Starting phenix.real_space_refine on Sun Jul 5 18:40:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jvc_22506/07_2026/7jvc_22506.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jvc_22506/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7jvc_22506/07_2026/7jvc_22506.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jvc_22506/07_2026/7jvc_22506.cif" model { file = "/net/cci-nas-00/data/ceres_data/7jvc_22506/07_2026/7jvc_22506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jvc_22506/07_2026/7jvc_22506.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jvc_22506/07_2026/7jvc_22506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jvc_22506/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 11 Time building chain proxies: 6.25, per 1000 atoms: 0.21 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: 2.34 Conformation dependent library (CDL) restraints added in 1.4 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: 1.39 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: 9.12 Time building geometry restraints manager: 3.14 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 - 17.70: 16859 17.70 - 35.40: 372 35.40 - 53.11: 101 53.11 - 70.81: 30 70.81 - 88.51: 18 Dihedral angle restraints: 17380 sinusoidal: 5080 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 17377 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: 4.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.200 Find NCS groups from input model: 0.730 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: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 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 : 9.632 88.509 9259 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/Z covalent geometry : bond 0.01318 / 0.73 (30098) covalent geometry : angle 1.41829 / 0.96 (41278) SS BOND : bond 0.00757 / 0.45 ( 51) SS BOND : angle 3.09303 / 2.10 ( 102) hydrogen bonds : bond 0.16748 / 10.82 ( 1407) hydrogen bonds : angle 8.30025 / 5.86 ( 3987) link_BETA1-4 : bond 0.06789 / 3.70 ( 18) link_BETA1-4 : angle 4.08518 / 2.56 ( 54) link_NAG-ASN : bond 0.06906 / 4.28 ( 48) link_NAG-ASN : angle 2.38572 / 1.60 ( 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 : 0.729 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: 0.1765 time to fit residues: 129.7034 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 : 1.204 ------------------------------------------------------------------------------- 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... A 207 HIS A 321 GLN A 388 ASN A 607 GLN A 965 GLN B 207 HIS B 321 GLN B 388 ASN 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.171232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.112587 restraints weight = 51307.208| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.89 r_work: 0.3262 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30215 Z= 0.146 Angle : 0.646 12.972 41578 Z= 0.328 Chirality : 0.046 0.232 5148 Planarity : 0.004 0.031 5427 Dihedral : 4.490 35.115 4413 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.55 % Favored : 98.38 % Rotamer: Outliers : 1.23 % Allowed : 8.08 % Favored : 90.70 % 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: 1.13 (0.13), residues: 4194 helix: 0.83 (0.19), residues: 741 sheet: 1.39 (0.14), residues: 1317 loop : 0.42 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 237 TYR 0.025 0.002 TYR E1138 PHE 0.018 0.002 PHE B 65 TRP 0.006 0.001 TRP E 104 HIS 0.007 0.001 HIS E1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (30098) covalent geometry : angle 0.60842 / 0.32 (41278) SS BOND : bond 0.00607 / 0.37 ( 51) SS BOND : angle 1.99884 / 1.30 ( 102) hydrogen bonds : bond 0.04418 / 2.88 ( 1407) hydrogen bonds : angle 5.93652 / 4.22 ( 3987) link_BETA1-4 : bond 0.00606 / 0.33 ( 18) link_BETA1-4 : angle 2.85334 / 1.79 ( 54) link_NAG-ASN : bond 0.00605 / 0.38 ( 48) link_NAG-ASN : angle 2.89529 / 1.95 ( 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 243 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8785 (p) cc_final: 0.8570 (t) REVERT: A 353 TRP cc_start: 0.5989 (p-90) cc_final: 0.5120 (p-90) REVERT: A 365 TYR cc_start: 0.7818 (m-80) cc_final: 0.7581 (m-80) REVERT: A 377 PHE cc_start: 0.7145 (t80) cc_final: 0.6901 (t80) REVERT: A 751 ASN cc_start: 0.8247 (m-40) cc_final: 0.8030 (m-40) REVERT: A 796 ASP cc_start: 0.8378 (t0) cc_final: 0.7955 (p0) REVERT: A 1019 ARG cc_start: 0.8860 (tpt170) cc_final: 