Starting phenix.real_space_refine on Sun May 18 06:47:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bnp_44733/05_2025/9bnp_44733.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bnp_44733/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bnp_44733/05_2025/9bnp_44733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bnp_44733/05_2025/9bnp_44733.map" model { file = "/net/cci-nas-00/data/ceres_data/9bnp_44733/05_2025/9bnp_44733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bnp_44733/05_2025/9bnp_44733.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.01, per 1000 atoms: 0.73 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: 5.85 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.94 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: 5.46 Time building geometry restraints manager: 6.55 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 505 or resid 601 throu \ gh 604)) selection = chain 'E' selection = (chain 'I' and (resid 33 through 184 or resid 188 through 397 or resid 412 throu \ gh 505 or resid 601 through 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: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 42.440 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.580 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (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 TRP 0.063 0.003 TRP J 631 HIS 0.006 0.001 HIS A 374 PHE 0.038 0.003 PHE L 87 TYR 0.026 0.002 TYR F 638 ARG 0.007 0.001 ARG E 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 54) link_NAG-ASN : angle 2.94799 ( 162) 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_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) hydrogen bonds : bond 0.14406 ( 485) hydrogen bonds : angle 6.56977 ( 1305) SS BOND : bond 0.00453 ( 38) SS BOND : angle 2.04233 ( 76) covalent geometry : bond 0.00565 (16851) covalent geometry : angle 1.19690 (22873) *********************** 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 : 1.692 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: 0.8575 (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: 0.2995 time to fit residues: 85.4857 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 : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.5980 chunk 142 optimal weight: 0.0970 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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** I 130 GLN L 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.087687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.067730 restraints weight = 40579.704| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.95 r_work: 0.2977 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16996 Z= 0.119 Angle : 0.649 11.411 23270 Z= 0.300 Chirality : 0.045 0.415 2886 Planarity : 0.003 0.042 2767 Dihedral : 10.662 82.159 4250 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.89 % Allowed : 6.79 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1879 helix: 1.48 (0.27), residues: 402 sheet: -0.60 (0.22), residues: 536 loop : -0.47 (0.21), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 479 HIS 0.003 0.001 HIS E 105 PHE 0.011 0.001 PHE L 87 TYR 0.009 0.001 TYR I 318 ARG 0.005 0.000 ARG L 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 54) link_NAG-ASN : angle 2.30785 ( 162) link_ALPHA1-6 : bond 0.00611 ( 4) link_ALPHA1-6 : angle 2.00891 ( 12) link_BETA1-4 : bond 0.00485 ( 43) link_BETA1-4 : angle 1.81499 ( 129) link_ALPHA1-2 : bond 0.01327 ( 2) link_ALPHA1-2 : angle 3.26823 ( 6) link_ALPHA1-3 : bond 0.01031 ( 4) link_ALPHA1-3 : angle 2.36685 ( 12) hydrogen bonds : bond 0.04238 ( 485) hydrogen bonds : angle 5.20611 ( 1305) SS BOND : bond 0.00193 ( 38) SS BOND : angle 0.92328 ( 76) covalent geometry : bond 0.00263 (16851) covalent geometry : angle 0.60127 (22873) *********************** 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 184 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6862 (tmtt) cc_final: 0.6254 (tptt) REVERT: A 