Starting phenix.real_space_refine on Sun Aug 24 03:24:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bnp_44733/08_2025/9bnp_44733.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bnp_44733/08_2025/9bnp_44733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bnp_44733/08_2025/9bnp_44733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bnp_44733/08_2025/9bnp_44733.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bnp_44733/08_2025/9bnp_44733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bnp_44733/08_2025/9bnp_44733.map" } resolution = 3.17 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= 0.014 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 112 5.16 5 C 10322 2.51 5 N 2722 2.21 5 O 3381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16537 Number of models: 1 Model: "" Number of chains: 49 Chain: "A" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3434 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 3 Chain: "B" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "E" Number of atoms: 3428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3428 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 3 Chain: "F" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "H" Number of atoms: 1016 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 132, 1006 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 127} Unresolved chain links: 4 Unresolved chain link angles: 12 Unresolved chain link dihedrals: 12 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Conformer: "A" Number of residues, atoms: 132, 1006 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 127} Unresolved chain links: 4 Unresolved chain link angles: 12 Unresolved chain link dihedrals: 12 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 bond proxies already assigned to first conformer: 1014 Chain: "I" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3450 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "J" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "L" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "a" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" OG SER H 7 " occ=0.82 ... (4 atoms not shown) pdb=" CB ASER H 7 " occ=0.85 Time building chain proxies: 4.65, per 1000 atoms: 0.28 Number of scatterers: 16537 At special positions: 0 Unit cell: (124.5, 126.99, 161.02, 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 112 16.00 O 3381 8.00 N 2722 7.00 C 10322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.02 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.04 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN Z 4 " - " MAN Z 5 " " MAN a 4 " - " MAN a 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA W 3 " - " MAN W 4 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA Z 3 " - " MAN Z 6 " " BMA a 3 " - " MAN a 6 " " MAN a 6 " - " MAN a 7 " " BMA l 3 " - " MAN l 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " NAG-ASN " NAG A 601 " - " ASN A 448 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 88 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 234 " " NAG C 1 " - " ASN A 363 " " NAG D 1 " - " ASN A 392 " " NAG E 601 " - " ASN E 355 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 339 " " NAG E 604 " - " ASN E 234 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN A 386 " " NAG I 601 " - " ASN I 448 " " NAG I 602 " - " ASN I 276 " " NAG I 603 " - " ASN I 355 " " NAG I 604 " - " ASN I 88 " " NAG I 605 " - " ASN I 339 " " NAG J 701 " - " ASN J 637 " " NAG J 702 " - " ASN J 618 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 276 " " NAG N 1 " - " ASN A 355 " " NAG O 1 " - " ASN A 295 " " NAG P 1 " - " ASN A 160 " " NAG Q 1 " - " ASN A 156 " " NAG R 1 " - " ASN A 197 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN E 363 " " NAG U 1 " - " ASN E 392 " " NAG V 1 " - " ASN E 386 " " NAG W 1 " - " ASN E 262 " " NAG X 1 " - " ASN E 276 " " NAG Y 1 " - " ASN E 295 " " NAG Z 1 " - " ASN E 160 " " NAG a 1 " - " ASN E 156 " " NAG b 1 " - " ASN E 197 " " NAG c 1 " - " ASN E 88 " " NAG d 1 " - " ASN E 332 " " NAG e 1 " - " ASN E 301 " " NAG f 1 " - " ASN E 448 " " NAG g 1 " - " ASN I 363 " " NAG h 1 " - " ASN I 392 " " NAG i 1 " - " ASN I 386 " " NAG j 1 " - " ASN I 262 " " NAG k 1 " - " ASN I 295 " " NAG l 1 " - " ASN I 160 " " NAG m 1 " - " ASN I 156 " " NAG n 1 " - " ASN I 197 " " NAG o 1 " - " ASN I 133 " " NAG p 1 " - " ASN I 332 " " NAG q 1 " - " ASN I 301 " " NAG r 1 " - " ASN I 234 " Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 826.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3572 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 28 sheets defined 25.0% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.739A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.870A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.704A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 475 through 481 removed outlier: 4.073A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.563A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.271A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.908A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.584A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.809A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 463 Processing helix chain 'E' and resid 474 through 481 removed outlier: 3.749A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 527 removed outlier: 4.402A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 535 Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.042A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 4.113A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 664 removed outlier: 3.525A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.891A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'I' and resid 98 through 117 removed outlier: 4.454A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.617A pdb=" N CYS I 126 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 354 Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.508A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 390 Processing helix chain 'I' and resid 475 through 481 removed outlier: 3.812A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 527 removed outlier: 4.505A pdb=" N GLY J 527 " --> pdb=" O GLY J 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 536 through 543 removed outlier: 4.249A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 595 Processing helix chain 'J' and resid 618 through 623 removed outlier: 3.736A pdb=" N ILE J 622 " --> pdb=" O ASN J 618 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 664 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 4.949A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.588A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.751A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA6, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA7, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.356A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 297 removed outlier: 7.400A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 330 through 334 current: chain 'A' and resid 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 382 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.947A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 494 through 499 removed outlier: 4.931A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.582A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.829A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AB6, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.578A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 260 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 7.510A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 59 current: chain 'H' and resid 100O through 103 Processing sheet with id=AC1, first strand: chain 'I' and resid 495 through 499 removed outlier: 5.294A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.588A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 75 through 76 removed outlier: 3.785A pdb=" N VAL I 75 " --> pdb=" O CYS I 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'I' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 259 through 261 current: chain 'I' and resid 284 through 298 removed outlier: 7.256A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 330 through 334 current: chain 'I' and resid 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 382 through 385 current: chain 'I' and resid 465 through 470 Processing sheet with id=AC7, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.747A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 423 through 424 Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.572A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 13 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 485 hydrogen bonds defined for protein. 1305 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: 3.50 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4341 1.33 - 1.46: 4129 1.46 - 1.58: 8232 1.58 - 1.70: 1 1.70 - 1.83: 148 Bond restraints: 16851 Sorted by residual: bond pdb=" N LYS L 50 " pdb=" CA LYS L 50 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.35e-02 5.49e+03 9.80e+00 bond pdb=" CB ASP F 632 " pdb=" CG ASP F 632 " ideal model delta sigma weight residual 1.516 1.582 -0.066 2.50e-02 1.60e+03 7.03e+00 bond pdb=" CB ASN E 80 " pdb=" CG ASN E 80 " ideal model delta sigma weight residual 1.516 1.580 -0.064 2.50e-02 1.60e+03 6.58e+00 bond pdb=" C ASN E 80 " pdb=" N PRO E 81 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.52e+00 bond pdb=" N PHE E 233 " pdb=" CA PHE E 233 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.27e-02 6.20e+03 6.02e+00 ... (remaining 16846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.00: 22551 4.00 - 7.99: 278 7.99 - 11.99: 32 11.99 - 15.98: 9 15.98 - 19.98: 3 Bond angle restraints: 22873 Sorted by residual: angle pdb=" C THR A 139 " pdb=" N ASP A 151 " pdb=" CA ASP A 151 " ideal model delta sigma weight residual 122.07 140.72 -18.65 1.70e+00 3.46e-01 1.20e+02 angle pdb=" CB MET A 475 " pdb=" CG MET A 475 " pdb=" SD MET A 475 " ideal model delta sigma weight residual 112.70 130.54 -17.84 3.00e+00 1.11e-01 3.54e+01 angle pdb=" CA MET H 34 " pdb=" CB MET H 34 " pdb=" CG MET H 34 " ideal model delta sigma weight residual 114.10 125.73 -11.63 2.00e+00 2.50e-01 3.38e+01 angle pdb=" C ASN E 80 " pdb=" CA ASN E 80 " pdb=" CB ASN E 80 " ideal model delta sigma weight residual 111.14 120.16 -9.02 1.56e+00 4.11e-01 3.34e+01 angle pdb=" CA LEU I 259 " pdb=" CB LEU I 259 " pdb=" CG LEU I 259 " ideal model delta sigma weight residual 116.30 136.28 -19.98 3.50e+00 8.16e-02 3.26e+01 ... (remaining 22868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.41: 10617 21.41 - 42.83: 645 42.83 - 64.24: 132 64.24 - 85.66: 75 85.66 - 107.07: 33 Dihedral angle restraints: 11502 sinusoidal: 5976 harmonic: 5526 Sorted by residual: dihedral pdb=" CA THR A 139 " pdb=" C THR A 139 " pdb=" N ASP A 151 " pdb=" CA ASP A 151 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CB CYS I 119 " pdb=" SG CYS I 119 " pdb=" SG CYS I 205 " pdb=" CB CYS I 205 " ideal model delta sinusoidal sigma weight residual -86.00 -135.88 49.88 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -132.73 46.73 1 1.00e+01 1.00e-02 3.02e+01 ... (remaining 11499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2663 0.117 - 0.234: 205 0.234 - 0.351: 13 0.351 - 0.468: 4 0.468 - 0.585: 1 Chirality restraints: 2886 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A 276 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.54e+00 chirality pdb=" C1 NAG A 605 " pdb=" ND2 ASN A 301 " pdb=" C2 NAG A 605 " pdb=" O5 NAG A 605 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" CB ILE A 138 " pdb=" CA ILE A 138 " pdb=" CG1 ILE A 138 " pdb=" CG2 ILE A 138 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.60e+00 ... (remaining 2883 not shown) Planarity restraints: 2821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 604 " 