0.8237 (ttp-170) REVERT: B 133 PHE cc_start: 0.6217 (m-80) cc_final: 0.6013 (m-80) REVERT: B 190 ARG cc_start: 0.7881 (mtt-85) cc_final: 0.7435 (mtt180) REVERT: B 654 GLU cc_start: 0.9032 (tt0) cc_final: 0.8800 (mt-10) REVERT: B 725 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8376 (tt0) REVERT: B 1019 ARG cc_start: 0.8731 (tpt170) cc_final: 0.8165 (ttm-80) REVERT: E 271 GLN cc_start: 0.7875 (mt0) cc_final: 0.7133 (tt0) REVERT: E 353 TRP cc_start: 0.5703 (p-90) cc_final: 0.4825 (p-90) REVERT: E 377 PHE cc_start: 0.6961 (t80) cc_final: 0.4889 (p90) REVERT: E 796 ASP cc_start: 0.8390 (t0) cc_final: 0.8026 (p0) REVERT: E 1019 ARG cc_start: 0.8716 (tpt170) cc_final: 0.8138 (ttp80) outliers start: 29 outliers final: 15 residues processed: 241 average time/residue: 0.1619 time to fit residues: 66.1652 Evaluate side-chains 181 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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: 50.0000 chunk 137 optimal weight: 40.0000 chunk 307 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 405 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 251 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 804 GLN A 914 ASN A 926 GLN A 965 GLN A1048 HIS A1071 GLN B 804 GLN B1048 HIS B1071 GLN E 901 GLN E1048 HIS E1071 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.162548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.101254 restraints weight = 52032.728| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.21 r_work: 0.3028 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.128 30215 Z= 0.538 Angle : 0.879 14.764 41578 Z= 0.444 Chirality : 0.056 0.454 5148 Planarity : 0.006 0.064 5427 Dihedral : 4.987 23.776 4413 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.07 % Allowed : 9.64 % Favored : 88.29 % 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: 0.39 (0.13), residues: 4194 helix: 0.31 (0.19), residues: 714 sheet: 0.80 (0.13), residues: 1437 loop : -0.05 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E1014 TYR 0.030 0.003 TYR B1067 PHE 0.033 0.004 PHE B1103 TRP 0.025 0.003 TRP A 886 HIS 0.012 0.004 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01289 / 0.54 (30098) covalent geometry : angle 0.85236 / 0.44 (41278) SS BOND : bond 0.00848 / 0.52 ( 51) SS BOND : angle 2.10383 / 1.43 ( 102) hydrogen bonds : bond 0.05227 / 3.51 ( 1407) hydrogen bonds : angle 6.00234 / 4.24 ( 3987) link_BETA1-4 : bond 0.00627 / 0.36 ( 18) link_BETA1-4 : angle 2.45899 / 1.56 ( 54) link_NAG-ASN : bond 0.01064 / 0.68 ( 48) link_NAG-ASN : angle 3.08470 / 2.08 ( 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 203 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 154 time to evaluate : 1.118 Fit side-chains REVERT: A 353 TRP cc_start: 0.6023 (p-90) cc_final: 0.5219 (p-90) REVERT: A 365 TYR cc_start: 0.7889 (m-80) cc_final: 0.7582 (m-80) REVERT: A 377 PHE cc_start: 0.7213 (t80) cc_final: 0.5719 (p90) REVERT: A 1004 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9297 (tt) REVERT: A 1019 ARG cc_start: 0.9005 (tpt170) cc_final: 0.8354 (ttp-170) REVERT: B 133 PHE cc_start: 0.6669 (m-80) cc_final: 0.6265 (t80) REVERT: B 377 PHE cc_start: 0.7293 (t80) cc_final: 0.5898 (p90) REVERT: B 554 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8389 (mp0) REVERT: B 957 GLN cc_start: 0.8638 (tt0) cc_final: 0.8375 (tp-100) REVERT: B 1019 ARG cc_start: 0.8734 (tpt170) cc_final: 0.8211 (ttm-80) REVERT: E 271 GLN cc_start: 0.8184 (mt0) cc_final: 0.7540 (tt0) REVERT: E 1019 ARG cc_start: 0.8813 (tpt170) cc_final: 0.8204 (ttp80) outliers start: 49 outliers final: 32 residues processed: 200 average time/residue: 0.1496 time to fit residues: 52.7943 Evaluate side-chains 172 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL 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 84 LEU 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: 0.8980 chunk 415 optimal weight: 50.0000 chunk 293 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 406 optimal weight: 50.0000 chunk 311 optimal weight: 0.3980 chunk 86 optimal weight: 0.7980 chunk 118 optimal weight: 50.0000 chunk 342 optimal weight: 0.8980 chunk 239 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.166925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108457 restraints weight = 51610.618| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.31 r_work: 0.3141 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30215 