271 MET cc_start: 0.7883 (mmm) cc_final: 0.7555 (mmt) REVERT: B 542 ARG cc_start: 0.9024 (ptm160) cc_final: 0.8684 (ptm160) REVERT: B 633 LYS cc_start: 0.9320 (mptt) cc_final: 0.8996 (mptt) REVERT: E 169 LYS cc_start: 0.8580 (mttt) cc_final: 0.8358 (mttt) REVERT: F 543 ASN cc_start: 0.9148 (m-40) cc_final: 0.8897 (m110) REVERT: F 584 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8600 (mt-10) REVERT: F 588 ARG cc_start: 0.8048 (mtt-85) cc_final: 0.7754 (ttm110) REVERT: F 621 GLU cc_start: 0.8634 (tp30) cc_final: 0.8424 (tp30) REVERT: F 647 GLU cc_start: 0.8582 (tt0) cc_final: 0.8182 (tt0) REVERT: H 43 LYS cc_start: 0.9036 (ptpp) cc_final: 0.8803 (ptpp) REVERT: I 161 MET cc_start: 0.9053 (tpt) cc_final: 0.8574 (tpt) REVERT: I 173 TYR cc_start: 0.8990 (p90) cc_final: 0.8573 (p90) REVERT: I 188 ASN cc_start: 0.7845 (p0) cc_final: 0.7606 (p0) REVERT: J 535 MET cc_start: 0.9267 (mmt) cc_final: 0.9059 (mpp) REVERT: J 624 ASP cc_start: 0.8697 (m-30) cc_final: 0.8133 (m-30) REVERT: J 632 ASP cc_start: 0.9311 (t0) cc_final: 0.9054 (t0) REVERT: J 657 GLU cc_start: 0.8085 (tp30) cc_final: 0.7737 (tt0) REVERT: L 17 ASP cc_start: 0.7243 (t0) cc_final: 0.6949 (t0) outliers start: 15 outliers final: 6 residues processed: 178 average time/residue: 0.2751 time to fit residues: 74.6462 Evaluate side-chains 162 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 156 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 67 optimal weight: 3.9990 chunk 112 optimal weight: 0.0870 chunk 108 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.080608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.060002 restraints weight = 41170.038| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 4.04 r_work: 0.2794 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16996 Z= 0.199 Angle : 0.666 10.676 23270 Z= 0.313 Chirality : 0.046 0.399 2886 Planarity : 0.004 0.039 2767 Dihedral : 8.887 69.579 4250 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.24 % Allowed : 8.33 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1879 helix: 1.39 (0.27), residues: 409 sheet: -0.42 (0.22), residues: 517 loop : -0.47 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 479 HIS 0.004 0.001 HIS E 330 PHE 0.018 0.002 PHE H 58 TYR 0.014 0.002 TYR A 173 ARG 0.004 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 54) link_NAG-ASN : angle 2.28567 ( 162) link_ALPHA1-6 : bond 0.00687 ( 4) link_ALPHA1-6 : angle 2.30598 ( 12) link_BETA1-4 : bond 0.00365 ( 43) link_BETA1-4 : angle 1.79648 ( 129) link_ALPHA1-2 : bond 0.01477 ( 2) link_ALPHA1-2 : angle 2.35087 ( 6) link_ALPHA1-3 : bond 0.00992 ( 4) link_ALPHA1-3 : angle 1.99999 ( 12) hydrogen bonds : bond 0.04172 ( 485) hydrogen bonds : angle 4.78772 ( 1305) SS BOND : bond 0.00267 ( 38) SS BOND : angle 1.02465 ( 76) covalent geometry : bond 0.00469 (16851) covalent geometry : angle 0.62123 (22873) *********************** 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 189 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.7225 (tmtt) cc_final: 0.6766 (tptt) REVERT: A 271 MET cc_start: 0.8153 (mmm) cc_final: 0.7848 (mmt) REVERT: A 475 MET cc_start: 0.8539 (tpp) cc_final: 0.7951 (tpp) REVERT: B 540 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7388 (mp-120) REVERT: B 542 ARG cc_start: 0.9080 (ptm160) cc_final: 0.8732 (ptm160) REVERT: E 169 LYS cc_start: 0.8632 (mttt) cc_final: 0.8379 (mttt) REVERT: F 584 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8429 (mt-10) REVERT: F 588 ARG cc_start: 0.8139 (mtt-85) cc_final: 0.7799 (ttm110) REVERT: F 621 GLU cc_start: 0.8718 (tp30) cc_final: 0.8410 (tp30) REVERT: F 625 ASN cc_start: 0.8470 (t0) cc_final: 0.8175 (t0) REVERT: F 647 GLU cc_start: 0.8660 (tt0) cc_final: 0.8254 (tt0) REVERT: H 43 LYS cc_start: 0.9009 (ptpp) cc_final: 0.8759 (ptpp) REVERT: H 83 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.7928 (mtt90) REVERT: I 173 TYR cc_start: 0.9035 (p90) cc_final: 0.8665 (p90) REVERT: I 188 ASN cc_start: 