Starting phenix.real_space_refine on Mon Jul 6 21:36:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x6u_33027/07_2026/7x6u_33027.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x6u_33027/07_2026/7x6u_33027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x6u_33027/07_2026/7x6u_33027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x6u_33027/07_2026/7x6u_33027.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x6u_33027/07_2026/7x6u_33027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x6u_33027/07_2026/7x6u_33027.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7x6u_33027/07_2026/7x6u_33027.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x6u_33027/07_2026/7x6u_33027.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 426 5.16 5 C 24384 2.51 5 N 6852 2.21 5 O 7662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 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: 39324 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3342 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 23, 'TRANS': 431} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3145 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'ASP:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "C" 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: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "E" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3342 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 23, 'TRANS': 431} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "F" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3145 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'ASP:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "G" 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: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "I" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3342 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 23, 'TRANS': 431} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "J" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3145 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'ASP:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "K" 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: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3342 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 23, 'TRANS': 431} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "N" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3145 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'ASP:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 56 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "Q" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3342 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 23, 'TRANS': 431} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "R" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3145 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'ASP:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 56 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "U" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3342 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 23, 'TRANS': 431} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "V" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3145 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'ASP:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 56 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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 Time building chain proxies: 7.89, per 1000 atoms: 0.20 Number of scatterers: 39324 At special positions: 0 Unit cell: (196.56, 201.96, 197.64, 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 426 16.00 O 7662 8.00 N 6852 7.00 C 24384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=126, symmetry=0 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 49 " distance=2.03 Simple disulfide: pdb=" SG CYS A 143 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 327 " distance=2.03 Simple disulfide: pdb=" SG CYS A 206 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 258 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 280 " distance=2.04 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 1 " - pdb=" SG CYS B 42 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 24 " distance=2.03 Simple disulfide: pdb=" SG CYS B 67 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 279 " distance=2.02 Simple disulfide: pdb=" SG CYS B 88 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 125 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.02 Simple disulfide: pdb=" SG CYS B 247 " - pdb=" SG CYS B 261 " distance=2.06 Simple disulfide: pdb=" SG CYS B 346 " - pdb=" SG CYS B 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 356 " - pdb=" SG CYS B 359 " distance=2.02 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS E 26 " - pdb=" SG CYS E 49 " distance=2.03 Simple disulfide: pdb=" SG CYS E 143 " - pdb=" SG CYS E 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 180 " - pdb=" SG CYS E 327 " distance=2.03 Simple disulfide: pdb=" SG CYS E 206 " - pdb=" SG CYS E 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 258 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 266 " - pdb=" SG CYS E 303 " distance=2.03 Simple disulfide: pdb=" SG CYS E 274 " - pdb=" SG CYS E 280 " distance=2.03 Simple disulfide: pdb=" SG CYS E 287 " - pdb=" SG CYS E 292 " distance=2.03 Simple disulfide: pdb=" SG CYS F 1 " - pdb=" SG CYS F 42 " distance=2.03 Simple disulfide: pdb=" SG CYS F 14 " - pdb=" SG CYS F 24 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 163 " distance=2.03 Simple disulfide: pdb=" SG CYS F 82 " - pdb=" SG CYS F 279 " distance=2.02 Simple disulfide: pdb=" SG CYS F 88 " - pdb=" SG CYS F 136 " distance=2.03 Simple disulfide: pdb=" SG CYS F 94 " - pdb=" SG CYS F 143 " distance=2.03 Simple disulfide: pdb=" SG CYS F 98 " - pdb=" SG CYS F 125 " distance=2.03 Simple disulfide: pdb=" SG CYS F 129 " - pdb=" SG CYS F 134 " distance=2.03 Simple disulfide: pdb=" SG CYS F 216 " - pdb=" SG CYS F 231 " distance=2.02 Simple disulfide: pdb=" SG CYS F 247 " - pdb=" SG CYS F 261 " distance=2.06 Simple disulfide: pdb=" SG CYS F 346 " - pdb=" SG CYS F 416 " distance=2.03 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F 359 " distance=2.02 Simple disulfide: pdb=" SG CYS F 381 " - pdb=" SG CYS F 412 " distance=2.03 Simple disulfide: pdb=" SG CYS I 26 " - pdb=" SG CYS I 49 " distance=2.03 Simple disulfide: pdb=" SG CYS I 143 " - pdb=" SG CYS I 156 " distance=2.03 Simple disulfide: pdb=" SG CYS I 180 " - pdb=" SG CYS I 327 " distance=2.03 Simple disulfide: pdb=" SG CYS I 206 " - pdb=" SG CYS I 216 " distance=2.03 Simple disulfide: pdb=" SG CYS I 258 " - pdb=" SG CYS I 305 " distance=2.03 Simple disulfide: pdb=" SG CYS I 266 " - pdb=" SG CYS I 303 " distance=2.03 Simple disulfide: pdb=" SG CYS I 274 " - pdb=" SG CYS I 280 " distance=2.04 Simple disulfide: pdb=" SG CYS I 287 " - pdb=" SG CYS I 292 " distance=2.03 Simple disulfide: pdb=" SG CYS J 1 " - pdb=" SG CYS J 42 " distance=2.03 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS J 24 " distance=2.03 Simple disulfide: pdb=" SG CYS J 67 " - pdb=" SG CYS J 163 " distance=2.03 Simple disulfide: pdb=" SG CYS J 82 " - pdb=" SG CYS J 279 " distance=2.02 Simple disulfide: pdb=" SG CYS J 88 " - pdb=" SG CYS J 136 " distance=2.03 Simple disulfide: pdb=" SG CYS J 94 " - pdb=" SG CYS J 143 " distance=2.03 Simple disulfide: pdb=" SG CYS J 98 " - pdb=" SG CYS J 125 " distance=2.03 Simple disulfide: pdb=" SG CYS J 129 " - pdb=" SG CYS J 134 " distance=2.03 Simple disulfide: pdb=" SG CYS J 216 " - pdb=" SG CYS J 231 " distance=2.02 Simple disulfide: pdb=" SG CYS J 247 " - pdb=" SG CYS J 261 " distance=2.06 Simple disulfide: pdb=" SG CYS J 346 " - pdb=" SG CYS J 416 " distance=2.03 Simple disulfide: pdb=" SG CYS J 356 " - pdb=" SG CYS J 359 " distance=2.02 Simple disulfide: pdb=" SG CYS J 381 " - pdb=" SG CYS J 412 " distance=2.03 Simple disulfide: pdb=" SG CYS M 26 " - pdb=" SG CYS M 49 " distance=2.03 Simple disulfide: pdb=" SG CYS M 143 " - pdb=" SG CYS M 156 " distance=2.03 Simple disulfide: pdb=" SG CYS M 180 " - pdb=" SG CYS M 327 " distance=2.03 Simple disulfide: pdb=" SG CYS M 206 " - pdb=" SG CYS M 216 " distance=2.03 Simple disulfide: pdb=" SG CYS M 258 " - pdb=" SG CYS M 305 " distance=2.03 Simple disulfide: pdb=" SG CYS M 266 " - pdb=" SG CYS M 303 " distance=2.03 Simple disulfide: pdb=" SG CYS M 274 " - pdb=" SG CYS M 280 " distance=2.04 Simple disulfide: pdb=" SG CYS M 287 " - pdb=" SG CYS M 292 " distance=2.03 Simple disulfide: pdb=" SG CYS N 1 " - pdb=" SG CYS N 42 " distance=2.03 Simple disulfide: pdb=" SG CYS N 14 " - pdb=" SG CYS N 24 " distance=2.03 Simple disulfide: pdb=" SG CYS N 67 " - pdb=" SG CYS N 163 " distance=2.03 Simple disulfide: pdb=" SG CYS N 82 " - pdb=" SG CYS N 279 " distance=2.02 Simple disulfide: pdb=" SG CYS N 88 " - pdb=" SG CYS N 136 " distance=2.03 Simple disulfide: pdb=" SG CYS N 94 " - pdb=" SG CYS N 143 " distance=2.03 Simple disulfide: pdb=" SG CYS N 98 " - pdb=" SG CYS N 125 " distance=2.03 Simple disulfide: pdb=" SG CYS N 129 " - pdb=" SG CYS N 134 " distance=2.03 Simple disulfide: pdb=" SG CYS N 216 " - pdb=" SG CYS N 231 " distance=2.02 Simple disulfide: pdb=" SG CYS N 247 " - pdb=" SG CYS N 261 " distance=2.06 Simple disulfide: pdb=" SG CYS N 346 " - pdb=" SG CYS N 416 " distance=2.03 Simple disulfide: pdb=" SG CYS N 356 " - pdb=" SG CYS N 359 " distance=2.02 Simple disulfide: pdb=" SG CYS N 381 " - pdb=" SG CYS N 412 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 26 " - pdb=" SG CYS Q 49 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 143 " - pdb=" SG CYS Q 156 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 180 " - pdb=" SG CYS Q 327 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 206 " - pdb=" SG CYS Q 216 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 258 " - pdb=" SG CYS Q 305 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 266 " - pdb=" SG CYS Q 303 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 274 " - pdb=" SG CYS Q 280 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 287 " - pdb=" SG CYS Q 292 " distance=2.03 Simple disulfide: pdb=" SG CYS R 1 " - pdb=" SG CYS R 42 " distance=2.03 Simple disulfide: pdb=" SG CYS R 14 " - pdb=" SG CYS R 24 " distance=2.03 Simple disulfide: pdb=" SG CYS R 67 " - pdb=" SG CYS R 163 " distance=2.03 Simple disulfide: pdb=" SG CYS R 82 " - pdb=" SG CYS R 279 " distance=2.02 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 136 " distance=2.03 Simple disulfide: pdb=" SG CYS R 94 " - pdb=" SG CYS R 143 " distance=2.03 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 125 " distance=2.03 Simple disulfide: pdb=" SG CYS R 129 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 216 " - pdb=" SG CYS R 231 " distance=2.02 Simple disulfide: pdb=" SG CYS R 247 " - pdb=" SG CYS R 261 " distance=2.06 Simple disulfide: pdb=" SG CYS R 346 " - pdb=" SG CYS R 416 " distance=2.03 Simple disulfide: pdb=" SG CYS R 356 " - pdb=" SG CYS R 359 " distance=2.02 Simple disulfide: pdb=" SG CYS R 381 " - pdb=" SG CYS R 412 " distance=2.03 Simple disulfide: pdb=" SG CYS U 26 " - pdb=" SG CYS U 49 " distance=2.03 Simple disulfide: pdb=" SG CYS U 143 " - pdb=" SG CYS U 156 " distance=2.03 Simple disulfide: pdb=" SG CYS U 180 " - pdb=" SG CYS U 327 " distance=2.03 Simple disulfide: pdb=" SG CYS U 206 " - pdb=" SG CYS U 216 " distance=2.03 Simple disulfide: pdb=" SG CYS U 258 " - pdb=" SG CYS U 305 " distance=2.03 Simple disulfide: pdb=" SG CYS U 266 " - pdb=" SG CYS U 303 " distance=2.03 Simple disulfide: pdb=" SG CYS U 274 " - pdb=" SG CYS U 280 " distance=2.04 Simple disulfide: pdb=" SG CYS U 287 " - pdb=" SG CYS U 292 " distance=2.03 Simple disulfide: pdb=" SG CYS V 1 " - pdb=" SG CYS V 42 " distance=2.03 Simple disulfide: pdb=" SG CYS V 14 " - pdb=" SG CYS V 24 " distance=2.03 Simple disulfide: pdb=" SG CYS V 67 " - pdb=" SG CYS V 163 " distance=2.03 Simple disulfide: pdb=" SG CYS V 82 " - pdb=" SG CYS V 279 " distance=2.02 Simple disulfide: pdb=" SG CYS V 88 " - pdb=" SG CYS V 136 " distance=2.03 Simple disulfide: pdb=" SG CYS V 94 " - pdb=" SG CYS V 143 " distance=2.03 Simple disulfide: pdb=" SG CYS V 98 " - pdb=" SG CYS V 125 " distance=2.03 Simple disulfide: pdb=" SG CYS V 129 " - pdb=" SG CYS V 134 " distance=2.03 Simple disulfide: pdb=" SG CYS V 216 " - pdb=" SG CYS V 231 " distance=2.02 Simple disulfide: pdb=" SG CYS V 247 " - pdb=" SG CYS V 261 " distance=2.06 Simple disulfide: pdb=" SG CYS V 346 " - pdb=" SG CYS V 416 " distance=2.03 Simple disulfide: pdb=" SG CYS V 356 " - pdb=" SG CYS V 359 " distance=2.02 Simple disulfide: pdb=" SG CYS V 381 " - pdb=" SG CYS V 412 " 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=25, symmetry=0 Links applied ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG H 2 " - " MAN H 3 " " NAG L 2 " - " MAN L 3 " " NAG P 2 " - " MAN P 3 " " NAG T 2 " - " MAN T 3 " " NAG X 2 " - " MAN X 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG D 1 " - " ASN