0.066 2.00e-02 2.50e+03 5.54e-02 3.83e+01 pdb=" C7 NAG E 604 " -0.013 2.00e-02 2.50e+03 pdb=" C8 NAG E 604 " -0.018 2.00e-02 2.50e+03 pdb=" N2 NAG E 604 " -0.088 2.00e-02 2.50e+03 pdb=" O7 NAG E 604 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 631 " -0.031 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP J 631 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP J 631 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP J 631 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 631 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP J 631 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP J 631 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 631 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 631 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP J 631 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 632 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" CG ASP F 632 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASP F 632 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP F 632 " 0.017 2.00e-02 2.50e+03 ... (remaining 2818 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1226 2.75 - 3.28: 16214 3.28 - 3.82: 26517 3.82 - 4.36: 31443 4.36 - 4.90: 55151 Nonbonded interactions: 130551 Sorted by model distance: nonbonded pdb=" O VAL I 36 " pdb=" OG1 THR J 606 " model vdw 2.207 3.040 nonbonded pdb=" NE2 GLN A 258 " pdb=" O VAL A 371 " model vdw 2.291 3.120 nonbonded pdb=" OG SER E 334 " pdb=" OG1 THR E 337 " model vdw 2.306 3.040 nonbonded pdb=" O ASP H 98 " pdb=" OH TYR H 100M" model vdw 2.318 3.040 nonbonded pdb=" ND2 ASN A 195 " pdb=" OG1 THR A 198 " model vdw 2.327 3.120 ... (remaining 130546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 184 or resid 188 through 604)) selection = chain 'E' selection = (chain 'I' and (resid 33 through 184 or resid 188 through 397 or resid 412 throu \ gh 604)) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 520 through 664) selection = (chain 'J' and resid 520 through 664) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } ncs_group { reference = chain 'K' selection = chain 'W' selection = chain 'l' } ncs_group { reference = (chain 'Z' and (resid 1 or resid 4 through 6)) selection = (chain 'a' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'j' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.930 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 27.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 0.006 0.073 16996 Z= 0.268 Angle : 1.236 19.978 23270 Z= 0.620 Chirality : 0.067 0.585 2886 Planarity : 0.005 0.055 2767 Dihedral : 15.568 107.070 7816 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.19), residues: 1879 helix: 1.05 (0.26), residues: 407 sheet: -0.75 (0.22), residues: 523 loop : -0.71 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 476 TYR 0.026 0.002 TYR F 638 PHE 0.038 0.003 PHE L 87 TRP 0.063 0.003 TRP J 631 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00565 (16851) covalent geometry : angle 1.19690 (22873) SS BOND : bond 0.00453 ( 38) SS BOND : angle 2.04233 ( 76) hydrogen bonds : bond 0.14406 ( 485) hydrogen bonds : angle 6.56977 ( 1305) link_ALPHA1-2 : bond 0.01292 ( 2) link_ALPHA1-2 : angle 2.70373 ( 6) link_ALPHA1-3 : bond 0.00682 ( 4) link_ALPHA1-3 : angle 1.46855 ( 12) link_ALPHA1-6 : bond 0.00540 ( 4) link_ALPHA1-6 : angle 1.69099 ( 12) link_BETA1-4 : bond 0.01058 ( 43) link_BETA1-4 : angle 2.70866 ( 129) link_NAG-ASN : bond 0.00445 ( 54) link_NAG-ASN : angle 2.94799 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6728 (tmtt) cc_final: 0.6077 (tptt) REVERT: B 542 ARG cc_start: 0.8858 (ptm160) cc_final: 0.8576 (ptm160) REVERT: E 169 LYS cc_start: 0.8413 (mttt) cc_final: 0.8148 (mttt) REVERT: E 356 ASN cc_start: 0.9040 (m-40) cc_final: 0.8719 (p0) REVERT: F 588 ARG cc_start: 0.7939 (mtt-85) cc_final: 0.7587 (ttm110) REVERT: H 31 ASP cc_start: 0.8277 (m-30) cc_final: 0.7983 (m-30) REVERT: I 161 MET cc_start: 0.8946 (tpt) cc_final: 0.8460 (tpt) REVERT: J 624 ASP cc_start: 0.8668 (m-30) cc_final: 0.8105 (m-30) REVERT: J 631 TRP cc_start: 0.8320 (t-100) cc_final: 0.8043 (t-100) REVERT: J 632 ASP cc_start: 0.9320 (t0) cc_final: 0.9077 (t0) REVERT: J 633 LYS cc_start: 0.9312 (mttt) cc_final: 0.8811 (mmtm) REVERT: L 17 ASP cc_start: 0.7311 (t0) cc_final: 0.6948 (t0) REVERT: L 45 LYS cc_start: 0.7935 (ttmm) cc_final: 0.7675 (tttp) REVERT: L 76 ASN cc_start: 0.8871 (m-40) cc_final: 0.8612 (p0) REVERT: L 90 GLN cc_start: 0.9231 (pp30) cc_final: 0.8928 (pp30) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1472 time to fit residues: 42.2783 Evaluate side-chains 162 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN B 651 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS L 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.082102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.061684 restraints weight = 40908.020| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.93 r_work: 0.2839 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 16996 Z= 0.270 Angle : 0.741 11.594 23270 Z= 0.347 Chirality : 0.049 0.409 2886 Planarity : 0.004 0.047 2767 Dihedral : 10.399 80.634 4250 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.30 % Allowed : 7.50 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.19), residues: 1879 helix: 1.29 (0.27), residues: 405 sheet: -0.69 (0.22), residues: 515 loop : -0.59 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 542 TYR 0.012 0.002 TYR I 318 PHE 0.020 0.002 PHE E 233 TRP 0.021 0.002 TRP A 479 HIS 0.006 0.002 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00632 (16851) covalent geometry : angle 0.69287 (22873) SS BOND : bond 0.00337 ( 38) SS BOND : angle 1.13907 ( 76) hydrogen bonds : bond 0.04594 ( 485) hydrogen bonds : angle 5.15897 ( 1305) link_ALPHA1-2 : bond 0.01683 ( 2) link_ALPHA1-2 : angle 3.28627 ( 6) link_ALPHA1-3 : bond 0.00924 ( 4) link_ALPHA1-3 : angle 2.97819 ( 12) link_ALPHA1-6 : bond 0.00672 ( 4) link_ALPHA1-6 : angle 2.41694 ( 12) link_BETA1-4 : bond 0.00477 ( 