Z= 0.137 Angle : 0.583 16.308 41578 Z= 0.287 Chirality : 0.045 0.399 5148 Planarity : 0.004 0.040 5427 Dihedral : 4.246 19.689 4413 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.07 % Allowed : 10.57 % 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: 0.79 (0.13), residues: 4194 helix: 1.28 (0.20), residues: 708 sheet: 1.00 (0.13), residues: 1359 loop : 0.03 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 646 TYR 0.016 0.001 TYR B1067 PHE 0.022 0.001 PHE E 374 TRP 0.010 0.001 TRP E 436 HIS 0.004 0.001 HIS E1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (30098) covalent geometry : angle 0.55175 / 0.28 (41278) SS BOND : bond 0.00331 / 0.20 ( 51) SS BOND : angle 1.53352 / 1.05 ( 102) hydrogen bonds : bond 0.03516 / 2.31 ( 1407) hydrogen bonds : angle 5.42212 / 3.84 ( 3987) link_BETA1-4 : bond 0.00637 / 0.35 ( 18) link_BETA1-4 : angle 2.18239 / 1.43 ( 54) link_NAG-ASN : bond 0.00502 / 0.30 ( 48) link_NAG-ASN : angle 2.73903 / 1.84 ( 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 214 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 165 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 135 PHE cc_start: 0.5454 (OUTLIER) cc_final: 0.5202 (m-80) REVERT: A 287 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8330 (m-30) REVERT: A 365 TYR cc_start: 0.7755 (m-80) cc_final: 0.7530 (m-80) REVERT: A 957 GLN cc_start: 0.8638 (tt0) cc_final: 0.8340 (tt0) REVERT: A 1004 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9087 (tt) REVERT: A 1019 ARG cc_start: 0.8812 (tpt170) cc_final: 0.8264 (ttp-170) REVERT: B 133 PHE cc_start: 0.6464 (m-80) cc_final: 0.6125 (t80) REVERT: B 1019 ARG cc_start: 0.8629 (tpt170) cc_final: 0.8134 (ttm-80) REVERT: E 135 PHE cc_start: 0.5185 (OUTLIER) cc_final: 0.4894 (m-80) REVERT: E 271 GLN cc_start: 0.8191 (mt0) cc_final: 0.7524 (tt0) REVERT: E 619 GLU cc_start: 0.7065 (mp0) cc_final: 0.6845 (mp0) REVERT: E 900 MET cc_start: 0.8832 (mtp) cc_final: 0.8577 (mtp) REVERT: E 1019 ARG cc_start: 0.8594 (tpt170) cc_final: 0.8144 (ttp-110) outliers start: 49 outliers final: 19 residues processed: 205 average time/residue: 0.1566 time to fit residues: 54.7090 Evaluate side-chains 164 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 560 LEU 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 244 LEU 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 101 ILE Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 434 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 348 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 chunk 414 optimal weight: 10.0000 chunk 388 optimal weight: 0.0470 chunk 125 optimal weight: 20.0000 chunk 115 optimal weight: 50.0000 chunk 398 optimal weight: 7.9990 chunk 419 optimal weight: 30.0000 chunk 273 optimal weight: 50.0000 chunk 54 optimal weight: 0.4980 chunk 361 optimal weight: 1.9990 overall best weight: 2.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN A 914 ASN B 804 GLN B 901 GLN B 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.163501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.102851 restraints weight = 51323.891| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.94 r_work: 0.3087 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 30215 Z= 0.352 Angle : 0.706 15.835 41578 Z= 0.349 Chirality : 0.050 0.522 5148 Planarity : 0.005 0.043 5427 Dihedral : 4.511 20.641 4413 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.83 % Allowed : 10.27 % Favored : 86.89 % 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: 0.47 (0.13), residues: 4194 helix: 0.97 (0.20), residues: 708 sheet: 0.65 (0.13), residues: 1404 loop : -0.06 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 646 TYR 0.024 0.002 TYR B1067 PHE 0.022 0.003 PHE B 140 TRP 0.011 0.002 TRP A 104 HIS 0.007 0.002 HIS E1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00843 / 0.35 (30098) covalent geometry : angle 0.68119 / 0.34 (41278) SS BOND : bond 0.00673 / 0.41 ( 51) SS BOND : angle 1.68646 / 1.13 ( 102) hydrogen bonds : bond 0.04237 / 2.83 ( 1407) hydrogen bonds : angle 5.55344 / 3.91 ( 3987) link_BETA1-4 : bond 0.00558 / 0.30 ( 18) link_BETA1-4 : angle 2.07822 / 1.37 ( 54) link_NAG-ASN : bond 0.00672 / 0.43 ( 48) link_NAG-ASN : angle 2.65887 / 1.81 ( 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 208 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 141 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.5804 (OUTLIER) cc_final: 0.5442 (m-80) REVERT: A 165 ASN cc_start: 0.5751 (OUTLIER) cc_final: 0.5525 (p0) REVERT: A 287 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8558 (m-30) REVERT: A 365 TYR cc_start: 0.7948 (m-80) cc_final: 0.7694 (m-80) REVERT: A 619 GLU cc_start: 0.7570 (mp0) cc_final: 0.7325 (mp0) REVERT: A 902 MET cc_start: 0.8966 (tpt) cc_final: 0.8645 (mmt) REVERT: A 957 GLN cc_start: 0.8957 (tt0) cc_final: 0.8700 (tt0) REVERT: A 1004 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9252 (tt) REVERT: A 1019 ARG cc_start: 0.9101 (tpt170) cc_final: 0.8427 (ttp-170) REVERT: B 135 PHE cc_start: 0.5373 (OUTLIER) cc_final: 0.4750 (m-80) REVERT: B 1019 ARG cc_start: 0.8921 (tpt170) cc_final: 0.8362 (ttm-80) REVERT: E 133 PHE cc_start: 0.7137 (m-80) cc_final: 0.5324 (t80) REVERT: E 135 PHE cc_start: 0.5590 (OUTLIER) cc_final: 0.5019 (m-80) REVERT: E 271 GLN cc_start: 0.8289 (mt0) cc_final: 0.7606 (tt0) REVERT: E 619 GLU cc_start: 0.7435 (mp0) cc_final: 0.7181 (mp0) REVERT: E 900 MET cc_start: 0.9074 (mtp) cc_final: 0.8848 (mtp) REVERT: E 957 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8235 (tm-30) REVERT: E 1019 ARG cc_start: 0.8933 (tpt170) cc_final: 0.8401 (ttm110) outliers start: 67 outliers final: 49 residues processed: 198 average time/residue: 0.1416 time to fit residues: 48.6532 Evaluate side-chains 190 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 135 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 546 LEU 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 711 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET 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 1133 VAL 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 284 THR Chi-restraints excluded: chain B residue 546 LEU 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 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 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 166 CYS Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 284 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 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 758 SER 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 1133 VAL 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: 0.1980 chunk 41 optimal weight: 9.9990 chunk 296 optimal weight: 0.6980 chunk 242 optimal weight: 0.5980 chunk 240 optimal weight: 0.8980 chunk 257 optimal weight: 0.0980 chunk 361 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 145 optimal weight: 0.5980 chunk 318 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 957 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.167137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.107679 restraints weight = 51322.851| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.79 r_work: 0.3195 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 30215 Z= 0.106 Angle : 0.552 16.374 41578 Z= 0.268 Chirality : 0.045 0.480 5148 Planarity : 0.004 0.042 5427 Dihedral : 3.968 19.346 4413 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.61 % Allowed : 11.42 % Favored : 86.98 % 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: 0.68 (0.13), residues: 4194 helix: 1.31 (0.20), residues: 747 sheet: 0.82 (0.14), residues: 1341 loop : -0.02 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 646 TYR 0.013 0.001 TYR B 369 PHE 0.018 0.001 PHE E 133 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.000 HIS E1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (30098) covalent geometry : angle 0.52462 / 0.26 (41278) SS BOND : bond 0.00270 / 0.16 ( 51) SS BOND : angle 1.33301 / 0.90 ( 102) hydrogen bonds : bond 0.03071 / 2.02 ( 1407) hydrogen bonds : angle 5.17457 / 3.66 ( 3987) link_BETA1-4 : bond 0.00587 / 0.31 ( 18) link_BETA1-4 : angle 1.97684 / 1.32 ( 54) link_NAG-ASN : bond 0.00626 / 0.37 ( 48) link_NAG-ASN : angle 2.54343 / 1.73 ( 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 198 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 1.138 Fit side-chains REVERT: A 135 PHE cc_start: 0.5821 (OUTLIER) cc_final: 0.5087 (m-80) REVERT: A 165 ASN cc_start: 0.5430 (OUTLIER) cc_final: 0.5167 (p0) REVERT: A 287 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8462 (m-30) REVERT: A 365 TYR cc_start: 0.7852 (m-80) cc_final: 0.7584 (m-80) REVERT: A 619 GLU cc_start: 0.7544 (mp0) cc_final: 0.7263 (mp0) REVERT: A 957 GLN cc_start: 0.8865 (tt0) cc_final: 0.8609 (tt0) REVERT: A 1004 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9022 (tt) REVERT: A 1019 ARG cc_start: 0.8957 (tpt170) cc_final: 0.8337 (ttp-170) REVERT: B 133 PHE cc_start: 0.6500 (m-80) cc_final: 0.6004 (t80) REVERT: B 135 PHE cc_start: 0.5131 (OUTLIER) cc_final: 0.4382 (m-80) REVERT: B 619 GLU cc_start: 0.7105 (mp0) cc_final: 0.6807 (mp0) REVERT: B 957 GLN cc_start: 0.8526 (tt0) cc_final: 0.8239 (tp-100) REVERT: B 1019 ARG cc_start: 0.8800 (tpt170) cc_final: 0.8192 (ttm-80) REVERT: E 133 PHE cc_start: 0.7154 (m-80) cc_final: 0.5539 (t80) REVERT: E 135 PHE cc_start: 0.5640 (OUTLIER) cc_final: 0.5134 (m-80) REVERT: E 271 GLN cc_start: 0.8322 (mt0) cc_final: 0.7608 (tt0) REVERT: E 619 GLU cc_start: 0.7345 (mp0) cc_final: 0.7064 (mp0) REVERT: E 674 TYR cc_start: 0.9029 (t80) cc_final: 0.8798 (t80) REVERT: E 900 MET cc_start: 0.8937 (mtp) cc_final: 0.8668 (mtp) REVERT: E 1019 ARG cc_start: 0.8786 (tpt170) cc_final: 0.8221 (ttp-110) outliers start: 38 outliers final: 18 residues processed: 189 average time/residue: 0.1459 time to fit residues: 47.6639 Evaluate side-chains 176 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 560 LEU 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 B residue 135 PHE Chi-restraints excluded: chain B residue 166 CYS 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 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR 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: 5.9990 chunk 46 optimal weight: 0.0870 chunk 55 optimal weight: 1.9990 chunk 390 optimal weight: 50.0000 chunk 170 optimal weight: 7.9990 chunk 425 optimal weight: 50.0000 chunk 305 optimal weight: 0.0020 chunk 216 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 overall best weight: 1.2172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.165513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.105357 restraints weight = 50961.412| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.17 r_work: 0.3115 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 30215 Z= 0.178 Angle : 0.572 16.221 41578 Z= 0.278 Chirality : 0.046 0.511 5148 Planarity : 0.004 0.041 5427 Dihedral : 3.970 20.050 4413 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.78 % Allowed : 11.46 % Favored : 86.77 % 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 (0.13), residues: 4194 helix: 1.44 (0.20), residues: 726 sheet: 0.79 (0.14), residues: 1344 loop : -0.00 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.017 0.001 TYR B1067 PHE 0.015 0.001 PHE B 140 TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS E1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (30098) covalent geometry : angle 0.54661 / 0.27 (41278) SS BOND : bond 0.00340 / 0.20 ( 51) SS BOND : angle 1.34821 / 0.91 ( 102) hydrogen bonds : bond 0.03303 / 2.18 ( 1407) hydrogen bonds : angle 5.13072 / 3.62 ( 3987) link_BETA1-4 : bond 0.00547 / 0.30 ( 18) link_BETA1-4 : angle 1.89127 / 1.27 ( 54) link_NAG-ASN : bond 0.00539 / 0.33 ( 48) link_NAG-ASN : angle 2.47484 / 1.72 ( 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 199 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 1.093 Fit side-chains REVERT: A 135 PHE cc_start: 0.5585 (OUTLIER) cc_final: 0.5276 (m-80) REVERT: A 165 ASN cc_start: 0.5677 (OUTLIER) cc_final: 0.5460 (p0) REVERT: A 287 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8318 (m-30) REVERT: A 365 TYR cc_start: 0.7808 (m-80) cc_final: 0.7528 (m-80) REVERT: A 619 GLU cc_start: 0.7444 (mp0) cc_final: 0.7184 (mp0) REVERT: A 957 GLN cc_start: 0.8696 (tt0) cc_final: 0.8434 (tt0) REVERT: A 1004 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9164 (tt) REVERT: A 1019 ARG cc_start: 0.8838 (tpt170) cc_final: 0.8322 (ttp-170) REVERT: B 135 PHE cc_start: 0.5038 (OUTLIER) cc_final: 0.4484 (m-80) REVERT: B 619 GLU cc_start: 0.7058 (mp0) cc_final: 0.6822 (mp0) REVERT: B 1019 ARG cc_start: 0.8705 (tpt170) cc_final: 0.8220 (ttm110) REVERT: E 131 CYS cc_start: 0.2867 (OUTLIER) cc_final: 0.2420 (m) REVERT: E 133 PHE cc_start: 0.7117 (m-80) cc_final: 0.5374 (t80) REVERT: E 135 PHE cc_start: 0.5381 (OUTLIER) cc_final: 0.4906 (m-80) REVERT: E 271 GLN cc_start: 0.8263 (mt0) cc_final: 0.7619 (tt0) REVERT: E 619 GLU cc_start: 0.7309 (mp0) cc_final: 0.7058 (mp0) REVERT: E 900 MET cc_start: 0.8875 (mtp) cc_final: 0.8606 (mtp) REVERT: E 1019 ARG cc_start: 0.8646 (tpt170) cc_final: 0.8227 (ttp-170) outliers start: 42 outliers final: 31 residues