A 63 " " NAG H 1 " - " ASN E 63 " " NAG L 1 " - " ASN I 63 " " NAG P 1 " - " ASN M 63 " " NAG T 1 " - " ASN Q 63 " " NAG X 1 " - " ASN U 63 " TRANS " LEU A 155 " - " GLU E 297 " " ALA E 298 " - " GLU A 154 " " SER E 299 " - " LEU A 155 " " ALA M 298 " - " GLU I 154 " " LEU Q 155 " - " GLU U 297 " " ALA U 298 " - " GLU Q 154 " Number of additional bonds: simple=25, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.68 Conformation dependent library (CDL) restraints added in 1.6 seconds 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9624 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 96 sheets defined 13.6% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 43 through 53 removed outlier: 3.986A pdb=" N LYS A 47 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 48 " --> pdb=" O TYR A 44 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N CYS A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 64 removed outlier: 3.858A pdb=" N SER A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 97 through 102 removed outlier: 3.583A pdb=" N ASP A 102 " --> pdb=" O CYS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.521A pdb=" N PHE A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 Processing helix chain 'A' and resid 451 through 457 removed outlier: 3.981A pdb=" N PHE A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 476 removed outlier: 3.534A pdb=" N TYR A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 438 through 448 removed outlier: 3.982A pdb=" N TYR B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET B 443 " --> pdb=" O ASP B 439 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER B 448 " --> pdb=" O GLN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 456 removed outlier: 3.965A pdb=" N ASN B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 467 removed outlier: 3.569A pdb=" N THR B 460 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN B 464 " --> pdb=" O THR B 460 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 53 removed outlier: 3.987A pdb=" N LYS E 47 " --> pdb=" O GLY E 43 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE E 48 " --> pdb=" O TYR E 44 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N CYS E 49 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN E 50 " --> pdb=" O GLU E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 64 removed outlier: 3.858A pdb=" N SER E 58 " --> pdb=" O LEU E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 92 Processing helix chain 'E' and resid 97 through 102 removed outlier: 3.582A pdb=" N ASP E 102 " --> pdb=" O CYS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.521A pdb=" N PHE E 202 " --> pdb=" O SER E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 274 Processing helix chain 'E' and resid 451 through 457 removed outlier: 3.980A pdb=" N PHE E 455 " --> pdb=" O LYS E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 476 removed outlier: 3.534A pdb=" N TYR E 464 " --> pdb=" O ILE E 460 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU E 467 " --> pdb=" O GLY E 463 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 470 " --> pdb=" O GLY E 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 253 Processing helix chain 'F' and resid 438 through 448 removed outlier: 3.982A pdb=" N TYR F 442 " --> pdb=" O VAL F 438 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET F 443 " --> pdb=" O ASP F 439 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER F 448 " --> pdb=" O GLN F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 456 removed outlier: 3.965A pdb=" N ASN F 455 " --> pdb=" O PRO F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 467 removed outlier: 3.569A pdb=" N THR F 460 " --> pdb=" O ILE F 456 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN F 464 " --> pdb=" O THR F 460 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE F 467 " --> pdb=" O LEU F 463 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 53 removed outlier: 3.986A pdb=" N LYS I 47 " --> pdb=" O GLY I 43 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE I 48 " --> pdb=" O TYR I 44 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N CYS I 49 " --> pdb=" O SER I 45 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN I 50 " --> pdb=" O GLU I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 64 removed outlier: 3.858A pdb=" N SER I 58 " --> pdb=" O LEU I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 92 Processing helix chain 'I' and resid 97 through 102 removed outlier: 3.583A pdb=" N ASP I 102 " --> pdb=" O CYS I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 163 Processing helix chain 'I' and resid 187 through 202 removed outlier: 3.521A pdb=" N PHE I 202 " --> pdb=" O SER I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 274 Processing helix chain 'I' and resid 451 through 457 removed outlier: 3.981A pdb=" N PHE I 455 " --> pdb=" O LYS I 451 " (cutoff:3.500A) Processing helix chain 'I' and resid 460 through 476 removed outlier: 3.533A pdb=" N TYR I 464 " --> pdb=" O ILE I 460 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU I 467 " --> pdb=" O GLY I 463 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU I 470 " --> pdb=" O GLY I 466 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 253 Processing helix chain 'J' and resid 438 through 448 removed outlier: 3.982A pdb=" N TYR J 442 " --> pdb=" O VAL J 438 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET J 443 " --> pdb=" O ASP J 439 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER J 448 " --> pdb=" O GLN J 444 " (cutoff:3.500A) Processing helix chain 'J' and resid 450 through 456 removed outlier: 3.965A pdb=" N ASN J 455 " --> pdb=" O PRO J 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 456 through 467 removed outlier: 3.568A pdb=" N THR J 460 " --> pdb=" O ILE J 456 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN J 464 " --> pdb=" O THR J 460 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE J 467 " --> pdb=" O LEU J 463 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 53 removed outlier: 3.987A pdb=" N LYS M 47 " --> pdb=" O GLY M 43 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE M 48 " --> pdb=" O TYR M 44 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N CYS M 49 " --> pdb=" O SER M 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN M 50 " --> pdb=" O GLU M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 64 removed outlier: 3.857A pdb=" N SER M 58 " --> pdb=" O LEU M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 92 Processing helix chain 'M' and resid 97 through 102 removed outlier: 3.583A pdb=" N ASP M 102 " --> pdb=" O CYS M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 163 Processing helix chain 'M' and resid 187 through 202 removed outlier: 3.521A pdb=" N PHE M 202 " --> pdb=" O SER M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 267 through 274 Processing helix chain 'M' and resid 451 through 457 removed outlier: 3.980A pdb=" N PHE M 455 " --> pdb=" O LYS M 451 " (cutoff:3.500A) Processing helix chain 'M' and resid 460 through 476 removed outlier: 3.535A pdb=" N TYR M 464 " --> pdb=" O ILE M 460 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU M 467 " --> pdb=" O GLY M 463 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU M 470 " --> pdb=" O GLY M 466 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 253 Processing helix chain 'N' and resid 438 through 448 removed outlier: 3.982A pdb=" N TYR N 442 " --> pdb=" O VAL N 438 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET N 443 " --> pdb=" O ASP N 439 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER N 448 " --> pdb=" O GLN N 444 " (cutoff:3.500A) Processing helix chain 'N' and resid 450 through 456 removed outlier: 3.965A pdb=" N ASN N 455 " --> pdb=" O PRO N 451 " (cutoff:3.500A) Processing helix chain 'N' and resid 456 through 467 removed outlier: 3.568A pdb=" N THR N 460 " --> pdb=" O ILE N 456 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN N 464 " --> pdb=" O THR N 460 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE N 467 " --> pdb=" O LEU N 463 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 53 removed outlier: 3.987A pdb=" N LYS Q 47 " --> pdb=" O GLY Q 43 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE Q 48 " --> pdb=" O TYR Q 44 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N CYS Q 49 " --> pdb=" O SER Q 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN Q 50 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 64 removed outlier: 3.858A pdb=" N SER Q 58 " --> pdb=" O LEU Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 92 Processing helix chain 'Q' and resid 97 through 102 removed outlier: 3.583A pdb=" N ASP Q 102 " --> pdb=" O CYS Q 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 163 Processing helix chain 'Q' and resid 187 through 202 removed outlier: 3.521A pdb=" N PHE Q 202 " --> pdb=" O SER Q 198 " (cutoff:3.500A) Processing helix chain 'Q' and resid 267 through 274 Processing helix chain 'Q' and resid 451 through 457 removed outlier: 3.981A pdb=" N PHE Q 455 " --> pdb=" O LYS Q 451 " (cutoff:3.500A) Processing helix chain 'Q' and resid 460 through 476 removed outlier: 3.534A pdb=" N TYR Q 464 " --> pdb=" O ILE Q 460 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU Q 467 " --> pdb=" O GLY Q 463 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU Q 470 " --> pdb=" O GLY Q 466 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 253 Processing helix chain 'R' and resid 438 through 448 removed outlier: 3.983A pdb=" N TYR R 442 " --> pdb=" O VAL R 438 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET R 443 " --> pdb=" O ASP R 439 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER R 448 " --> pdb=" O GLN R 444 " (cutoff:3.500A) Processing helix chain 'R' and resid 450 through 456 removed outlier: 3.965A pdb=" N ASN R 455 " --> pdb=" O PRO R 451 " (cutoff:3.500A) Processing helix chain 'R' and resid 456 through 467 removed outlier: 3.569A pdb=" N THR R 460 " --> pdb=" O ILE R 456 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN R 464 " --> pdb=" O THR R 460 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE R 467 " --> pdb=" O LEU R 463 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 53 removed outlier: 3.986A pdb=" N LYS U 47 " --> pdb=" O GLY U 43 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE U 48 " --> pdb=" O TYR U 44 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N CYS U 49 " --> pdb=" O SER U 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN U 50 " --> pdb=" O GLU U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 64 removed outlier: 3.858A pdb=" N SER U 58 " --> pdb=" O LEU U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 92 Processing helix chain 'U' and resid 97 through 102 removed outlier: 3.584A pdb=" N ASP U 102 " --> pdb=" O CYS U 99 " (cutoff:3.500A) Processing helix chain 'U' and resid 160 through 163 Processing helix chain 'U' and resid 187 through 202 removed outlier: 3.520A pdb=" N PHE U 202 " --> pdb=" O SER U 198 " (cutoff:3.500A) Processing helix chain 'U' and resid 267 through 274 Processing helix chain 'U' and resid 451 through 457 removed outlier: 3.981A pdb=" N PHE U 455 " --> pdb=" O LYS U 451 " (cutoff:3.500A) Processing helix chain 'U' and resid 460 through 476 removed outlier: 3.534A pdb=" N TYR U 464 " --> pdb=" O ILE U 460 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU U 467 " --> pdb=" O GLY U 463 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU U 470 " --> pdb=" O GLY U 466 " (cutoff:3.500A) Processing helix chain 'V' and resid 249 through 253 Processing helix chain 'V' and resid 438 through 448 removed outlier: 3.981A pdb=" N TYR V 442 " --> pdb=" O VAL V 438 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET V 443 " --> pdb=" O ASP V 439 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER V 448 " --> pdb=" O GLN V 444 " (cutoff:3.500A) Processing helix chain 'V' and resid 450 through 456 removed outlier: 3.965A pdb=" N ASN V 455 " --> pdb=" O PRO V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 456 through 467 removed outlier: 3.569A pdb=" N THR V 460 " --> pdb=" O ILE V 456 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN V 464 " --> pdb=" O THR V 460 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE V 467 " --> pdb=" O LEU V 463 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 109 through 110 removed outlier: 3.665A pdb=" N TRP A 141 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE A 130 " --> pdb=" O TRP A 141 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 129 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 147 through 148 Processing sheet with id=3, first strand: chain 'A' and resid 177 through 180 removed outlier: 3.886A pdb=" N CYS A 327 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER A 331 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL A 227 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA A 228 " --> pdb=" O MET A 240 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 