m-30) REVERT: A 619 GLU cc_start: 0.7423 (mp0) cc_final: 0.7096 (mp0) REVERT: A 1004 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9106 (tt) REVERT: A 1019 ARG cc_start: 0.8960 (tpt170) cc_final: 0.8342 (ttp-170) REVERT: B 135 PHE cc_start: 0.5062 (OUTLIER) cc_final: 0.4503 (m-80) REVERT: B 165 ASN cc_start: 0.5202 (OUTLIER) cc_final: 0.4889 (p0) REVERT: B 326 ILE cc_start: 0.8723 (mm) cc_final: 0.8451 (pt) REVERT: B 619 GLU cc_start: 0.7532 (mp0) cc_final: 0.7169 (mp0) REVERT: B 1019 ARG cc_start: 0.8738 (tpt170) cc_final: 0.8224 (ttm-80) REVERT: E 133 PHE cc_start: 0.6875 (m-80) cc_final: 0.5558 (t80) REVERT: E 135 PHE cc_start: 0.5364 (OUTLIER) cc_final: 0.5044 (m-80) REVERT: E 271 GLN cc_start: 0.8422 (mt0) cc_final: 0.7666 (tt0) REVERT: E 900 MET cc_start: 0.8973 (mtp) cc_final: 0.8695 (mtp) REVERT: E 1019 ARG cc_start: 0.8750 (tpt170) cc_final: 0.8209 (ttp-110) outliers start: 44 outliers final: 34 residues processed: 188 average time/residue: 0.1525 time to fit residues: 49.5794 Evaluate side-chains 192 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 166 CYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 338 PHE Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 6 optimal weight: 2.9990 chunk 329 optimal weight: 0.9990 chunk 245 optimal weight: 30.0000 chunk 139 optimal weight: 0.0970 chunk 12 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 262 optimal weight: 0.5980 chunk 361 optimal weight: 0.7980 chunk 299 optimal weight: 3.9990 chunk 293 optimal weight: 0.6980 chunk 206 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.170382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.112009 restraints weight = 50316.063| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.37 r_work: 0.3153 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30215 Z= 0.113 Angle : 0.534 17.027 41578 Z= 0.254 Chirality : 0.044 0.411 5148 Planarity : 0.004 0.039 5427 Dihedral : 4.493 56.135 5793 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.65 % Allowed : 11.33 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.13), residues: 4194 helix: 1.64 (0.20), residues: 747 sheet: 1.09 (0.14), residues: 1332 loop : 0.07 (0.14), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.018 0.001 TYR B1138 PHE 0.013 0.001 PHE E 374 TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00257 (30098) covalent geometry : angle 0.49940 (41278) SS BOND : bond 0.00235 ( 51) SS BOND : angle 1.08696 ( 102) hydrogen bonds : bond 0.02876 ( 1407) hydrogen bonds : angle 4.77217 ( 3987) link_BETA1-4 : bond 0.00596 ( 18) link_BETA1-4 : angle 1.88566 ( 54) link_NAG-ASN : bond 0.00791 ( 48) link_NAG-ASN : angle 2.95788 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8511.57 seconds wall clock time: 145 minutes 22.16 seconds (8722.16 seconds total)