processed: 185 average time/residue: 0.1487 time to fit residues: 47.8159 Evaluate side-chains 188 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 165 ASN 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 560 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 166 CYS 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 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 E residue 47 VAL Chi-restraints excluded: chain E residue 131 CYS 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 560 LEU 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 973 ILE Chi-restraints excluded: chain E residue 1017 GLU Chi-restraints excluded: chain E residue 1130 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 347 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 319 optimal weight: 20.0000 chunk 293 optimal weight: 0.0370 chunk 140 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 236 optimal weight: 0.8980 chunk 420 optimal weight: 0.0070 chunk 356 optimal weight: 0.9980 chunk 222 optimal weight: 0.6980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 957 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.167401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.107961 restraints weight = 51800.491| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.09 r_work: 0.3181 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 30215 Z= 0.102 Angle : 0.527 16.569 41578 Z= 0.254 Chirality : 0.044 0.402 5148 Planarity : 0.004 0.043 5427 Dihedral : 3.742 20.616 4413 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.73 % Allowed : 11.63 % Favored : 86.64 % 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: 0.85 (0.13), residues: 4194 helix: 1.64 (0.20), residues: 726 sheet: 0.90 (0.14), residues: 1341 loop : 0.04 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 646 TYR 0.012 0.001 TYR E1067 PHE 0.014 0.001 PHE E 133 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (30098) covalent geometry : angle 0.50174 / 0.25 (41278) SS BOND : bond 0.00227 / 0.13 ( 51) SS BOND : angle 1.16044 / 0.77 ( 102) hydrogen bonds : bond 0.02891 / 1.88 ( 1407) hydrogen bonds : angle 4.96831 / 3.49 ( 3987) link_BETA1-4 : bond 0.00586 / 0.31 ( 18) link_BETA1-4 : angle 1.84185 / 1.25 ( 54) link_NAG-ASN : bond 0.00582 / 0.36 ( 48) link_NAG-ASN : angle 2.40218 / 1.66 ( 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 197 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 ASN cc_start: 0.5586 (OUTLIER) cc_final: 0.5340 (p0) REVERT: A 287 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8533 (m-30) REVERT: A 365 TYR cc_start: 0.7815 (m-80) cc_final: 0.7584 (m-80) REVERT: A 619 GLU cc_start: 0.7633 (mp0) cc_final: 0.7305 (mp0) REVERT: A 1004 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9068 (tt) REVERT: A 1019 ARG cc_start: 0.8991 (tpt170) cc_final: 0.8359 (ttp-170) REVERT: B 133 PHE cc_start: 0.6601 (m-80) cc_final: 0.6104 (t80) REVERT: B 135 PHE cc_start: 0.5103 (OUTLIER) cc_final: 0.4467 (m-80) REVERT: B 326 ILE cc_start: 0.8770 (mm) cc_final: 0.8475 (pt) REVERT: B 619 GLU cc_start: 0.7262 (mp0) cc_final: 0.6865 (mp0) REVERT: B 1019 ARG cc_start: 0.8765 (tpt170) cc_final: 0.8229 (ttm-80) REVERT: E 131 CYS cc_start: 0.3183 (OUTLIER) cc_final: 0.2550 (m) REVERT: E 133 PHE cc_start: 0.6897 (m-80) cc_final: 0.6088 (t80) REVERT: E 271 GLN cc_start: 0.8347 (mt0) cc_final: 0.7643 (tt0) REVERT: E 619 GLU cc_start: 0.7439 (mp0) cc_final: 0.7128 (mp0) REVERT: E 674 TYR cc_start: 0.9078 (t80) cc_final: 0.8818 (t80) REVERT: E 900 MET cc_start: 0.8981 (mtp) cc_final: 0.8713 (mtp) REVERT: E 1019 ARG cc_start: 0.8809 (tpt170) cc_final: 0.8252 (ttp-110) outliers start: 41 outliers final: 27 residues processed: 188 average time/residue: 0.1479 time to fit residues: 47.9152 Evaluate side-chains 184 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 165 ASN 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 560 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 47 VAL 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 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 131 CYS 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 560 LEU 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 1017 GLU Chi-restraints excluded: chain E residue 1130 ILE 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: 2.9990 chunk 191 optimal weight: 0.9980 chunk 129 optimal weight: 50.0000 chunk 92 