240 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 238 " --> pdb=" O MET A 230 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 207 through 208 Processing sheet with id=5, first strand: chain 'A' and resid 244 through 248 Processing sheet with id=6, first strand: chain 'A' and resid 257 through 259 removed outlier: 3.644A pdb=" N TYR A 259 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 304 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 352 through 353 Processing sheet with id=8, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.792A pdb=" N GLY B 28 " --> pdb=" O ARG B 325 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 322 " --> pdb=" O TYR B 202 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'B' and resid 40 through 41 removed outlier: 6.382A pdb=" N VAL B 171 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE B 63 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER B 169 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU B 65 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL B 167 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE B 172 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE B 184 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.546A pdb=" N TRP B 158 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 219 " --> pdb=" O LYS B 159 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 229 " --> pdb=" O CYS B 216 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 79 through 81 Processing sheet with id=12, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=13, first strand: chain 'B' and resid 268 through 271 Processing sheet with id=14, first strand: chain 'B' and resid 346 through 347 removed outlier: 3.541A pdb=" N THR B 347 " --> pdb=" O HIS B 370 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS B 370 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N SER B 366 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'B' and resid 346 through 347 removed outlier: 3.541A pdb=" N THR B 347 " --> pdb=" O HIS B 370 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS B 370 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE B 367 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'B' and resid 375 through 376 removed outlier: 3.857A pdb=" N SER B 375 " --> pdb=" O GLU B 392 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'E' and resid 109 through 110 removed outlier: 3.665A pdb=" N TRP E 141 " --> pdb=" O PHE E 130 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE E 130 " --> pdb=" O TRP E 141 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU E 129 " --> pdb=" O LEU E 173 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'E' and resid 147 through 148 Processing sheet with id=19, first strand: chain 'E' and resid 177 through 180 removed outlier: 3.886A pdb=" N CYS E 327 " --> pdb=" O ASP E 231 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER E 331 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL E 227 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA E 228 " --> pdb=" O MET E 240 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET E 240 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE E 238 " --> pdb=" O MET E 230 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'E' and resid 207 through 208 Processing sheet with id=21, first strand: chain 'E' and resid 244 through 248 Processing sheet with id=22, first strand: chain 'E' and resid 257 through 259 removed outlier: 3.645A pdb=" N TYR E 259 " --> pdb=" O ARG E 304 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG E 304 " --> pdb=" O TYR E 259 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 352 through 353 Processing sheet with id=24, first strand: chain 'F' and resid 28 through 29 removed outlier: 3.793A pdb=" N GLY F 28 " --> pdb=" O ARG F 325 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR F 322 " --> pdb=" O TYR F 202 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'F' and resid 40 through 41 removed outlier: 6.382A pdb=" N VAL F 171 " --> pdb=" O LYS F 61 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE F 63 " --> pdb=" O SER F 169 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER F 169 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU F 65 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL F 167 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE F 172 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE F 184 " --> pdb=" O ILE F 172 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'F' and resid 73 through 75 removed outlier: 3.546A pdb=" N TRP F 158 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU F 219 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA F 229 " --> pdb=" O CYS F 216 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'F' and resid 79 through 81 Processing sheet with id=28, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=29, first strand: chain 'F' and resid 268 through 271 Processing sheet with id=30, first strand: chain 'F' and resid 346 through 347 removed outlier: 3.542A pdb=" N THR F 347 " --> pdb=" O HIS F 370 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS F 370 " --> pdb=" O THR F 347 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N SER F 366 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'F' and resid 346 through 347 removed outlier: 3.542A pdb=" N THR F 347 " --> pdb=" O HIS F 370 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS F 370 " --> pdb=" O THR F 347 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE F 367 " --> pdb=" O VAL F 399 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'F' and resid 375 through 376 removed outlier: 3.858A pdb=" N SER F 375 " --> pdb=" O GLU F 392 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'I' and resid 109 through 110 removed outlier: 3.665A pdb=" N TRP I 141 " --> pdb=" O PHE I 130 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE I 130 " --> pdb=" O TRP I 141 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU I 129 " --> pdb=" O LEU I 173 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'I' and resid 147 through 148 Processing sheet with id=35, first strand: chain 'I' and resid 177 through 180 removed outlier: 3.885A pdb=" N CYS I 327 " --> pdb=" O ASP I 231 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER I 331 " --> pdb=" O VAL I 227 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL I 227 " --> pdb=" O SER I 331 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA I 228 " --> pdb=" O MET I 240 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET I 240 " --> pdb=" O ALA I 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE I 238 " --> pdb=" O MET I 230 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'I' and resid 207 through 208 Processing sheet with id=37, first strand: chain 'I' and resid 244 through 248 Processing sheet with id=38, first strand: chain 'I' and resid 257 through 259 removed outlier: 3.644A pdb=" N TYR I 259 " --> pdb=" O ARG I 304 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG I 304 " --> pdb=" O TYR I 259 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'I' and resid 352 through 353 Processing sheet with id=40, first strand: chain 'J' and resid 28 through 29 removed outlier: 3.793A pdb=" N GLY J 28 " --> pdb=" O ARG J 325 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR J 322 " --> pdb=" O TYR J 202 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'J' and resid 40 through 41 removed outlier: 6.382A pdb=" N VAL J 171 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE J 63 " --> pdb=" O SER J 169 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N SER J 169 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU J 65 " --> pdb=" O VAL J 167 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL J 167 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE J 172 " --> pdb=" O PHE J 184 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE J 184 " --> pdb=" O ILE J 172 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'J' and resid 73 through 75 removed outlier: 3.545A pdb=" N TRP J 158 " --> pdb=" O VAL J 75 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU J 219 " --> pdb=" O LYS J 159 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA J 229 " --> pdb=" O CYS J 216 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'J' and resid 79 through 81 Processing sheet with id=44, first strand: chain 'J' and resid 84 through 85 Processing sheet with id=45, first strand: chain 'J' and resid 268 through 271 Processing sheet with id=46, first strand: chain 'J' and resid 346 through 347 removed outlier: 3.541A pdb=" N THR J 347 " --> pdb=" O HIS J 370 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS J 370 " --> pdb=" O THR J 347 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER J 366 " --> pdb=" O THR J 351 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'J' and resid 346 through 347 removed outlier: 3.541A pdb=" N THR J 347 " --> pdb=" O HIS J 370 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS J 370 " --> pdb=" O THR J 347 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE J 367 " --> pdb=" O VAL J 399 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'J' and resid 375 through 376 removed outlier: 3.857A pdb=" N SER J 375 " --> pdb=" O GLU J 392 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'M' and resid 109 through 110 removed outlier: 3.665A pdb=" N TRP M 141 " --> pdb=" O PHE M 130 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE M 130 " --> pdb=" O TRP M 141 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU M 129 " --> pdb=" O LEU M 173 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'M' and resid 147 through 148 Processing sheet with id=51, first strand: chain 'M' and resid 177 through 180 removed outlier: 3.886A pdb=" N CYS M 327 " --> pdb=" O ASP M 231 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER M 331 " --> pdb=" O VAL M 227 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL M 227 " --> pdb=" O SER M 331 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA M 228 " --> pdb=" O MET M 240 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET M 240 " --> pdb=" O ALA M 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE M 238 " --> pdb=" O MET M 230 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'M' and resid 207 through 208 Processing sheet with id=53, first strand: chain 'M' and resid 244 through 248 Processing sheet with id=54, first strand: chain 'M' and resid 257 through 259 removed outlier: 3.644A pdb=" N TYR M 259 " --> pdb=" O ARG M 304 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG M 304 " --> pdb=" O TYR M 259 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'M' and resid 352 through 353 Processing sheet with id=56, first strand: chain 'N' and resid 28 through 29 removed outlier: 3.793A pdb=" N GLY N 28 " --> pdb=" O ARG N 325 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR N 322 " --> pdb=" O TYR N 202 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'N' and resid 40 through 41 removed outlier: 6.382A pdb=" N VAL N 171 " --> pdb=" O LYS N 61 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE N 63 " --> pdb=" O SER N 169 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER N 169 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU N 65 " --> pdb=" O VAL N 167 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL N 167 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE N 172 " --> pdb=" O PHE N 184 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE N 184 " --> pdb=" O ILE N 172 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'N' and resid 73 through 75 removed outlier: 3.545A pdb=" N TRP N 158 " --> pdb=" O VAL N 75 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU N 219 " --> pdb=" O LYS N 159 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA N 229 " --> pdb=" O CYS N 216 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'N' and resid 79 through 81 Processing sheet with id=60, first strand: chain 'N' and resid 84 through 85 Processing sheet with id=61, first strand: chain 'N' and resid 268 through 271 Processing sheet with id=62, first strand: chain 'N' and resid 346 through 347 removed outlier: 3.542A pdb=" N THR N 347 " --> pdb=" O HIS N 370 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS N 370 " --> pdb=" O THR N 347 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N SER N 366 " --> pdb=" O THR N 351 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'N' and resid 346 through 347 removed outlier: 3.542A pdb=" N THR N 347 " --> pdb=" O HIS N 370 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS N 370 " --> pdb=" O THR N 347 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE N 367 " --> pdb=" O VAL N 399 " (cutoff:3.500A) Processing sheet with id=64, first strand: chain 'N' and resid 375 through 376 removed outlier: 3.856A pdb=" N SER N 375 " --> pdb=" O GLU N 392 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'Q' and resid 109 through 110 