43) link_BETA1-4 : angle 1.95977 ( 129) link_NAG-ASN : bond 0.00460 ( 54) link_NAG-ASN : angle 2.43688 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.7200 (tmtt) cc_final: 0.6735 (tptt) REVERT: B 530 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.6772 (mtt) REVERT: B 542 ARG cc_start: 0.9062 (ptm160) cc_final: 0.8699 (ptm160) REVERT: B 633 LYS cc_start: 0.9340 (mptt) cc_final: 0.9014 (mptt) REVERT: E 169 LYS cc_start: 0.8493 (mttt) cc_final: 0.8235 (mttt) REVERT: F 543 ASN cc_start: 0.9158 (m-40) cc_final: 0.8820 (m110) REVERT: F 584 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8519 (mt-10) REVERT: F 588 ARG cc_start: 0.8072 (mtt-85) cc_final: 0.7714 (ttm110) REVERT: F 621 GLU cc_start: 0.8602 (tp30) cc_final: 0.8320 (tp30) REVERT: F 625 ASN cc_start: 0.8499 (t0) cc_final: 0.8281 (t0) REVERT: H 31 ASP cc_start: 0.8520 (m-30) cc_final: 0.8293 (m-30) REVERT: H 43 LYS cc_start: 0.8989 (ptpp) cc_final: 0.8750 (ptpp) REVERT: I 173 TYR cc_start: 0.9005 (p90) cc_final: 0.8658 (p90) REVERT: I 188 ASN cc_start: 0.7859 (p0) cc_final: 0.7638 (p0) REVERT: J 535 MET cc_start: 0.9297 (mmt) cc_final: 0.8969 (mpp) REVERT: J 624 ASP cc_start: 0.8884 (m-30) cc_final: 0.8438 (m-30) REVERT: J 632 ASP cc_start: 0.9385 (t0) cc_final: 0.9106 (t0) REVERT: J 657 GLU cc_start: 0.8023 (tp30) cc_final: 0.7674 (tt0) REVERT: L 39 LYS cc_start: 0.8649 (mmtp) cc_final: 0.8383 (mmtm) REVERT: L 100 GLN cc_start: 0.8878 (mp10) cc_final: 0.8673 (mp-120) REVERT: L 105 GLU cc_start: 0.4636 (OUTLIER) cc_final: 0.4129 (tp30) outliers start: 22 outliers final: 12 residues processed: 173 average time/residue: 0.1353 time to fit residues: 35.5854 Evaluate side-chains 163 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 87 PHE Chi-restraints excluded: chain L residue 105 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 99 optimal weight: 6.9990 chunk 12 optimal weight: 0.2980 chunk 184 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS I 66 HIS L 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.080549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.059979 restraints weight = 41537.824| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 4.06 r_work: 0.2790 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16996 Z= 0.163 Angle : 0.638 11.630 23270 Z= 0.296 Chirality : 0.045 0.403 2886 Planarity : 0.003 0.038 2767 Dihedral : 8.882 68.862 4250 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.18 % Allowed : 8.51 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.19), residues: 1879 helix: 1.48 (0.27), residues: 405 sheet: -0.52 (0.22), residues: 536 loop : -0.50 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 38 TYR 0.011 0.001 TYR L 49 PHE 0.015 0.001 PHE H 58 TRP 0.011 0.001 TRP J 631 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00382 (16851) covalent geometry : angle 0.59233 (22873) SS BOND : bond 0.00228 ( 38) SS BOND : angle 0.95920 ( 76) hydrogen bonds : bond 0.04005 ( 485) hydrogen bonds : angle 4.81570 ( 1305) link_ALPHA1-2 : bond 0.01441 ( 2) link_ALPHA1-2 : angle 2.49080 ( 6) link_ALPHA1-3 : bond 0.01027 ( 4) link_ALPHA1-3 : angle 1.90903 ( 12) link_ALPHA1-6 : bond 0.00704 ( 4) link_ALPHA1-6 : angle 2.14016 ( 12) link_BETA1-4 : bond 0.00370 ( 43) link_BETA1-4 : angle 1.74268 ( 129) link_NAG-ASN : bond 0.00286 ( 54) link_NAG-ASN : angle 2.27332 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9073 (tpt) cc_final: 0.8823 (tpt) REVERT: A 207 LYS cc_start: 0.7387 (tmtt) cc_final: 0.6947 (tptt) REVERT: A 475 MET cc_start: 0.8530 (tpp) cc_final: 0.8169 (tpp) REVERT: B 540 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7391 (mp-120) REVERT: B 542 ARG cc_start: 0.9063 (ptm160) cc_final: 0.8721 (ptm160) REVERT: E 114 GLN cc_start: 0.8777 (tt0) cc_final: 0.8496 (tt0) REVERT: E 169 LYS cc_start: 0.8646 (mttt) cc_final: 0.8389 (mttt) REVERT: F 588 ARG cc_start: 0.8161 (mtt-85) cc_final: 0.7815 (ttm110) REVERT: F 621 GLU cc_start: 0.8574 (tp30) cc_final: 0.8156 (tp30) REVERT: F 625 ASN cc_start: 0.8556 (t0) cc_final: 0.8105 (t0) REVERT: F 647 GLU cc_start: 0.8663 (tt0) cc_final: 0.8274 (tt0) REVERT: H 31 ASP cc_start: 0.8507 (m-30) cc_final: 0.8282 (m-30) REVERT: H 43 LYS cc_start: 0.9010 (ptpp) cc_final: 0.8761 (ptpp) REVERT: I 173 TYR cc_start: 0.9045 (p90) cc_final: 0.8729 (p90) REVERT: I 188 ASN cc_start: 0.7879 (p0) cc_final: 0.7657 (p0) REVERT: J 535 MET cc_start: 0.9312 (mmt) cc_final: 0.9040 (mpp) REVERT: J 624 ASP cc_start: 0.8921 (m-30) cc_final: 0.8489 (m-30) REVERT: J 632 ASP cc_start: 0.9385 (t0) cc_final: 0.9075 (t0) REVERT: J 633 LYS cc_start: 0.9451 (mmtp) cc_final: 0.8886 (mmtm) REVERT: J 657 GLU cc_start: 0.8105 (tp30) cc_final: 0.7750 (tt0) REVERT: L 38 ARG cc_start: 0.8214 (ttt90) cc_final: 0.7494 (ttt90) REVERT: L 79 GLN cc_start: 0.7872 (mm110) cc_final: 0.7514 (mm110) REVERT: L 82 ASP cc_start: 0.6001 (m-30) cc_final: 0.5705 (m-30) REVERT: L 100 GLN cc_start: 0.8956 (mp10) cc_final: 0.8706 (mp-120) outliers start: 20 outliers final: 10 residues processed: 177 average time/residue: 0.1364 time to fit residues: 36.3837 Evaluate side-chains 168 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 87 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 186 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN J 540 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.078977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.058348 restraints weight = 41672.065| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 4.04 r_work: 0.2753 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16996 Z= 0.210 Angle : 0.651 11.503 23270 Z= 0.303 Chirality : 0.045 0.406 2886 Planarity : 0.004 0.036 2767 Dihedral : 8.213 59.345 4250 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.71 % Allowed : 9.39 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.20), residues: 1879 helix: 1.41 (0.27), residues: 402 sheet: -0.55 (0.22), residues: 538 loop : -0.47 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 38 TYR 0.013 0.001 TYR L 49 PHE 0.017 0.002 PHE