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 251 optimal weight: 20.0000 chunk 192 optimal weight: 0.0060 chunk 125 optimal weight: 20.0000 chunk 122 optimal weight: 50.0000 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.167360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.106991 restraints weight = 49841.869| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.85 r_work: 0.3141 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 30215 Z= 0.193 Angle : 0.572 16.141 41578 Z= 0.278 Chirality : 0.046 0.412 5148 Planarity : 0.004 0.045 5427 Dihedral : 3.884 20.993 4413 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.78 % Allowed : 11.71 % Favored : 86.51 % 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: 0.78 (0.13), residues: 4194 helix: 1.51 (0.20), residues: 723 sheet: 0.88 (0.14), residues: 1344 loop : 0.01 (0.14), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 765 TYR 0.018 0.001 TYR B1067 PHE 0.015 0.002 PHE B 140 TRP 0.009 0.001 TRP A 436 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (30098) covalent geometry : angle 0.54771 / 0.27 (41278) SS BOND : bond 0.00341 / 0.20 ( 51) SS BOND : angle 1.36786 / 0.90 ( 102) hydrogen bonds : bond 0.03314 / 2.18 ( 1407) hydrogen bonds : angle 5.02799 / 3.54 ( 3987) link_BETA1-4 : bond 0.00537 / 0.28 ( 18) link_BETA1-4 : angle 1.80071 / 1.22 ( 54) link_NAG-ASN : bond 0.00539 / 0.34 ( 48) link_NAG-ASN : angle 2.40306 / 1.66 ( 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 196 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.5703 (OUTLIER) cc_final: 0.5374 (m-80) REVERT: A 287 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8519 (m-30) REVERT: A 365 TYR cc_start: 0.7896 (m-80) cc_final: 0.7674 (m-80) REVERT: A 377 PHE cc_start: 0.7235 (t80) cc_final: 0.5432 (p90) REVERT: A 619 GLU cc_start: 0.7728 (mp0) cc_final: 0.7355 (mp0) REVERT: A 674 TYR cc_start: 0.9172 (t80) cc_final: 0.8891 (t80) REVERT: A 957 GLN cc_start: 0.8792 (tt0) cc_final: 0.8491 (tt0) REVERT: A 1004 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9180 (tt) REVERT: A 1019 ARG cc_start: 0.9012 (tpt170) cc_final: 0.8429 (ttp-170) REVERT: B 133 PHE cc_start: 0.6551 (m-80) cc_final: 0.6216 (t80) REVERT: B 135 PHE cc_start: 0.5188 (OUTLIER) cc_final: 0.4569 (m-80) REVERT: B 619 GLU cc_start: 0.7259 (mp0) cc_final: 0.6896 (mp0) REVERT: B 1019 ARG cc_start: 0.8916 (tpt170) cc_final: 0.8370 (ttm110) REVERT: E 133 PHE cc_start: 0.7167 (m-80) cc_final: 0.5423 (t80) REVERT: E 135 PHE cc_start: 0.5662 (OUTLIER) cc_final: 0.5175 (m-80) REVERT: E 271 GLN cc_start: 0.8405 (mt0) cc_final: 0.7727 (tt0) REVERT: E 592 PHE cc_start: 0.8336 (p90) cc_final: 0.7953 (p90) REVERT: E 619 GLU cc_start: 0.7496 (mp0) cc_final: 0.7172 (mp0) REVERT: E 900 MET cc_start: 0.9037 (mtp) cc_final: 0.8774 (mtp) REVERT: E 1019 ARG cc_start: 0.8857 (tpt170) cc_final: 0.8338 (ttp-170) outliers start: 42 outliers final: 34 residues processed: 186 average time/residue: 0.1508 time to fit residues: 48.5854 Evaluate side-chains 192 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 131 CYS 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 560 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET 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 47 VAL 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 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 E residue 47 VAL Chi-restraints excluded: chain E residue 131 CYS 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 546 LEU Chi-restraints excluded: chain E residue 560 LEU 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 1017 GLU Chi-restraints excluded: chain E residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 166 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 373 optimal weight: 0.6980 chunk 36 optimal weight: 0.0040 chunk 213 optimal weight: 0.5980 chunk 196 optimal weight: 1.9990 chunk 372 optimal weight: 0.3980 chunk 211 optimal weight: 1.9990 chunk 341 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.167351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110887 restraints weight = 51182.037| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.14 r_work: 0.3159 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 30215 Z= 0.105 Angle : 0.524 16.193 41578 Z= 0.253 Chirality : 0.044 0.376 5148 Planarity : 0.004 0.039 5427 Dihedral : 3.699 20.985 4413 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.56 % Allowed : 11.84 % Favored : 86.60 % 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: 0.86 (0.13), residues: 4194 helix: 1.54 (0.20), residues: 747 sheet: 0.93 (0.14), residues: 1383 loop : 0.03 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.013 0.001 TYR B1067 PHE 0.013 0.001 PHE A 377 TRP 0.010 0.000 TRP A 436 HIS 0.002 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (30098) covalent geometry : angle 0.50027 / 0.25 (41278) SS BOND : bond 0.00241 / 0.14 ( 51) SS BOND : angle 1.17949 / 0.77 ( 102) hydrogen bonds : bond 0.02893 / 1.89 ( 1407) hydrogen bonds : angle 4.89166 / 3.44 ( 3987) link_BETA1-4 : bond 0.00573 / 0.31 ( 18) link_BETA1-4 : angle 1.76492 / 1.20 ( 54) link_NAG-ASN : bond 0.00513 / 0.32 ( 48) link_NAG-ASN : angle 2.32609 / 1.61 ( 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 189 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8317 (m-30) REVERT: A 377 PHE cc_start: 0.7238 (t80) cc_final: 0.5434 (p90) REVERT: A 619 GLU cc_start: 0.7506 (mp0) cc_final: 0.7203 (mp0) REVERT: A 957 GLN cc_start: 0.8512 (tt0) cc_final: 0.8186 (tt0) REVERT: A 1004 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9055 (tt) REVERT: A 1019 ARG cc_start: 0.8810 (tpt170) cc_final: 0.8273 (ttp-170) REVERT: B 133 PHE cc_start: 0.6453 (m-80) cc_final: 0.6122 (t80) REVERT: B 135 PHE cc_start: 0.5097 (OUTLIER) cc_final: 0.4520 (m-80) REVERT: B 326 ILE cc_start: 0.8669 (mm) cc_final: 0.8408 (pt) REVERT: B 619 GLU cc_start: 0.7129 (mp0) cc_final: 0.6741 (mp0) REVERT: B 1019 ARG cc_start: 0.8640 (tpt170) cc_final: 0.8145 (ttm110) REVERT: E 133 PHE cc_start: 0.6790 (m-80) cc_final: 0.5989 (t80) REVERT: E 271 GLN cc_start: 0.8226 (mt0) cc_final: 0.7585 (tt0) REVERT: E 619 GLU cc_start: 0.7322 (mp0) cc_final: 0.7031 (mp0) REVERT: E 674 TYR cc_start: 0.8989 (t80) cc_final: 0.8787 (t80) REVERT: E 900 MET cc_start: 0.8847 (mtp) cc_final: 0.8576 (mtp) REVERT: E 1019 ARG cc_start: 0.8627 (tpt170) cc_final: 0.8156 (ttp-110) outliers start: 37 outliers final: 31 residues processed: 182 average time/residue: 0.1458 time to fit residues: 45.4812 Evaluate side-chains 181 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 131 CYS 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 560 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET 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 47 VAL 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 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 131 CYS 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 560 LEU 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 1017 GLU Chi-restraints excluded: chain E residue 1130 ILE 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: 5.9990 chunk 245 optimal weight: 40.0000 chunk 139 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 262 optimal weight: 40.0000 chunk 361 optimal weight: 1.9990 chunk 299 optimal weight: 0.4980 chunk 293 optimal weight: 0.0980 chunk 206 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 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 = 0.4237 r_free = 0.4237 target = 0.165564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.104198 restraints weight = 50902.266| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.01 r_work: 0.3123 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30215 Z= 0.185 Angle : 0.562 15.352 41578 Z= 0.274 Chirality : 0.045 0.381 5148 Planarity : 0.004 0.041 5427 Dihedral : 3.836 21.062 4413 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.90 % Allowed : 11.67 % Favored : 86.43 % 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: 0.77 (0.13), residues: 4194 helix: 1.40 (0.20), residues: 747 sheet: 0.86 (0.14), residues: 1374 loop : 0.01 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.017 0.001 TYR B1067 PHE 0.015 0.002 PHE B 140 TRP 0.010 0.001 TRP A 436 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 (30098) covalent geometry : angle 0.54023 / 0.27 (41278) SS BOND : bond 0.00337 / 0.20 ( 51) SS BOND : angle 1.28301 / 0.86 ( 102) hydrogen bonds : bond 0.03268 / 2.16 ( 1407) hydrogen bonds : angle 4.96592 / 3.49 ( 3987) link_BETA1-4 : bond 0.00536 / 0.27 ( 18) link_BETA1-4 : angle 1.73704 / 1.19 ( 54) link_NAG-ASN : bond 0.00492 / 0.31 ( 48) link_NAG-ASN : angle 2.31816 / 1.61 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7899.94 seconds wall clock time: 135 minutes 7.71 seconds (8107.71 seconds total)