removed outlier: 3.665A pdb=" N TRP Q 141 " --> pdb=" O PHE Q 130 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE Q 130 " --> pdb=" O TRP Q 141 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU Q 129 " --> pdb=" O LEU Q 173 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'Q' and resid 147 through 148 Processing sheet with id=67, first strand: chain 'Q' and resid 177 through 180 removed outlier: 3.886A pdb=" N CYS Q 327 " --> pdb=" O ASP Q 231 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER Q 331 " --> pdb=" O VAL Q 227 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL Q 227 " --> pdb=" O SER Q 331 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA Q 228 " --> pdb=" O MET Q 240 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET Q 240 " --> pdb=" O ALA Q 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE Q 238 " --> pdb=" O MET Q 230 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'Q' and resid 207 through 208 Processing sheet with id=69, first strand: chain 'Q' and resid 244 through 248 Processing sheet with id=70, first strand: chain 'Q' and resid 257 through 259 removed outlier: 3.643A pdb=" N TYR Q 259 " --> pdb=" O ARG Q 304 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG Q 304 " --> pdb=" O TYR Q 259 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'Q' and resid 352 through 353 Processing sheet with id=72, first strand: chain 'R' and resid 28 through 29 removed outlier: 3.792A pdb=" N GLY R 28 " --> pdb=" O ARG R 325 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR R 322 " --> pdb=" O TYR R 202 " (cutoff:3.500A) Processing sheet with id=73, first strand: chain 'R' and resid 40 through 41 removed outlier: 6.382A pdb=" N VAL R 171 " --> pdb=" O LYS R 61 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE R 63 " --> pdb=" O SER R 169 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER R 169 " --> pdb=" O ILE R 63 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU R 65 " --> pdb=" O VAL R 167 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL R 167 " --> pdb=" O LEU R 65 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE R 172 " --> pdb=" O PHE R 184 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE R 184 " --> pdb=" O ILE R 172 " (cutoff:3.500A) Processing sheet with id=74, first strand: chain 'R' and resid 73 through 75 removed outlier: 3.545A pdb=" N TRP R 158 " --> pdb=" O VAL R 75 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU R 219 " --> pdb=" O LYS R 159 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA R 229 " --> pdb=" O CYS R 216 " (cutoff:3.500A) Processing sheet with id=75, first strand: chain 'R' and resid 79 through 81 Processing sheet with id=76, first strand: chain 'R' and resid 84 through 85 Processing sheet with id=77, first strand: chain 'R' and resid 268 through 271 Processing sheet with id=78, first strand: chain 'R' and resid 346 through 347 removed outlier: 3.542A pdb=" N THR R 347 " --> pdb=" O HIS R 370 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS R 370 " --> pdb=" O THR R 347 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N SER R 366 " --> pdb=" O THR R 351 " (cutoff:3.500A) Processing sheet with id=79, first strand: chain 'R' and resid 346 through 347 removed outlier: 3.542A pdb=" N THR R 347 " --> pdb=" O HIS R 370 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS R 370 " --> pdb=" O THR R 347 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE R 367 " --> pdb=" O VAL R 399 " (cutoff:3.500A) Processing sheet with id=80, first strand: chain 'R' and resid 375 through 376 removed outlier: 3.857A pdb=" N SER R 375 " --> pdb=" O GLU R 392 " (cutoff:3.500A) Processing sheet with id=81, first strand: chain 'U' and resid 109 through 110 removed outlier: 3.665A pdb=" N TRP U 141 " --> pdb=" O PHE U 130 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE U 130 " --> pdb=" O TRP U 141 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU U 129 " --> pdb=" O LEU U 173 " (cutoff:3.500A) Processing sheet with id=82, first strand: chain 'U' and resid 147 through 148 Processing sheet with id=83, first strand: chain 'U' and resid 177 through 180 removed outlier: 3.886A pdb=" N CYS U 327 " --> pdb=" O ASP U 231 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER U 331 " --> pdb=" O VAL U 227 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL U 227 " --> pdb=" O SER U 331 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA U 228 " --> pdb=" O MET U 240 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET U 240 " --> pdb=" O ALA U 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE U 238 " --> pdb=" O MET U 230 " (cutoff:3.500A) Processing sheet with id=84, first strand: chain 'U' and resid 207 through 208 Processing sheet with id=85, first strand: chain 'U' and resid 244 through 248 Processing sheet with id=86, first strand: chain 'U' and resid 257 through 259 removed outlier: 3.644A pdb=" N TYR U 259 " --> pdb=" O ARG U 304 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG U 304 " --> pdb=" O TYR U 259 " (cutoff:3.500A) Processing sheet with id=87, first strand: chain 'U' and resid 352 through 353 Processing sheet with id=88, first strand: chain 'V' and resid 28 through 29 removed outlier: 3.792A pdb=" N GLY V 28 " --> pdb=" O ARG V 325 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR V 322 " --> pdb=" O TYR V 202 " (cutoff:3.500A) Processing sheet with id=89, first strand: chain 'V' and resid 40 through 41 removed outlier: 6.382A pdb=" N VAL V 171 " --> pdb=" O LYS V 61 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE V 63 " --> pdb=" O SER V 169 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER V 169 " --> pdb=" O ILE V 63 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU V 65 " --> pdb=" O VAL V 167 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL V 167 " --> pdb=" O LEU V 65 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE V 172 " --> pdb=" O PHE V 184 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE V 184 " --> pdb=" O ILE V 172 " (cutoff:3.500A) Processing sheet with id=90, first strand: chain 'V' and resid 73 through 75 removed outlier: 3.546A pdb=" N TRP V 158 " --> pdb=" O VAL V 75 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU V 219 " --> pdb=" O LYS V 159 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA V 229 " --> pdb=" O CYS V 216 " (cutoff:3.500A) Processing sheet with id=91, first strand: chain 'V' and resid 79 through 81 Processing sheet with id=92, first strand: chain 'V' and resid 84 through 85 Processing sheet with id=93, first strand: chain 'V' and resid 268 through 271 Processing sheet with id=94, first strand: chain 'V' and resid 346 through 347 removed outlier: 3.540A pdb=" N THR V 347 " --> pdb=" O HIS V 370 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS V 370 " --> pdb=" O THR V 347 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER V 366 " --> pdb=" O THR V 351 " (cutoff:3.500A) Processing sheet with id=95, first strand: chain 'V' and resid 346 through 347 removed outlier: 3.540A pdb=" N THR V 347 " --> pdb=" O HIS V 370 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS V 370 " --> pdb=" O THR V 347 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE V 367 " --> pdb=" O VAL V 399 " (cutoff:3.500A) Processing sheet with id=96, first strand: chain 'V' and resid 375 through 376 removed outlier: 3.857A pdb=" N SER V 375 " --> pdb=" O GLU V 392 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 1728 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: 7.19 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 13062 1.35 - 1.47: 9509 1.47 - 1.59: 17011 1.59 - 1.72: 0 1.72 - 1.84: 540 Bond restraints: 40122 Sorted by residual: bond pdb=" C1 MAN T 3 " pdb=" C2 MAN T 3 " ideal model delta sigma weight residual 1.526 1.578 -0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" C1 MAN D 3 " pdb=" C2 MAN D 3 " ideal model delta sigma weight residual 1.526 1.577 -0.051 2.00e-02 2.50e+03 6.58e+00 bond pdb=" C1 MAN X 3 " pdb=" C2 MAN X 3 " ideal model delta sigma weight residual 1.526 1.577 -0.051 2.00e-02 2.50e+03 6.56e+00 bond pdb=" C1 MAN P 3 " pdb=" C2 MAN P 3 " ideal model delta sigma weight residual 1.526 1.577 -0.051 2.00e-02 2.50e+03 6.48e+00 bond pdb=" C1 MAN H 3 " pdb=" C2 MAN H 3 " ideal model delta sigma weight residual 1.526 1.577 -0.051 2.00e-02 2.50e+03 6.47e+00 ... (remaining 40117 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 53334 2.94 - 5.87: 810 5.87 - 8.81: 108 8.81 - 11.75: 12 11.75 - 14.69: 6 Bond angle restraints: 54270 Sorted by residual: angle pdb=" N PRO U 445 " pdb=" CA PRO U 445 " pdb=" CB PRO U 445 " ideal model delta sigma weight residual 103.36 110.40 -7.04 8.80e-01 1.29e+00 6.40e+01 angle pdb=" N PRO A 445 " pdb=" CA PRO A 445 " pdb=" CB PRO A 445 " ideal model delta sigma weight residual 103.36 110.37 -7.01 8.80e-01 1.29e+00 6.34e+01 angle pdb=" N PRO M 445 " pdb=" CA PRO M 445 " pdb=" CB PRO M 445 " ideal model delta sigma weight residual 103.36 110.35 -6.99 8.80e-01 1.29e+00 6.31e+01 angle pdb=" N PRO Q 445 " pdb=" CA PRO Q 445 " pdb=" CB PRO Q 445 " ideal model delta sigma weight residual 103.36 110.35 -6.99 8.80e-01 1.29e+00 6.31e+01 angle pdb=" N PRO I 445 " pdb=" CA PRO I 445 " pdb=" CB PRO I 445 " ideal model delta sigma weight residual 103.36 110.34 -6.98 8.80e-01 1.29e+00 6.30e+01 ... (remaining 54265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.44: 23269 28.44 - 56.89: 746 56.89 - 85.33: 102 85.33 - 113.77: 1 113.77 - 142.22: 2 Dihedral angle restraints: 24120 sinusoidal: 9084 harmonic: 15036 Sorted by residual: dihedral pdb=" CA LEU A 155 " pdb=" N LEU A 155 " pdb=" C GLU E 297 " pdb=" CA GLU E 297 " ideal model delta harmonic sigma weight residual -180.00 -37.78 -142.22 0 5.00e+00 4.00e-02 8.09e+02 dihedral pdb=" CA LEU Q 155 " pdb=" N LEU Q 155 " pdb=" C GLU U 297 " pdb=" CA GLU U 297 " ideal model delta harmonic sigma weight residual -180.00 -40.16 -139.84 0 5.00e+00 4.00e-02 7.82e+02 dihedral pdb=" CA LEU A 155 " pdb=" C LEU A 155 " pdb=" N SER E 299 " pdb=" CA SER E 299 " ideal model delta harmonic sigma weight residual 180.00 80.43 99.57 0 5.00e+00 4.00e-02 3.97e+02 ... (remaining 24117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4641 0.053 - 0.106: 1134 0.106 - 0.159: 237 0.159 - 0.212: 30 0.212 - 0.265: 36 Chirality restraints: 6078 Sorted by residual: chirality pdb=" CA CYS F 261 " pdb=" N CYS F 261 " pdb=" C CYS F 261 " pdb=" CB CYS F 261 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA CYS B 261 " pdb=" N CYS B 261 " pdb=" C CYS B 261 " pdb=" CB CYS B 261 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA CYS R 261 " pdb=" N CYS R 261 " pdb=" C CYS R 261 " pdb=" CB CYS R 261 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 6075 not shown) Planarity restraints: 7038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N LEU Q 155 " 0.093 2.00e-02 2.50e+03 2.22e-01 4.93e+02 pdb=" CA GLU U 297 " 0.150 2.00e-02 2.50e+03 pdb=" C GLU U 297 " -0.383 2.00e-02 2.50e+03 pdb=" O GLU U 297 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N LEU A 155 " 0.099 2.00e-02 2.50e+03 2.17e-01 4.71e+02 pdb=" CA GLU E 297 " 0.146 2.00e-02 2.50e+03 pdb=" C GLU E 297 " -0.375 2.00e-02 2.50e+03 pdb=" O GLU E 297 " 0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 154 " -0.014 2.00e-02 2.50e+03 2.12e-01 4.49e+02 pdb=" C GLU A 154 " -0.291 2.00e-02 2.50e+03 pdb=" O GLU A 154 " -0.002 2.00e-02 2.50e+03 pdb=" N ALA E 298 " 0.307 2.00e-02 2.50e+03 ... (remaining 7035 not shown) Histogram of nonbonded interaction distances: 0.51 - 1.39: 55 1.39 - 2.26: 371 2.26 - 3.14: 33686 3.14 - 4.02: 96022 4.02 - 4.90: 157485 Warning: very small nonbonded interaction distances. Nonbonded interactions: 287619 Sorted by model distance: nonbonded pdb=" O CYS A 156 " pdb=" OG SER E 299 " model vdw 0.507 3.040 nonbonded pdb=" O CYS Q 156 " pdb=" OG SER U 299 " model vdw 0.517 3.040 nonbonded pdb=" O CYS I 156 " pdb=" OG SER M 299 " model vdw 0.582 3.040 nonbonded pdb=" C LEU I 155 " pdb=" CA SER M 299 " model vdw 0.628 3.700 nonbonded pdb=" O GLU A 154 " pdb=" CA ALA E 298 " model vdw 0.782 2.776 ... (remaining 287614 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'R' selection = chain 'V' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'S' selection = chain 'W' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' selection = chain 'T' selection = chain 'X' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'Q' selection = chain 'U' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'R' selection = chain 'V' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'S' selection = chain 'W' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' selection = chain 'T' selection = chain 'X' } Set refine NCS operators NCS operators will be refined. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.710 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: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 33.530 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 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 : 0.009 0.727 40303 Z= 0.770 Angle : 1.329 83.340 54612 Z= 0.757 Chirality : 0.052 0.265 6078 Planarity : 0.006 0.073 7026 Dihedral : 13.203 78.106 14100 Min Nonbonded Distance : 0.507 Molprobity Statistics. All-atom Clashscore : 29.59 Ramachandran Plot: Outliers : 0.57 % Allowed : 10.09 % Favored : 89.34 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.10), residues: 5280 helix: -0.60 (0.21), residues: 612 sheet: -2.16 (0.14), residues: 1194 loop : -2.84 (0.09), residues: 3474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 380 TYR 0.028 0.002 TYR J 280 PHE 0.031 0.002 PHE E 330 TRP 0.026 0.003 TRP E 174 HIS 0.007 0.002 HIS V 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.22 (40122) covalent geometry : angle 0.94458 / 0.55 (54270) SS BOND : bond 0.00685 / 0.48 ( 126) SS BOND : angle 2.89391 / 2.07 ( 252) hydrogen bonds : bond 0.32560 / 21.87 ( 702) hydrogen bonds : angle 10.12827 / 7.06 ( 1728) Misc. bond : bond 0.23735 / 17.16 ( 25) link_ALPHA1-4 : bond 0.00634 / 0.44 ( 6) link_ALPHA1-4 : angle 2.73883 / 1.76 ( 18) link_BETA1-4 : bond 0.00785 / 0.56 ( 12) link_BETA1-4 : angle 1.70176 / 1.10 ( 36) link_NAG-ASN : bond 0.00028 / 0.02 ( 6) link_NAG-ASN : angle 1.78255 / 1.06 ( 18) link_TRANS : bond 0.50883 / 38.47 ( 6) link_TRANS : angle 50.32494 / 31.73 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8644 (m100) cc_final: 0.8392 (m-10) REVERT: A 96 LEU cc_start: 0.8195 (tt) cc_final: 0.6987 (mp) REVERT: A 103 TRP cc_start: 0.7856 (t-100) cc_final: 0.6537 (t-100) REVERT: A 166 LEU cc_start: 0.6598 (tp) cc_final: 0.6287 (tp) REVERT: A 230 MET cc_start: 0.7901 (ppp) cc_final: 0.7490 (ppp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0519 time to fit residues: 4.5996 Evaluate side-chains 52 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.092 Evaluate side-chains 75 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 ARG cc_start: 0.7873 (mmt90) cc_final: 0.7615 (mmt-90) REVERT: B 270 ILE cc_start: 0.8673 (tp) cc_final: 0.8408 (tp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0577 time to fit residues: 5.3307 Evaluate side-chains 59 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.114 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 8.9990 chunk 430 optimal weight: 6.9990 chunk 41 optimal weight: 0.0070 chunk 265 optimal weight: 8.9990 chunk 523 optimal weight: 10.0000 chunk 497 optimal weight: 0.1980 chunk 414 optimal weight: 10.0000 chunk 310 optimal weight: 7.9990 chunk 488 optimal weight: 10.0000 chunk 366 optimal weight: 0.1980 chunk 223 optimal weight: 0.0970 overall best weight: 1.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN A 199 GLN B 154 HIS B 370 HIS B 411 GLN B 413 GLN ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.142340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.128633 restraints weight = 14116.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.129538 restraints weight = 10579.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.130145 restraints weight = 8432.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.130112 restraints weight = 8161.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.130326 restraints weight = 7482.232| |-----------------------------------------------------------------------------| r_work (final): 0.3925 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.158768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.143651 restraints weight = 10484.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.145888 restraints weight = 6657.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.147448 restraints weight = 4661.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.148412 restraints weight = 3535.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.149293 restraints weight = 2890.955| |-----------------------------------------------------------------------------| r_work (final): 0.4007 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.209466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.201636 restraints weight = 656.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.201634 restraints weight = 689.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.201634 restraints weight = 689.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.201634 restraints weight = 689.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.201634 restraints weight = 689.055| |-----------------------------------------------------------------------------| r_work (final): 0.3574 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.134442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132488 restraints weight = 116.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.133840 restraints weight = 29.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.134179 restraints weight = 7.580 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.134235 restraints weight = 2.177 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.134284 restraints weight = 0.872 | |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5703 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.822 40303 Z= 0.469 Angle : 1.204 68.814 54612 Z= 0.693 Chirality : 0.050 0.256 6078 Planarity : 0.007 0.112 7026 Dihedral : 7.117 57.880 5592 Min Nonbonded Distance : 1.460 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.57 % Allowed : 10.57 % Favored : 88.86 % Rotamer: Outliers : 0.58 % Allowed : 6.12 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -3.41 (0.10), residues: 5280 helix: -0.47 (0.19), residues: 648 sheet: -1.87 (0.14), residues: 1194 loop : -2.95 (0.08), residues: 3438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 29 TYR 0.022 0.002 TYR E 328 PHE 0.032 0.003 PHE V 195 TRP 0.017 0.002 TRP N 149 HIS 0.007 0.001 HIS M 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.28 (40122) covalent geometry : angle 0.88727 / 0.51 (54270) SS BOND : bond 0.00954 / 0.64 ( 126) SS BOND : angle 2.39701 / 1.62 ( 252) hydrogen bonds : bond 0.05005 / 3.33 ( 702) hydrogen bonds : angle 6.99989 / 4.86 ( 1728) Misc. bond : bond 0.05967 / 4.45 ( 25) link_ALPHA1-4 : bond 0.01348 / 0.94 ( 6) link_ALPHA1-4 : angle 2.12999 / 1.43 ( 18) link_BETA1-4 : bond 0.00163 / 0.12 ( 12) link_BETA1-4 : angle 1.34886 / 0.86 ( 36) link_NAG-ASN : bond 0.00022 / 0.02 ( 6) link_NAG-ASN : angle 1.96506 / 1.17 ( 18) link_TRANS : bond 0.39553 / 22.81 ( 6) link_TRANS : angle 43.99452 / 25.49 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8481 (m100) cc_final: 0.8030 (m-90) REVERT: A 96 LEU cc_start: 0.7546 (tt) cc_final: 0.6520 (mp) REVERT: A 166 LEU cc_start: 0.6254 (tp) cc_final: 0.5954 (tp) REVERT: A 183 MET cc_start: 0.8224 (ppp) cc_final: 0.7893 (ppp) REVERT: A 230 MET cc_start: 0.7988 (ppp) cc_final: 0.7646 (ppp) REVERT: A 369 GLU cc_start: 0.6877 (mp0) cc_final: 0.5852 (mp0) outliers start: 2 outliers final: 1 residues processed: 77 average time/residue: 0.0652 time to fit residues: 5.9717 Evaluate side-chains 54 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.113 Evaluate side-chains 77 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 ARG cc_start: 0.8058 (mmt90) cc_final: 0.7444 (mmt180) REVERT: B 225 LYS cc_start: 0.5215 (mmtm) cc_final: 0.4693 (tppt) REVERT: B 245 ILE cc_start: 0.8917 (mm) cc_final: 0.8198 (mm) REVERT: B 246 GLN cc_start: 0.7555 (pm20) cc_final: 0.6724 (pt0) REVERT: B 295 ILE cc_start: 0.8470 (mp) cc_final: 0.8129 (tp) REVERT: B 328 PHE cc_start: 0.8560 (m-80) cc_final: 0.8240 (m-80) outliers start: 2 outliers final: 0 residues processed: 77 average time/residue: 0.0569 time to fit residues: 5.4086 Evaluate side-chains 63 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.085 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 189 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 470 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 489 optimal weight: 8.9990 chunk 362 optimal weight: 6.9990 chunk 256 optimal weight: 4.9990 chunk 445 optimal weight: 0.0970 chunk 177 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 HIS B 370 HIS B 374 ASN B 415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.143882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.129911 restraints weight = 14268.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.131677 restraints weight = 9666.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.132895 restraints weight = 7129.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.133754 restraints weight = 5654.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.134338 restraints weight = 4742.839| |-----------------------------------------------------------------------------| r_work (final): 0.3986 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.162139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.145884 restraints weight = 10300.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.148329 restraints weight = 6399.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.150042 restraints weight = 4441.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.151228 restraints weight = 3353.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.152056 restraints weight = 2710.460| |-----------------------------------------------------------------------------| r_work (final): 0.4044 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.204944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.196666 restraints weight = 603.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.195876 restraints weight = 663.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.195874 restraints weight = 591.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.195873 restraints weight = 591.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.195873 restraints weight = 591.823| |-----------------------------------------------------------------------------| r_work (final): 0.4175 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.137562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.135680 restraints weight = 104.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.137096 restraints weight = 30.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.137336 restraints weight = 8.152 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.137460 restraints weight = 2.216 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.137447 restraints weight = 0.709 | |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5671 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.788 40303 Z= 0.481 Angle : 1.150 63.511 54612 Z= 0.644 Chirality : 0.048 0.193 6078 Planarity : 0.006 0.083 7026 Dihedral : 6.629 33.516 5592 Min Nonbonded Distance : 1.508 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.77 % Favored : 89.77 % Rotamer: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.40 (0.10), residues: 5280 helix: -0.27 (0.20), residues: 648 sheet: -1.88 (0.15), residues: 1032 loop : -2.97 (0.08), residues: 3600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG V 87 TYR 0.013 0.001 TYR E 138 PHE 0.041 0.003 PHE R 107 TRP 0.045 0.003 TRP M 247 HIS 0.008 0.001 HIS U 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.30 (40122) covalent geometry : angle 0.86185 / 0.48 (54270) SS BOND : bond 0.00459 / 0.34 ( 126) SS BOND : angle 2.43891 / 1.69 ( 252) hydrogen bonds : bond 0.04013 / 2.69 ( 702) hydrogen bonds : angle 6.40082 / 4.43 ( 1728) Misc. bond : bond 0.05436 / 4.18 ( 25) link_ALPHA1-4 : bond 0.01551 / 1.09 ( 6) link_ALPHA1-4 : angle 2.19061 / 1.47 ( 18) link_BETA1-4 : bond 0.00309 / 0.23 ( 12) link_BETA1-4 : angle 1.22748 / 0.79 ( 36) link_NAG-ASN : bond 0.00235 / 0.16 ( 6) link_NAG-ASN : angle 1.43038 / 0.87 ( 18) link_TRANS : bond 0.40052 / 24.44 ( 6) link_TRANS : angle 41.01722 / 22.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8382 (m100) cc_final: 0.8144 (m-90) REVERT: A 96 LEU cc_start: 0.7639 (tt) cc_final: 0.6517 (mp) REVERT: A 166 LEU cc_start: 0.6119 (tp) cc_final: 0.5868 (tp) REVERT: A 194 LEU cc_start: 0.9231 (mm) cc_final: 0.8996 (tp) REVERT: A 230 MET cc_start: 0.7991 (ppp) cc_final: 0.7604 (ppp) REVERT: A 318 TYR cc_start: 0.8393 (t80) cc_final: 0.7889 (t80) REVERT: A 369 GLU cc_start: 0.6871 (mp0) cc_final: 0.4954 (mp0) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0718 time to fit residues: 6.2384 Evaluate side-chains 54 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.127 Evaluate side-chains 78 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.6600 (tmt170) cc_final: 0.4744 (pmt-80) REVERT: B 87 ARG cc_start: 0.8290 (mmt90) cc_final: 0.7572 (mmt180) REVERT: B 225 LYS cc_start: 0.4970 (mmtm) cc_final: 0.4599 (tppt) REVERT: B 295 ILE cc_start: 0.8343 (mp) cc_final: 0.8047 (tp) REVERT: B 328 PHE cc_start: 0.8514 (m-80) cc_final: 0.8250 (m-80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0667 time to fit residues: 6.3080 Evaluate side-chains 64 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.081 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0007 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 439 optimal weight: 0.0000 chunk 285 optimal weight: 3.9990 chunk 477 optimal weight: 0.0060 chunk 50 optimal weight: 6.9990 chunk 336 optimal weight: 0.0040 chunk 517 optimal weight: 0.0170 chunk 425 optimal weight: 9.9990 chunk 42 optimal weight: 30.0000 chunk 523 optimal weight: 8.9990 chunk 288 optimal weight: 10.0000 chunk 281 optimal weight: 10.0000 overall best weight: 0.8052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 HIS B 370 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.145849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.131805 restraints weight = 14184.