H 58 TRP 0.016 0.001 TRP I 112 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00494 (16851) covalent geometry : angle 0.60559 (22873) SS BOND : bond 0.00265 ( 38) SS BOND : angle 0.95143 ( 76) hydrogen bonds : bond 0.03897 ( 485) hydrogen bonds : angle 4.72238 ( 1305) link_ALPHA1-2 : bond 0.01453 ( 2) link_ALPHA1-2 : angle 2.75597 ( 6) link_ALPHA1-3 : bond 0.00998 ( 4) link_ALPHA1-3 : angle 2.31304 ( 12) link_ALPHA1-6 : bond 0.00824 ( 4) link_ALPHA1-6 : angle 2.16008 ( 12) link_BETA1-4 : bond 0.00338 ( 43) link_BETA1-4 : angle 1.69677 ( 129) link_NAG-ASN : bond 0.00386 ( 54) link_NAG-ASN : angle 2.29962 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9107 (tpt) cc_final: 0.8873 (tpt) REVERT: A 475 MET cc_start: 0.8601 (tpp) cc_final: 0.8208 (tpp) REVERT: B 542 ARG cc_start: 0.9079 (ptm160) cc_final: 0.8741 (ptm160) REVERT: B 633 LYS cc_start: 0.9404 (mptt) cc_final: 0.9098 (mptt) REVERT: E 99 ASN cc_start: 0.8902 (t0) cc_final: 0.8617 (t0) REVERT: E 169 LYS cc_start: 0.8565 (mttt) cc_final: 0.8318 (mtmm) REVERT: F 543 ASN cc_start: 0.9114 (m-40) cc_final: 0.8880 (m110) REVERT: F 588 ARG cc_start: 0.8206 (mtt-85) cc_final: 0.7875 (ttm110) REVERT: F 621 GLU cc_start: 0.8618 (tp30) cc_final: 0.8123 (tp30) REVERT: F 625 ASN cc_start: 0.8564 (t0) cc_final: 0.8031 (t0) REVERT: H 31 ASP cc_start: 0.8604 (m-30) cc_final: 0.8333 (m-30) REVERT: H 43 LYS cc_start: 0.9015 (ptpp) cc_final: 0.8748 (ptpp) REVERT: I 173 TYR cc_start: 0.9060 (p90) cc_final: 0.8811 (p90) REVERT: I 188 ASN cc_start: 0.7904 (p0) cc_final: 0.7663 (p0) REVERT: J 535 MET cc_start: 0.9300 (mmt) cc_final: 0.8921 (mpp) REVERT: J 632 ASP cc_start: 0.9430 (t0) cc_final: 0.9127 (t0) REVERT: J 633 LYS cc_start: 0.9526 (mmtp) cc_final: 0.9046 (mmtm) REVERT: J 657 GLU cc_start: 0.8064 (tp30) cc_final: 0.7727 (tt0) REVERT: L 38 ARG cc_start: 0.8249 (ttt90) cc_final: 0.7600 (ttt90) REVERT: L 79 GLN cc_start: 0.7789 (mm110) cc_final: 0.7426 (mm110) outliers start: 29 outliers final: 18 residues processed: 181 average time/residue: 0.1412 time to fit residues: 38.7361 Evaluate side-chains 174 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 660 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 87 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 54 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.078284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.057685 restraints weight = 41383.116| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 4.02 r_work: 0.2733 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16996 Z= 0.229 Angle : 0.661 11.899 23270 Z= 0.309 Chirality : 0.046 0.411 2886 Planarity : 0.004 0.038 2767 Dihedral : 8.107 58.672 4250 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.24 % Allowed : 10.16 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.20), residues: 1879 helix: 1.45 (0.27), residues: 405 sheet: -0.56 (0.22), residues: 536 loop : -0.54 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 38 TYR 0.014 0.001 TYR L 49 PHE 0.016 0.002 PHE H 58 TRP 0.019 0.001 TRP I 112 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00542 (16851) covalent geometry : angle 0.61478 (22873) SS BOND : bond 0.00298 ( 38) SS BOND : angle 1.42324 ( 76) hydrogen bonds : bond 0.03915 ( 485) hydrogen bonds : angle 4.71104 ( 1305) link_ALPHA1-2 : bond 0.01434 ( 2) link_ALPHA1-2 : angle 2.61382 ( 6) link_ALPHA1-3 : bond 0.01024 ( 4) link_ALPHA1-3 : angle 2.20180 ( 12) link_ALPHA1-6 : bond 0.00826 ( 4) link_ALPHA1-6 : angle 2.03235 ( 12) link_BETA1-4 : bond 0.00336 ( 43) link_BETA1-4 : angle 1.65324 ( 129) link_NAG-ASN : bond 0.00416 ( 54) link_NAG-ASN : angle 2.32454 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.7608 (tmtt) cc_final: 0.7174 (tptt) REVERT: A 376 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8547 (m-80) REVERT: A 475 MET cc_start: 0.8598 (tpp) cc_final: 0.8199 (tpp) REVERT: B 540 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7411 (mp-120) REVERT: B 542 ARG cc_start: 0.9075 (ptm160) cc_final: 0.8743 (ptm160) REVERT: B 633 LYS cc_start: 0.9394 (mptt) cc_final: 0.9097 (mptt) REVERT: E 69 TRP cc_start: 0.8026 (OUTLIER) cc_final: 0.7100 (m100) REVERT: F 543 ASN cc_start: 0.9141 (m-40) cc_final: 0.8926 (m-40) REVERT: F 588 ARG cc_start: 0.8216 (mtt-85) cc_final: 0.7880 (ttm110) REVERT: F 647 GLU cc_start: 0.8664 (tt0) cc_final: 0.8265 (tt0) REVERT: I 173 TYR cc_start: 0.9063 (p90) cc_final: 0.8809 (p90) REVERT: I 188 ASN cc_start: 0.7956 (p0) cc_final: 0.7689 (p0) REVERT: J 535 MET cc_start: 0.9298 (mmt) cc_final: 0.8917 (mpp) REVERT: J 630 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8521 (pm20) REVERT: J 632 ASP cc_start: 0.9433 (t0) cc_final: 0.9125 (t0) REVERT: J 633 LYS cc_start: 0.9541 (mmtp) cc_final: 0.9074 (mmtm) REVERT: J 657 GLU cc_start: 0.8119 (tp30) cc_final: 0.7769 (tt0) REVERT: L 38 ARG cc_start: 0.8275 (ttt90) cc_final: 0.7584 (ttt90) REVERT: L 39 LYS cc_start: 0.8385 (mmtm) cc_final: 0.7956 (mmtm) REVERT: L 79 GLN cc_start: 0.7732 (mm110) cc_final: 0.7365 (mm110) outliers start: 38 outliers final: 22 residues processed: 183 average time/residue: 0.1362 time to fit residues: 37.6501 Evaluate side-chains 178 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 87 PHE Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 154 optimal weight: 0.4980 chunk 176 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 179 optimal weight: 0.1980 chunk 60 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.080227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.059686 restraints weight = 41125.746| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 4.04 r_work: 0.2785 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16996 Z= 0.113 Angle : 0.590 11.520 23270 Z= 0.274 Chirality : 0.044 0.405 2886 Planarity : 0.003 0.037 2767 Dihedral : 7.562 57.424 4250 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.83 % Allowed : 10.99 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.20), residues: 1879 helix: 1.53 (0.27), residues: 408 sheet: -0.41 (0.22), residues: 533 loop : -0.47 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 38 TYR 0.010 0.001 TYR A 484 PHE 0.012 0.001 PHE H 58 TRP 0.011 0.001 TRP J 623 HIS 0.002 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00255 (16851) covalent geometry : angle 0.54737 (22873) SS BOND : bond 0.00205 ( 38) SS BOND : angle 0.90688 ( 76) hydrogen bonds : bond 0.03411 ( 485) hydrogen bonds : angle 4.49583 ( 1305) link_ALPHA1-2 : bond 0.01511 ( 2) link_ALPHA1-2 : angle 2.66576 ( 6) link_ALPHA1-3 : bond 0.01136 ( 4) link_ALPHA1-3 : angle 1.95042 ( 12) link_ALPHA1-6 : bond 0.00884 ( 4) link_ALPHA1-6 : angle 1.95028 ( 12) link_BETA1-4 : bond 0.00377 ( 43) link_BETA1-4 : angle 1.51377 ( 129) link_NAG-ASN : bond 0.00246 ( 54) link_NAG-ASN : angle 2.16224 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8545 (m-10) REVERT: A 426 MET cc_start: 0.7830 (tpt) cc_final: 0.7506 (tpt) REVERT: A 475 MET cc_start: 0.8571 (tpp) cc_final: 0.8132 (tpp) REVERT: B 540 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7392 (mp-120) REVERT: B 542 ARG cc_start: 0.9062 (ptm160) cc_final: 0.8744 (ptm160) REVERT: B 633 LYS cc_start: 0.9414 (mptt) cc_final: 0.9109 (mptt) REVERT: E 99 ASN cc_start: 0.8988 (t0) cc_final: 0.8643 (t0) REVERT: E 161 MET cc_start: 0.8986 (tpt) cc_final: 0.8471 (tpt) REVERT: F 543 ASN cc_start: 0.9110 (m-40) cc_final: 0.8883 (m-40) REVERT: F 588 ARG cc_start: 0.8201 (mtt-85) cc_final: 0.7871 (ttm110) REVERT: F 647 GLU cc_start: 0.8643 (tt0) cc_final: 0.8241 (tt0) REVERT: H 31 ASP cc_start: 0.8600 (m-30) cc_final: 0.8339 (m-30) REVERT: I 173 TYR cc_start: 0.9035 (p90) cc_final: 0.8781 (p90) REVERT: I 188 ASN cc_start: 0.7869 (p0) cc_final: 0.7602 (p0) REVERT: I 207 LYS cc_start: 0.8031 (tptt) cc_final: 0.7513 (tptp) REVERT: J 535 MET cc_start: 0.9265 (mmt) cc_final: 0.8929 (mpp) REVERT: J 630 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8517 (pm20) REVERT: J 632 ASP cc_start: 0.9364 (t0) cc_final: 0.9075 (t0) REVERT: J 633 LYS cc_start: 0.9535 (mmtp) cc_final: 0.9071 (mmtm) REVERT: J 657 GLU cc_start: 0.8110 (tp30) cc_final: 0.7744 (tt0) REVERT: L 38 ARG cc_start: 0.8269 (ttt90) cc_final: 0.7552 (ttt90) REVERT: L 39 LYS cc_start: 0.8365 (mmtm) cc_final: 0.7952 (mmtm) REVERT: L 79 GLN cc_start: 0.7684 (mm110) cc_final: 0.7361 (mm110) outliers start: 31 outliers final: 24 residues processed: 186 average time/residue: 0.1283 time to fit residues: 36.4040 Evaluate side-chains 187 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 87 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 18 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.079663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.059149 restraints weight = 41118.766| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 4.02 r_work: 0.2771 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16996 Z= 0.140 Angle : 0.596 11.226 23270 Z= 0.276 Chirality : 0.044 0.403 2886 Planarity : 0.003 0.036 2767 Dihedral : 7.418 57.686 4250 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.01 % Allowed : 11.52 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.20), residues: 1879 helix: 1.85 (0.27), residues: 396 sheet: -0.39 (0.22), residues: 533 loop : -0.49 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 298 TYR 0.020 0.001 TYR H 56 PHE 0.014 0.001 PHE H 58 TRP 0.010 0.001 TRP I 112 HIS 0.002 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00326 (16851) covalent geometry : angle 0.55432 (22873) SS BOND : bond 0.00221 ( 38) SS BOND : angle 0.89295 ( 76) hydrogen bonds : bond 0.03427 ( 485) hydrogen bonds : angle 4.46481 ( 1305) link_ALPHA1-2 : bond 0.01488 ( 2) link_ALPHA1-2 : angle 2.65329 ( 6) link_ALPHA1-3 : bond 0.01002 ( 4) link_ALPHA1-3 : angle 1.99246 ( 12) link_ALPHA1-6 : bond 0.00802 ( 4) link_ALPHA1-6 : angle 1.88407 ( 12) link_BETA1-4 : bond 0.00363 ( 43) link_BETA1-4 : angle 1.51937 ( 129) link_NAG-ASN : bond 0.00287 ( 54) link_NAG-ASN : angle 2.15654 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 CYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7324 (m) REVERT: A 376 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8587 (m-80) REVERT: A 426 MET cc_start: 0.7936 (tpt) cc_final: 0.7619 (tpt) REVERT: A 475 MET cc_start: 0.8565 (tpp) cc_final: 0.8127 (tpp) REVERT: B 540 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7324 (mp-120) REVERT: B 542 ARG cc_start: 0.9071 (ptm160) cc_final: 0.8736 (ptm160) REVERT: B 632 ASP cc_start: 0.9254 (t0) cc_final: 0.9040 (t0) REVERT: B 633 LYS cc_start: 0.9394 (mptt) cc_final: 0.9092 (mptt) REVERT: E 99 ASN cc_start: 0.9032 (t0) cc_final: 0.8693 (t0) REVERT: E 475 MET cc_start: 0.7182 (mpp) cc_final: 0.6577 (mmm) REVERT: F 543 ASN cc_start: 0.9116 (m-40) cc_final: 0.8865 (m-40) REVERT: F 588 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7870 (ttm110) REVERT: F 647 GLU cc_start: 0.8656 (tt0) cc_final: 0.8242 (tt0) REVERT: H 31 ASP cc_start: 0.8619 (m-30) cc_final: 0.8359 (m-30) REVERT: H 43 LYS cc_start: 0.9107 (ptpp) cc_final: 0.8683 (ptpp) REVERT: I 173 TYR cc_start: 0.9029 (p90) cc_final: 0.8780 (p90) REVERT: I 188 ASN cc_start: 0.7910 (p0) cc_final: 0.7641 (p0) REVERT: J 535 MET cc_start: 0.9257 (mmt) cc_final: 0.8933 (mpp) REVERT: J 630 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8513 (pm20) REVERT: J 632 ASP cc_start: 0.9372 (t0) cc_final: 0.9088 (t0) REVERT: J 633 LYS cc_start: 0.9538 (mmtp) cc_final: 0.9091 (mmtm) REVERT: J 657 GLU cc_start: 0.8127 (tp30) cc_final: 0.7762 (tt0) REVERT: L 38 ARG cc_start: 0.8282 (ttt90) cc_final: 0.7552 (ttt90) REVERT: L 39 LYS cc_start: 0.8360 (mmtm) cc_final: 0.7937 (mmtm) REVERT: L 79 GLN cc_start: 0.7615 (mm110) cc_final: 0.7281 (mm110) outliers start: 34 outliers final: 25 residues processed: 189 average time/residue: 0.1294 time to fit residues: 37.2401 Evaluate side-chains 192 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain J residue 660 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 87 PHE Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 0.0670 chunk 74 optimal