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.133515 restraints weight = 9607.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.134771 restraints weight = 7126.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.135669 restraints weight = 5664.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.136148 restraints weight = 4707.570| |-----------------------------------------------------------------------------| r_work (final): 0.4009 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.164128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.147788 restraints weight = 10272.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.150282 restraints weight = 6294.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.152026 restraints weight = 4330.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.153284 restraints weight = 3242.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.154083 restraints weight = 2599.257| |-----------------------------------------------------------------------------| r_work (final): 0.4067 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.205075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.203735 restraints weight = 52.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.203808 restraints weight = 6.810 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.203808 restraints weight = 0.332 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.203808 restraints weight = 0.332 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.203808 restraints weight = 0.332 | |-----------------------------------------------------------------------------| r_work (final): 0.4261 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.141649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.138793 restraints weight = 110.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.140657 restraints weight = 40.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.141105 restraints weight = 12.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.141260 restraints weight = 3.913 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.141331 restraints weight = 1.413 | |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5603 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.732 40303 Z= 0.478 Angle : 1.096 72.081 54612 Z= 0.602 Chirality : 0.048 0.306 6078 Planarity : 0.006 0.080 7026 Dihedral : 6.321 31.752 5592 Min Nonbonded Distance : 1.417 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.89 % Favored : 89.77 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.32 (0.10), residues: 5280 helix: 0.09 (0.20), residues: 612 sheet: -1.70 (0.15), residues: 1104 loop : -3.01 (0.08), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 304 TYR 0.020 0.001 TYR N 280 PHE 0.022 0.002 PHE J 107 TRP 0.028 0.002 TRP A 247 HIS 0.008 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.30 (40122) covalent geometry : angle 0.82167 / 0.45 (54270) SS BOND : bond 0.00373 / 0.28 ( 126) SS BOND : angle 2.12418 / 1.45 ( 252) hydrogen bonds : bond 0.03168 / 2.12 ( 702) hydrogen bonds : angle 5.95290 / 4.11 ( 1728) Misc. bond : bond 0.05216 / 3.91 ( 25) link_ALPHA1-4 : bond 0.01363 / 0.95 ( 6) link_ALPHA1-4 : angle 2.04793 / 1.35 ( 18) link_BETA1-4 : bond 0.00198 / 0.15 ( 12) link_BETA1-4 : angle 1.15168 / 0.74 ( 36) link_NAG-ASN : bond 0.00189 / 0.13 ( 6) link_NAG-ASN : angle 1.34636 / 0.83 ( 18) link_TRANS : bond 0.40033 / 25.07 ( 6) link_TRANS : angle 39.16663 / 21.04 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.5876 (tp) cc_final: 0.5662 (tp) REVERT: A 230 MET cc_start: 0.7963 (ppp) cc_final: 0.7517 (ppp) REVERT: A 369 GLU cc_start: 0.6844 (mp0) cc_final: 0.6618 (mp0) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0759 time to fit residues: 7.0013 Evaluate side-chains 59 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.082 Evaluate side-chains 85 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 SER cc_start: 0.9122 (p) cc_final: 0.8631 (p) REVERT: B 81 ARG cc_start: 0.6097 (mmm160) cc_final: 0.5623 (ttt180) REVERT: B 86 ARG cc_start: 0.6569 (tmt170) cc_final: 0.4707 (ppt170) REVERT: B 87 ARG cc_start: 0.8299 (mmt90) cc_final: 0.7423 (mmt180) REVERT: B 146 TRP cc_start: 0.8055 (p-90) cc_final: 0.7775 (p90) REVERT: B 225 LYS cc_start: 0.4778 (mmtm) cc_final: 0.4517 (tppt) REVERT: B 328 PHE cc_start: 0.8576 (m-80) cc_final: 0.8294 (m-80) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0700 time to fit residues: 7.0874 Evaluate side-chains 63 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.122 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 341 optimal weight: 1.9990 chunk 181 optimal weight: 30.0000 chunk 317 optimal weight: 10.0000 chunk 464 optimal weight: 2.9990 chunk 352 optimal weight: 30.0000 chunk 424 optimal weight: 7.9990 chunk 410 optimal weight: 20.0000 chunk 85 optimal weight: 0.0030 chunk 182 optimal weight: 6.9990 chunk 159 optimal weight: 0.6980 chunk 254 optimal weight: 5.9990 overall best weight: 2.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN B 370 HIS ** B 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.145396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.131441 restraints weight = 14336.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.132839 restraints weight = 10219.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.134826 restraints weight = 7640.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.134882 restraints weight = 5879.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.134991 restraints weight = 5508.579| |-----------------------------------------------------------------------------| r_work (final): 0.3993 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.163881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.147229 restraints weight = 10288.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.149746 restraints weight = 6351.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.151425 restraints weight = 4383.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.152667 restraints weight = 3309.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.153486 restraints weight = 2677.911| |-----------------------------------------------------------------------------| r_work (final): 0.4066 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.212589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.210668 restraints weight = 462.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.198485 restraints weight = 87.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.199756 restraints weight = 58.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.200198 restraints weight = 49.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.200197 restraints weight = 46.801| |-----------------------------------------------------------------------------| r_work (final): 0.4229 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.141671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.137684 restraints weight = 133.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.140048 restraints weight = 60.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.140979 restraints weight = 28.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.141393 restraints weight = 10.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.141560 restraints weight = 3.949 | |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5701 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.577 40303 Z= 0.410 Angle : 0.907 47.655 54612 Z= 0.491 Chirality : 0.048 0.296 6078 Planarity : 0.006 0.075 7026 Dihedral : 6.027 24.329 5592 Min Nonbonded Distance : 1.245 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.77 % Favored : 90.00 % Rotamer: Outliers : 0.15 % Allowed : 2.92 % Favored : 96.94 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.10), residues: 5280 helix: 0.41 (0.21), residues: 612 sheet: -1.67 (0.15), residues: 990 loop : -2.91 (0.08), residues: 3678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 304 TYR 0.012 0.001 TYR B 280 PHE 0.023 0.002 PHE N 107 TRP 0.027 0.002 TRP N 149 HIS 0.009 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.28 (40122) covalent geometry : angle 0.85200 / 0.47 (54270) SS BOND : bond 0.00421 / 0.33 ( 126) SS BOND : angle 2.09510 / 1.44 ( 252) hydrogen bonds : bond 0.02963 / 1.98 ( 702) hydrogen bonds : angle 5.78854 / 3.99 ( 1728) Misc. bond : bond 0.05258 / 3.95 ( 25) link_ALPHA1-4 : bond 0.01532 / 1.07 ( 6) link_ALPHA1-4 : angle 2.07874 / 1.41 ( 18) link_BETA1-4 : bond 0.00351 / 0.26 ( 12) link_BETA1-4 : angle 1.02118 / 0.66 ( 36) link_NAG-ASN : bond 0.00131 / 0.09 ( 6) link_NAG-ASN : angle 1.20155 / 0.75 ( 18) link_TRANS : bond 0.31068 / 19.11 ( 6) link_TRANS : angle 15.40020 / 7.48 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.6218 (tp) cc_final: 0.5992 (tp) REVERT: A 279 SER cc_start: 0.7622 (m) cc_final: 0.7373 (t) REVERT: A 369 GLU cc_start: 0.6873 (mp0) cc_final: 0.6656 (mp0) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.0578 time to fit residues: 5.4086 Evaluate side-chains 55 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.131 Evaluate side-chains 78 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 SER cc_start: 0.9182 (p) cc_final: 0.8742 (p) REVERT: B 86 ARG cc_start: 0.6606 (tmt170) cc_final: 0.4671 (ppt170) REVERT: B 87 ARG cc_start: 0.8104 (mmt90) cc_final: 0.7428 (mmt180) REVERT: B 146 TRP cc_start: 0.7970 (p-90) cc_final: 0.7730 (p90) REVERT: B 225 LYS cc_start: 0.4819 (mmtm) cc_final: 0.4520 (tppt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0713 time to fit residues: 6.6480 Evaluate side-chains 60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.119 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 204 optimal weight: 0.0010 chunk 146 optimal weight: 10.0000 chunk 130 optimal weight: 0.0060 chunk 315 optimal weight: 0.5980 chunk 241 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 169 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 3 optimal weight: 0.0570 chunk 295 optimal weight: 0.0670 overall best weight: 0.1458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN B 370 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.146846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.132496 restraints weight = 13661.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.134403 restraints weight = 9125.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.135693 restraints weight = 6669.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.136651 restraints weight = 5247.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.137161 restraints weight = 4366.098| |-----------------------------------------------------------------------------| r_work (final): 0.4034 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.181737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.174130 restraints weight = 11870.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.174990 restraints weight = 8910.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.175287 restraints weight = 7147.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.175762 restraints weight = 6213.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.175916 restraints weight = 5543.016| |-----------------------------------------------------------------------------| r_work (final): 0.4128 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.216858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.216772 restraints weight = 46.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.216772 restraints weight = 4.008 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.216772 restraints weight = 4.008 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.216772 restraints weight = 4.008 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.216772 restraints weight = 4.008 | |-----------------------------------------------------------------------------| r_work (final): 0.4447 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.141924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.138241 restraints weight = 128.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.140705 restraints weight = 50.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.141382 restraints weight = 17.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.141760 restraints weight = 7.021 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.141838 restraints weight = 2.391 | |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5603 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.985 40303 Z= 0.877 Angle : 1.096 49.555 54612 Z= 0.561 Chirality : 0.051 0.549 6078 Planarity : 0.007 0.116 7026 Dihedral : 5.911 23.426 5592 Min Nonbonded Distance : 1.357 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.86 % Favored : 90.80 % Rotamer: Outliers : 0.15 % Allowed : 2.77 % Favored : 97.08 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.10), residues: 5280 helix: 0.20 (0.21), residues: 648 sheet: -1.64 (0.14), residues: 1188 loop : -2.91 (0.08), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 87 TYR 0.014 0.001 TYR R 280 PHE 0.041 0.002 PHE E 330 TRP 0.039 0.003 TRP Q 247 HIS 0.015 0.001 HIS M 56 Details of bonding type rmsd/Z covalent geometry : bond 0.01834 / 0.84 (40122) covalent geometry : angle 1.03938 / 0.53 (54270) SS BOND : bond 0.00400 / 0.28 ( 126) SS BOND : angle 2.59004 / 1.77 ( 252) hydrogen bonds : bond 0.03339 / 2.25 ( 702) hydrogen bonds : angle 5.70457 / 3.96 ( 1728) Misc. bond : bond 0.05323 / 4.02 ( 25) link_ALPHA1-4 : bond 0.01275 / 0.89 ( 6) link_ALPHA1-4 : angle 2.11296 / 1.40 ( 18) link_BETA1-4 : bond 0.00025 / 0.02 ( 12) link_BETA1-4 : angle 1.09058 / 0.70 ( 36) link_NAG-ASN : bond 0.00099 / 0.07 ( 6) link_NAG-ASN : angle 1.03123 / 0.66 ( 18) link_TRANS : bond 0.25114 / 13.26 ( 6) link_TRANS : angle 16.93543 / 8.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.6137 (tp) cc_final: 0.5865 (tp) REVERT: A 230 MET cc_start: 0.7946 (ppp) cc_final: 0.7725 (ppp) outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.0582 time to fit residues: 5.1649 Evaluate side-chains 54 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.128 Evaluate side-chains 73 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 SER cc_start: 0.8704 (p) cc_final: 0.8360 (t) REVERT: B 86 ARG cc_start: 0.5440 (tmt170) cc_final: 0.3124 (pmt-80) REVERT: B 87 ARG cc_start: 0.6706 (mmt90) cc_final: 0.6248 (mmt-90) REVERT: B 225 LYS cc_start: 0.4802 (mmtm) cc_final: 0.4469 (tppt) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0766 time to fit residues: 6.7068 Evaluate side-chains 57 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.124 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 148 optimal weight: 6.9990 chunk 356 optimal weight: 0.0070 chunk 429 optimal weight: 0.0030 chunk 222 optimal weight: 6.9990 chunk 135 optimal weight: 0.1980 chunk 419 optimal weight: 9.9990 chunk 116 optimal weight: 0.0970 chunk 287 optimal weight: 0.9990 chunk 378 optimal weight: 0.9980 chunk 239 optimal weight: 5.9990 chunk 360 optimal weight: 20.0000 overall best weight: 0.2606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 370 HIS B 411 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.148071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.133123 restraints weight = 14049.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.135242 restraints weight = 9286.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.136689 restraints weight = 6694.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.137704 restraints weight = 5196.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.138352 restraints weight = 4291.485| |-----------------------------------------------------------------------------| r_work (final): 0.4043 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.169147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.153157 restraints weight = 10471.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.155398 restraints weight = 6629.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.156932 restraints weight = 4654.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.157994 restraints weight = 3577.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.158587 restraints weight = 2954.235| |-----------------------------------------------------------------------------| r_work (final): 0.4119 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.221320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.219015 restraints weight = 45.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.218716 restraints weight = 66.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.218716 restraints weight = 70.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.218716 restraints weight = 70.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.218716 restraints weight = 70.448| |-----------------------------------------------------------------------------| r_work (final): 0.4448 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.139511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.135050 restraints weight = 122.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.137706 restraints weight = 63.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.138669 restraints weight = 29.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.139080 restraints weight = 13.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.139305 restraints weight = 6.238 | |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5608 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.590 40303 Z= 0.328 Angle : 0.902 47.408 54612 Z= 0.452 Chirality : 0.048 0.287 6078 Planarity : 0.007 0.122 7026 Dihedral : 5.782 23.910 5592 Min Nonbonded Distance : 1.413 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.43 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.10), residues: 5280 helix: 0.40 (0.21), residues: 654 sheet: -1.72 (0.15), residues: 1062 loop : -2.89 (0.08), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG V 89 TYR 0.012 0.001 TYR E 138 PHE 0.025 0.002 PHE U 330 TRP 0.043 0.003 TRP A 247 HIS 0.011 0.001 HIS M 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.21 (40122) covalent geometry : angle 0.83458 / 0.42 (54270) SS BOND : bond 0.00397 / 0.29 ( 126) SS BOND : angle 2.48358 / 1.71 ( 252) hydrogen bonds : bond 0.03103 / 2.10 ( 702) hydrogen bonds : angle 5.61068 / 3.90 ( 1728) Misc. bond : bond 0.05223 / 3.76 ( 25) link_ALPHA1-4 : bond 0.01562 / 1.09 ( 6) link_ALPHA1-4 : angle 2.03352 / 1.38 ( 18) link_BETA1-4 : bond 0.00431 / 0.32 ( 12) link_BETA1-4 : angle 1.11388 / 0.72 ( 36) link_NAG-ASN : bond 0.00012 / 0.01 ( 6) link_NAG-ASN : angle 1.08836 / 0.71 ( 18) link_TRANS : bond 0.24363 / 12.36 ( 6) link_TRANS : angle 16.55216 / 8.73 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.7786 (tt) cc_final: 0.7051 (mm) REVERT: A 166 LEU cc_start: 0.6318 (tp) cc_final: 0.6091 (tp) REVERT: A 230 MET cc_start: 0.7989 (ppp) cc_final: 0.7752 (ppp) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0552 time to fit residues: 5.0393 Evaluate side-chains 55 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.139 Evaluate side-chains 71 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LYS cc_start: 0.4214 (mmmt) cc_final: 0.3859 (mmtt) REVERT: B 86 ARG cc_start: 0.6100 (tmt170) cc_final: 0.4390 (ppt170) REVERT: B 87 ARG cc_start: 0.7216 (mmt90) cc_final: 0.6654 (mmt180) REVERT: B 174 LEU cc_start: 0.8361 (tt) cc_final: 0.7785 (tt) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0702 time to fit residues: 6.0499 Evaluate side-chains 53 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.114 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 430 optimal weight: 0.0980 chunk 161 optimal weight: 0.0770 chunk 77 optimal weight: 0.1980 chunk 22 optimal weight: 4.9990 chunk 374 optimal weight: 3.9990 chunk 90 optimal weight: 0.0670 chunk 175 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 260 optimal weight: 0.1980 chunk 248 optimal weight: 0.0770 chunk 226 optimal weight: 0.0870 overall best weight: 0.0812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 HIS B 370 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.150521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.140827 restraints weight = 15170.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.140980 restraints weight = 12337.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.141253 restraints weight = 10202.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.141409 restraints weight = 10055.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.141500 restraints weight = 8912.694| |-----------------------------------------------------------------------------| r_work (final): 0.4059 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.169661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.153527 restraints weight = 10398.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.155783 restraints weight = 6665.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.157265 restraints weight = 4731.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.158254 restraints weight = 3679.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.158776 restraints weight = 3071.809| |-----------------------------------------------------------------------------| r_work (final): 0.4117 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.226751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.224000 restraints weight = 46.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.223981 restraints weight = 0.971 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.223985 restraints weight = 0.512 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.223985 restraints weight = 0.465 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.223985 restraints weight = 0.465 | |-----------------------------------------------------------------------------| r_work (final): 0.4588 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.138191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.133817 restraints weight = 135.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.136456 restraints weight = 59.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.137426 restraints weight = 24.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.137819 restraints weight = 9.953 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.138023 restraints weight = 4.191 | |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.599 40303 Z= 0.317 Angle : 0.881 47.634 54612 Z= 0.439 Chirality : 0.048 0.331 6078 Planarity : 0.005 0.046 7026 Dihedral : 5.530 24.245 5592 Min Nonbonded Distance : 1.435 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.32 % Favored : 90.45 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.10), residues: 5280 helix: 0.48 (0.21), residues: 654 sheet: -1.67 (0.15), residues: 1056 loop : -2.92 (0.08), residues: 3570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 304 TYR 0.015 0.001 TYR F 280 PHE 0.034 0.002 PHE V 107 TRP 0.037 0.003 TRP M 247 HIS 0.010 0.001 HIS M 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.19 (40122) covalent geometry : angle 0.81400 / 0.40 (54270) SS BOND : bond 0.00357 / 0.26 ( 126) SS BOND : angle 2.24113 / 1.55 ( 252) hydrogen bonds : bond 0.02839 / 1.93 ( 702) hydrogen bonds : angle 5.54510 / 3.84 ( 1728) Misc. bond : bond 0.05266 / 3.83 ( 25) link_ALPHA1-4 : bond 0.01197 / 0.84 ( 6) link_ALPHA1-4 : angle 2.01600 / 1.34 ( 18) link_BETA1-4 : bond 0.00089 / 0.07 ( 12) link_BETA1-4 : angle 0.88321 / 0.57 ( 36) link_NAG-ASN : bond 0.00025 / 0.02 ( 6) link_NAG-ASN : angle 1.01674 / 0.69 ( 18) link_TRANS : bond 0.24589 / 12.37 ( 6) link_TRANS : angle 16.81569 / 8.98 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.7787 (tt) cc_final: 0.6984 (mm) REVERT: A 166 LEU cc_start: 0.6392 (tp) cc_final: 0.6159 (tp) REVERT: A 230 MET cc_start: 0.8001 (ppp) cc_final: 0.7768 (ppp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0605 time to fit residues: 5.1933 Evaluate side-chains 59 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.118 Evaluate side-chains 74 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.6458 (tmt170) cc_final: 0.4550 (ppt170) REVERT: B 87 ARG cc_start: 0.6643 (mmt90) cc_final: 0.6349 (mmt180) REVERT: B 127 ASP cc_start: 0.5464 (t70) cc_final: 0.5153 (p0) REVERT: B 174 LEU cc_start: 0.8458 (tt) cc_final: 0.8194 (tt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0752 time to fit residues: 6.7184 Evaluate side-chains 61 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.121 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 212 optimal weight: 0.6980 chunk 468 optimal weight: 0.1980 chunk 176 optimal weight: 20.0000 chunk 282 optimal weight: 0.5980 chunk 164 optimal weight: 4.9990 chunk 317 optimal weight: 9.9990 chunk 210 optimal weight: 7.9990 chunk 259 optimal weight: 0.0980 chunk 201 optimal weight: 5.9990 chunk 524 optimal weight: 0.7980 chunk 357 optimal weight: 20.0000 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 HIS ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.151554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.141028 restraints weight = 15298.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.142120 restraints weight = 11166.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.142740 restraints weight = 8759.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.143368 restraints weight = 7372.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.143696 restraints weight = 6401.301| |-----------------------------------------------------------------------------| r_work (final): 0.4105 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.169875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.152366 restraints weight = 10672.