weight: 4.9990 chunk 151 optimal weight: 0.0370 chunk 112 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.080072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.059728 restraints weight = 41264.663| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 4.01 r_work: 0.2785 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16996 Z= 0.117 Angle : 0.587 11.880 23270 Z= 0.271 Chirality : 0.044 0.398 2886 Planarity : 0.003 0.037 2767 Dihedral : 7.257 56.830 4250 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.07 % Allowed : 11.64 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.20), residues: 1879 helix: 1.92 (0.27), residues: 399 sheet: -0.33 (0.22), residues: 532 loop : -0.45 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 38 TYR 0.010 0.001 TYR A 484 PHE 0.014 0.001 PHE H 58 TRP 0.010 0.001 TRP I 112 HIS 0.002 0.000 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00269 (16851) covalent geometry : angle 0.54760 (22873) SS BOND : bond 0.00250 ( 38) SS BOND : angle 0.82764 ( 76) hydrogen bonds : bond 0.03281 ( 485) hydrogen bonds : angle 4.39494 ( 1305) link_ALPHA1-2 : bond 0.01554 ( 2) link_ALPHA1-2 : angle 2.62292 ( 6) link_ALPHA1-3 : bond 0.01002 ( 4) link_ALPHA1-3 : angle 1.90086 ( 12) link_ALPHA1-6 : bond 0.00822 ( 4) link_ALPHA1-6 : angle 1.78534 ( 12) link_BETA1-4 : bond 0.00377 ( 43) link_BETA1-4 : angle 1.46944 ( 129) link_NAG-ASN : bond 0.00248 ( 54) link_NAG-ASN : angle 2.10032 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 CYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7469 (m) REVERT: A 376 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8611 (m-80) REVERT: A 426 MET cc_start: 0.7892 (tpt) cc_final: 0.7640 (tpt) REVERT: A 475 MET cc_start: 0.8532 (tpp) cc_final: 0.8084 (tpp) REVERT: B 540 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7287 (mp-120) REVERT: B 542 ARG cc_start: 0.9071 (ptm160) cc_final: 0.8756 (ptm160) REVERT: B 632 ASP cc_start: 0.9248 (t0) cc_final: 0.9003 (t0) REVERT: B 633 LYS cc_start: 0.9401 (mptt) cc_final: 0.9090 (mptt) REVERT: E 99 ASN cc_start: 0.9034 (t0) cc_final: 0.8691 (t0) REVERT: E 191 TYR cc_start: 0.9048 (m-80) cc_final: 0.8627 (m-80) REVERT: E 475 MET cc_start: 0.7180 (mpp) cc_final: 0.6582 (mmm) REVERT: F 543 ASN cc_start: 0.9112 (m-40) cc_final: 0.8858 (m-40) REVERT: F 588 ARG cc_start: 0.8192 (mtt-85) cc_final: 0.7867 (ttm110) REVERT: F 647 GLU cc_start: 0.8641 (tt0) cc_final: 0.8257 (tt0) REVERT: H 31 ASP cc_start: 0.8594 (m-30) cc_final: 0.8340 (m-30) REVERT: H 43 LYS cc_start: 0.9099 (ptpp) cc_final: 0.8673 (ptpp) REVERT: I 173 TYR cc_start: 0.9022 (p90) cc_final: 0.8771 (p90) REVERT: I 188 ASN cc_start: 0.7885 (p0) cc_final: 0.7609 (p0) REVERT: I 191 TYR cc_start: 0.9190 (m-80) cc_final: 0.8882 (m-80) REVERT: I 207 LYS cc_start: 0.8001 (tptt) cc_final: 0.7602 (tptp) REVERT: J 535 MET cc_start: 0.9255 (mmt) cc_final: 0.8915 (mpp) REVERT: J 630 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8558 (pm20) REVERT: J 632 ASP cc_start: 0.9358 (t0) cc_final: 0.9084 (t0) REVERT: J 657 GLU cc_start: 0.8131 (tp30) cc_final: 0.7767 (tt0) REVERT: L 38 ARG cc_start: 0.8274 (ttt90) cc_final: 0.7552 (ttt90) REVERT: L 39 LYS cc_start: 0.8325 (mmtm) cc_final: 0.7887 (mmtm) REVERT: L 45 LYS cc_start: 0.8270 (ttmm) cc_final: 0.7997 (ttmm) REVERT: L 79 GLN cc_start: 0.7571 (mm110) cc_final: 0.7236 (mm110) outliers start: 35 outliers final: 26 residues processed: 188 average time/residue: 0.1295 time to fit residues: 37.3962 Evaluate side-chains 191 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 87 PHE Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 97 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 166 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.078544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.058095 restraints weight = 41511.716| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 4.00 r_work: 0.2762 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16996 Z= 0.186 Angle : 0.627 11.964 23270 Z= 0.291 Chirality : 0.045 0.399 2886 Planarity : 0.003 0.037 2767 Dihedral : 7.375 58.358 4250 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.07 % Allowed : 11.81 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.20), residues: 1879 helix: 1.83 (0.27), residues: 398 sheet: -0.41 (0.22), residues: 539 loop : -0.49 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 298 TYR 0.021 0.001 TYR H 56 PHE 0.015 0.001 PHE H 58 TRP 0.018 0.001 TRP I 112 HIS 0.002 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00437 (16851) covalent geometry : angle 0.58657 (22873) SS BOND : bond 0.00264 ( 38) SS BOND : angle 0.95548 ( 76) hydrogen bonds : bond 0.03559 ( 485) hydrogen bonds : angle 4.48574 ( 1305) link_ALPHA1-2 : bond 0.01580 ( 2) link_ALPHA1-2 : angle 2.61815 ( 6) link_ALPHA1-3 : bond 0.00898 ( 4) link_ALPHA1-3 : angle 2.05170 ( 12) link_ALPHA1-6 : bond 0.00796 ( 4) link_ALPHA1-6 : angle 1.88681 ( 12) link_BETA1-4 : bond 0.00341 ( 43) link_BETA1-4 : angle 1.51157 ( 129) link_NAG-ASN : bond 0.00348 ( 54) link_NAG-ASN : angle 2.18776 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 CYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7470 (m) REVERT: A 376 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8668 (m-80) REVERT: A 426 MET cc_start: 0.8113 (tpt) cc_final: 0.7836 (tpt) REVERT: A 475 MET cc_start: 0.8534 (tpp) cc_final: 0.8091 (tpp) REVERT: B 540 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7342 (mp-120) REVERT: B 542 ARG cc_start: 0.9082 (ptm160) cc_final: 0.8764 (ptm160) REVERT: B 632 ASP cc_start: 0.9237 (t0) cc_final: 0.8987 (t0) REVERT: B 633 LYS cc_start: 0.9389 (mptt) cc_final: 0.9081 (mptt) REVERT: E 69 TRP cc_start: 0.7944 (OUTLIER) cc_final: 0.6834 (m100) REVERT: F 543 ASN cc_start: 0.9127 (m-40) cc_final: 0.8856 (m110) REVERT: F 588 ARG cc_start: 0.8212 (mtt-85) cc_final: 0.7884 (ttm110) REVERT: F 647 GLU cc_start: 0.8655 (tt0) cc_final: 0.8249 (tt0) REVERT: H 31 ASP cc_start: 0.8661 (m-30) cc_final: 0.8437 (m-30) REVERT: H 43 LYS