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.155078 restraints weight = 6415.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.156942 restraints weight = 4349.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.158163 restraints weight = 3235.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.158938 restraints weight = 2616.255| |-----------------------------------------------------------------------------| r_work (final): 0.4131 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.226665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.226585 restraints weight = 42.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.226608 restraints weight = 4.326 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.226661 restraints weight = 2.093 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.226648 restraints weight = 0.193 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.226648 restraints weight = 0.119 | |-----------------------------------------------------------------------------| r_work (final): 0.4547 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.139313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.134486 restraints weight = 132.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.137301 restraints weight = 59.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.138483 restraints weight = 25.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.138914 restraints weight = 10.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.139048 restraints weight = 3.982 | |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5554 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.594 40303 Z= 0.329 Angle : 0.922 47.453 54612 Z= 0.464 Chirality : 0.050 0.314 6078 Planarity : 0.008 0.199 7026 Dihedral : 5.638 28.012 5592 Min Nonbonded Distance : 1.448 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.09 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.10), residues: 5280 helix: 0.53 (0.21), residues: 654 sheet: -1.60 (0.15), residues: 1068 loop : -2.90 (0.08), residues: 3558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG V 87 TYR 0.029 0.001 TYR N 280 PHE 0.022 0.002 PHE V 107 TRP 0.091 0.004 TRP A 247 HIS 0.009 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.21 (40122) covalent geometry : angle 0.85900 / 0.43 (54270) SS BOND : bond 0.00410 / 0.30 ( 126) SS BOND : angle 2.21449 / 1.52 ( 252) hydrogen bonds : bond 0.03427 / 2.34 ( 702) hydrogen bonds : angle 5.85963 / 4.01 ( 1728) Misc. bond : bond 0.05226 / 3.80 ( 25) link_ALPHA1-4 : bond 0.01075 / 0.75 ( 6) link_ALPHA1-4 : angle 1.96294 / 1.31 ( 18) link_BETA1-4 : bond 0.00276 / 0.20 ( 12) link_BETA1-4 : angle 0.83919 / 0.55 ( 36) link_NAG-ASN : bond 0.00082 / 0.06 ( 6) link_NAG-ASN : angle 1.00843 / 0.69 ( 18) link_TRANS : bond 0.24437 / 12.36 ( 6) link_TRANS : angle 16.69316 / 9.05 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.7807 (tt) cc_final: 0.6917 (mm) REVERT: A 166 LEU cc_start: 0.6178 (tp) cc_final: 0.5944 (tp) REVERT: A 248 VAL cc_start: 0.7923 (p) cc_final: 0.7703 (m) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0670 time to fit residues: 5.8212 Evaluate side-chains 58 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.125 Evaluate side-chains 69 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.4913 (tmt170) cc_final: 0.4165 (ppt170) REVERT: B 90 TRP cc_start: 0.6776 (t60) cc_final: 0.6513 (t60) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0646 time to fit residues: 5.4012 Evaluate side-chains 53 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.079 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 189 optimal weight: 0.0870 chunk 371 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 181 optimal weight: 0.7980 chunk 493 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 259 optimal weight: 20.0000 chunk 338 optimal weight: 2.9990 chunk 179 optimal weight: 20.0000 chunk 359 optimal weight: 9.9990 chunk 282 optimal weight: 5.9990 overall best weight: 1.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 HIS A 64 HIS ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.151025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.140607 restraints weight = 15015.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.141750 restraints weight = 10981.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.142403 restraints weight = 8689.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.143045 restraints weight = 7176.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.143281 restraints weight = 6135.925| |-----------------------------------------------------------------------------| r_work (final): 0.4097 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.168752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.152701 restraints weight = 10390.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.154917 restraints weight = 6709.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.156444 restraints weight = 4786.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.157531 restraints weight = 3705.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.158229 restraints weight = 3063.092| |-----------------------------------------------------------------------------| r_work (final): 0.4124 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.219084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.218130 restraints weight = 42.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.218337 restraints weight = 46.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.218295 restraints weight = 16.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.218295 restraints weight = 5.807 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.218295 restraints weight = 5.807 | |-----------------------------------------------------------------------------| r_work (final): 0.4446 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.139523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.134495 restraints weight = 137.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.137333 restraints weight = 58.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.138569 restraints weight = 24.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.139036 restraints weight = 9.284 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.139158 restraints weight = 3.422 | |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5544 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.600 40303 Z= 0.316 Angle : 0.886 47.022 54612 Z= 0.447 Chirality : 0.047 0.283 6078 Planarity : 0.005 0.061 7026 Dihedral : 5.414 23.487 5592 Min Nonbonded Distance : 1.462 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.98 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.10), residues: 5280 helix: 0.57 (0.21), residues: 654 sheet: -1.35 (0.15), residues: 1026 loop : -2.92 (0.08), residues: 3600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 91 TYR 0.026 0.001 TYR J 280 PHE 0.017 0.002 PHE Q 420 TRP 0.031 0.003 TRP M 247 HIS 0.007 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.19 (40122) covalent geometry : angle 0.82119 / 0.41 (54270) SS BOND : bond 0.00297 / 0.22 ( 126) SS BOND : angle 2.13056 / 1.46 ( 252) hydrogen bonds : bond 0.03144 / 2.15 ( 702) hydrogen bonds : angle 5.63447 / 3.86 ( 1728) Misc. bond : bond 0.05499 / 4.06 ( 25) link_ALPHA1-4 : bond 0.01151 / 0.81 ( 6) link_ALPHA1-4 : angle 1.93310 / 1.30 ( 18) link_BETA1-4 : bond 0.00290 / 0.21 ( 12) link_BETA1-4 : angle 0.91465 / 0.60 ( 36) link_NAG-ASN : bond 0.00040 / 0.03 ( 6) link_NAG-ASN : angle 0.97610 / 0.68 ( 18) link_TRANS : bond 0.24687 / 12.49 ( 6) link_TRANS : angle 16.72206 / 9.22 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.7530 (tt) cc_final: 0.6197 (mp) REVERT: A 166 LEU cc_start: 0.6150 (tp) cc_final: 0.5878 (tp) REVERT: A 225 PHE cc_start: 0.8779 (t80) cc_final: 0.8526 (t80) REVERT: A 369 GLU cc_start: 0.5938 (mp0) cc_final: 0.5716 (mp0) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0659 time to fit residues: 5.8477 Evaluate side-chains 56 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.168 Evaluate side-chains 69 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 81 ARG cc_start: 0.7968 (mmp80) cc_final: 0.7709 (mmp-170) REVERT: B 86 ARG cc_start: 0.6992 (tmt170) cc_final: 0.5476 (ppt170) REVERT: B 149 TRP cc_start: 0.6929 (m-90) cc_final: 0.6625 (m-90) REVERT: B 225 LYS cc_start: 0.4843 (tppt) cc_final: 0.4293 (tppt) REVERT: B 378 HIS cc_start: 0.5925 (t70) cc_final: 0.5613 (t-90) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0731 time to fit residues: 6.0978 Evaluate side-chains 54 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.135 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 144 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 13 optimal weight: 0.0030 chunk 256 optimal weight: 7.9990 chunk 237 optimal weight: 4.9990 chunk 27 optimal weight: 30.0000 chunk 22 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 247 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 chunk 326 optimal weight: 7.9990 overall best weight: 4.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 HIS ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS B 370 HIS ** B 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.146841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.133019 restraints weight = 14086.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.135049 restraints weight = 9213.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.136442 restraints weight = 6596.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.137393 restraints weight = 5062.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.137944 restraints weight = 4156.810| |-----------------------------------------------------------------------------| r_work (final): 0.4046 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.165428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.148778 restraints weight = 10386.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.151150 restraints weight = 6567.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.152823 restraints weight = 4596.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.153975 restraints weight = 3526.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.154712 restraints weight = 2891.729| |-----------------------------------------------------------------------------| r_work (final): 0.4089 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.217612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.215423 restraints weight = 51.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.215423 restraints weight = 31.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.215423 restraints weight = 31.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.215423 restraints weight = 31.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.215423 restraints weight = 31.557| |-----------------------------------------------------------------------------| r_work (final): 0.4419 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.124996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.124014 restraints weight = 145.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.124668 restraints weight = 37.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.124869 restraints weight = 11.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.124932 restraints weight = 3.471 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.124948 restraints weight = 1.114 | |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5685 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.615 40303 Z= 0.324 Angle : 0.896 47.429 54612 Z= 0.455 Chirality : 0.047 0.248 6078 Planarity : 0.009 0.248 7026 Dihedral : 5.646 28.194 5592 Min Nonbonded Distance : 1.478 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.11 % Favored : 89.43 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.10), residues: 5280 helix: 0.67 (0.21), residues: 654 sheet: -1.31 (0.15), residues: 1038 loop : -2.90 (0.08), residues: 3588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG V 380 TYR 0.023 0.002 TYR J 280 PHE 0.030 0.002 PHE J 388 TRP 0.032 0.003 TRP U 92 HIS 0.005 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.20 (40122) covalent geometry : angle 0.83458 / 0.42 (54270) SS BOND : bond 0.00392 / 0.29 ( 126) SS BOND : angle 1.89306 / 1.29 ( 252) hydrogen bonds : bond 0.03296 / 2.28 ( 702) hydrogen bonds : angle 5.51217 / 3.80 ( 1728) Misc. bond : bond 0.05128 / 3.86 ( 25) link_ALPHA1-4 : bond 0.00931 / 0.65 ( 6) link_ALPHA1-4 : angle 1.79948 / 1.22 ( 18) link_BETA1-4 : bond 0.00211 / 0.16 ( 12) link_BETA1-4 : angle 0.87671 / 0.60 ( 36) link_NAG-ASN : bond 0.00141 / 0.10 ( 6) link_NAG-ASN : angle 1.14706 / 0.81 ( 18) link_TRANS : bond 0.25308 / 12.80 ( 6) link_TRANS : angle 16.73424 / 9.27 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3112.64 seconds wall clock time: 56 minutes 10.69 seconds (3370.69 seconds total)