cc_start: 0.9111 (ptpp) cc_final: 0.8793 (ptpp) REVERT: I 173 TYR cc_start: 0.9084 (p90) cc_final: 0.8839 (p90) REVERT: J 535 MET cc_start: 0.9232 (mmt) cc_final: 0.8864 (mpp) REVERT: J 630 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8568 (pm20) REVERT: J 632 ASP cc_start: 0.9397 (t0) cc_final: 0.9108 (t0) REVERT: J 657 GLU cc_start: 0.8125 (tp30) cc_final: 0.7777 (tt0) REVERT: L 38 ARG cc_start: 0.8353 (ttt90) cc_final: 0.7636 (ttt90) REVERT: L 42 LYS cc_start: 0.8463 (mttt) cc_final: 0.7915 (mtmm) REVERT: L 45 LYS cc_start: 0.8293 (ttmm) cc_final: 0.8034 (ttmm) REVERT: L 79 GLN cc_start: 0.7575 (mm110) cc_final: 0.7208 (mm110) outliers start: 35 outliers final: 26 residues processed: 184 average time/residue: 0.1333 time to fit residues: 37.3482 Evaluate side-chains 192 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 87 PHE Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 15 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.079729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.059463 restraints weight = 41016.712| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.99 r_work: 0.2781 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16996 Z= 0.121 Angle : 0.594 11.938 23270 Z= 0.276 Chirality : 0.044 0.398 2886 Planarity : 0.003 0.036 2767 Dihedral : 7.193 56.927 4250 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.95 % Allowed : 11.99 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.20), residues: 1879 helix: 1.91 (0.27), residues: 399 sheet: -0.31 (0.22), residues: 534 loop : -0.47 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 38 TYR 0.011 0.001 TYR A 484 PHE 0.013 0.001 PHE H 58 TRP 0.010 0.001 TRP I 112 HIS 0.002 0.000 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00280 (16851) covalent geometry : angle 0.55592 (22873) SS BOND : bond 0.00218 ( 38) SS BOND : angle 0.80784 ( 76) hydrogen bonds : bond 0.03311 ( 485) hydrogen bonds : angle 4.39632 ( 1305) link_ALPHA1-2 : bond 0.01559 ( 2) link_ALPHA1-2 : angle 2.57836 ( 6) link_ALPHA1-3 : bond 0.00968 ( 4) link_ALPHA1-3 : angle 1.87894 ( 12) link_ALPHA1-6 : bond 0.00806 ( 4) link_ALPHA1-6 : angle 1.72021 ( 12) link_BETA1-4 : bond 0.00376 ( 43) link_BETA1-4 : angle 1.43748 ( 129) link_NAG-ASN : bond 0.00249 ( 54) link_NAG-ASN : angle 2.09465 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 CYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7509 (m) REVERT: A 376 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8618 (m-80) REVERT: A 426 MET cc_start: 0.8029 (tpt) cc_final: 0.7819 (tpt) REVERT: A 475 MET cc_start: 0.8506 (tpp) cc_final: 0.8052 (tpp) REVERT: B 540 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7264 (mp-120) REVERT: B 542 ARG cc_start: 0.9079 (ptm160) cc_final: 0.8762 (ptm160) REVERT: B 632 ASP cc_start: 0.9209 (t0) cc_final: 0.8926 (t0) REVERT: B 633 LYS cc_start: 0.9377 (mptt) cc_final: 0.9061 (mptt) REVERT: E 475 MET cc_start: 0.7168 (mpp) cc_final: 0.6544 (mmm) REVERT: F 543 ASN cc_start: 0.9107 (m-40) cc_final: 0.8844 (m-40) REVERT: F 588 ARG cc_start: 0.8182 (mtt-85) cc_final: 0.7858 (ttm110) REVERT: F 647 GLU cc_start: 0.8646 (tt0) cc_final: 0.8257 (tt0) REVERT: H 31 ASP cc_start: 0.8689 (m-30) cc_final: 0.8437 (m-30) REVERT: H 43 LYS cc_start: 0.9113 (ptpp) cc_final: 0.8802 (ptpp) REVERT: I 173 TYR cc_start: 0.9029 (p90) cc_final: 0.8776 (p90) REVERT: I 191 TYR cc_start: 0.9180 (m-80) cc_final: 0.8964 (m-80) REVERT: J 535 MET cc_start: 0.9195 (mmt) cc_final: 0.8813 (mpp) REVERT: J 630 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8563 (pm20) REVERT: J 632 ASP cc_start: 0.9363 (t0) cc_final: 0.9075 (t0) REVERT: J 657 GLU cc_start: 0.8067 (tp30) cc_final: 0.7680 (tt0) REVERT: L 38 ARG cc_start: 0.8284 (ttt90) cc_final: 0.7571 (ttt90) REVERT: L 39 LYS cc_start: 0.8293 (mmtm) cc_final: 0.7357 (mmtm) REVERT: L 42 LYS cc_start: 0.8426 (mttt) cc_final: 0.7692 (ttpt) REVERT: L 45 LYS cc_start: 0.8268 (ttmm) cc_final: 0.8027 (ttmm) outliers start: 33 outliers final: 27 residues processed: 184 average time/residue: 0.1339 time to fit residues: 37.4944 Evaluate side-chains 191 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 87 PHE Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.5777 > 50: distance: 99 - 216: 3.340 distance: 135 - 145: 5.049 distance: 145 - 146: 3.323 distance: 146 - 147: 6.122 distance: 147 - 148: 4.541 distance: 147 - 150: 9.366 distance: 150 - 151: 10.656 distance: 150 - 156: 4.772 distance: 151 - 152: 9.322 distance: 151 - 154: 11.311 distance: 152 - 153: 5.914 distance: 152 - 157: 9.005 distance: 154 - 155: 3.930 distance: 155 - 156: 7.449 distance: 157 - 158: 5.458 distance: 157 - 163: 3.039 distance: 158 - 159: 5.204 distance: 158 - 161: 7.078 distance: 159 - 160: 4.442 distance: 159 - 164: 5.341 distance: 161 - 162: 6.899 distance: 162 - 163: 5.199 distance: 164 - 165: 7.028 distance: 165 - 166: 17.463 distance: 165 - 168: 4.944 distance: 166 - 167: 40.488 distance: 166 - 172: 13.714 distance: 168 - 169: 5.660 distance: 168 - 170: 6.162 distance: 169 - 171: 7.828 distance: 172 - 173: 20.064 distance: 173 - 174: 10.222 distance: 173 - 176: 19.867 distance: 174 - 175: 15.351 distance: 174 - 181: 15.208 distance: 176 - 177: 9.837 distance: 177 - 178: 10.272 distance: 178 - 179: 14.257 distance: 178 - 180: 9.546 distance: 181 - 182: 12.131 distance: 182 - 183: 12.642 distance: 183 - 184: 8.389 distance: 183 - 185: 7.571 distance: 185 - 186: 6.205 distance: 186 - 187: 4.201 distance: 186 - 189: 4.504 distance: 187 - 188: 5.639 distance: 187 - 192: 7.619 distance: 189 - 190: 9.049 distance: 189 - 191: 7.908 distance: 192 - 193: 5.617 distance: 193 - 194: 3.841 distance: 193 - 196: 5.658 distance: 194 - 195: 7.858 distance: 194 - 200: 4.600 distance: 196 - 197: 9.491 distance: 196 - 198: 13.268 distance: 197 - 199: 9.612 distance: 201 - 204: 4.000 distance: 204 - 205: 3.045 distance: 205 - 206: 5.248 distance: 208 - 209: 3.015 distance: 212 - 213: 3.194 distance: 212 - 215: 3.283 distance: 213 - 214: 4.358 distance: 215 - 216: 9.371