0.7832 (p0) cc_final: 0.7550 (p0) REVERT: J 535 MET cc_start: 0.9304 (mmt) cc_final: 0.9026 (mpp) REVERT: J 624 ASP cc_start: 0.8919 (m-30) cc_final: 0.8509 (m-30) REVERT: J 632 ASP cc_start: 0.9437 (t0) cc_final: 0.9125 (t0) REVERT: J 633 LYS cc_start: 0.9498 (mmtp) cc_final: 0.9007 (mmtm) REVERT: J 657 GLU cc_start: 0.8101 (tp30) cc_final: 0.7757 (tt0) REVERT: L 100 GLN cc_start: 0.8925 (mp10) cc_final: 0.8698 (mp-120) REVERT: L 105 GLU cc_start: 0.4545 (OUTLIER) cc_final: 0.4140 (tp30) outliers start: 21 outliers final: 14 residues processed: 179 average time/residue: 0.2953 time to fit residues: 79.2358 Evaluate side-chains 169 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 THR 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 599 SER Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain J residue 641 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 Chi-restraints excluded: chain L residue 105 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 118 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 0.0570 chunk 78 optimal weight: 0.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.081495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.061096 restraints weight = 40723.199| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 4.03 r_work: 0.2819 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 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 = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16996 Z= 0.124 Angle : 0.590 10.976 23270 Z= 0.272 Chirality : 0.044 0.396 2886 Planarity : 0.003 0.035 2767 Dihedral : 7.964 57.767 4250 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.36 % Allowed : 9.51 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.20), residues: 1879 helix: 1.50 (0.27), residues: 405 sheet: -0.31 (0.22), residues: 534 loop : -0.39 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 112 HIS 0.003 0.001 HIS E 105 PHE 0.015 0.001 PHE H 58 TYR 0.010 0.001 TYR I 318 ARG 0.004 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 54) link_NAG-ASN : angle 2.16142 ( 162) link_ALPHA1-6 : bond 0.00783 ( 4) link_ALPHA1-6 : angle 2.08659 ( 12) link_BETA1-4 : bond 0.00390 ( 43) link_BETA1-4 : angle 1.57623 ( 129) link_ALPHA1-2 : bond 0.01311 ( 2) link_ALPHA1-2 : angle 2.68028 ( 6) link_ALPHA1-3 : bond 0.01126 ( 4) link_ALPHA1-3 : angle 2.14280 ( 12) hydrogen bonds : bond 0.03513 ( 485) hydrogen bonds : angle 4.56797 ( 1305) SS BOND : bond 0.00197 ( 38) SS BOND : angle 0.79507 ( 76) covalent geometry : bond 0.00286 (16851) covalent geometry : angle 0.54581 (22873) *********************** 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 194 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9057 (tpt) cc_final: 0.8702 (tpt) REVERT: A 207 LYS cc_start: 0.7242 (tmtt) cc_final: 0.6724 (tptt) REVERT: A 271 MET cc_start: 0.8118 (mmm) cc_final: 0.7858 (mmt) REVERT: A 475 MET cc_start: 0.8502 (tpp) cc_final: 0.8105 (tpp) REVERT: B 542 ARG cc_start: 0.9058 (ptm160) cc_final: 0.8689 (ptm160) REVERT: B 633 LYS cc_start: 0.9411 (mptt) cc_final: 0.9101 (mptt) REVERT: E 169 LYS cc_start: 0.8579 (mttt) cc_final: 0.8323 (mttt) REVERT: F 584 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8315 (mt-10) REVERT: F 588 ARG cc_start: 0.8140 (mtt-85) cc_final: 0.7797 (ttm110) REVERT: F 647 GLU cc_start: 0.8616 (tt0) cc_final: 0.8225 (tt0) REVERT: H 43 LYS cc_start: 0.9019 (ptpp) cc_final: 0.8754 (ptpp) REVERT: I 173 TYR cc_start: 0.9029 (p90) cc_final: 0.8665 (p90) REVERT: I 188 ASN cc_start: 0.7807 (p0) cc_final: 0.7516 (p0) REVERT: I 207 LYS cc_start: 0.8160 (tptt) cc_final: 0.7683 (tptp) REVERT: J 535 MET cc_start: 0.9252 (mmt) cc_final: 0.8973 (mpp) REVERT: J 624 ASP cc_start: 0.8927 (m-30) cc_final: 0.8493 (m-30) REVERT: J 630 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8483 (pm20) REVERT: J 632 ASP cc_start: 0.9371 (t0) cc_final: 0.9048 (t0) REVERT: J 633 LYS cc_start: 0.9520 (mmtp) cc_final: 0.9023 (mmtm) REVERT: J 657 GLU cc_start: 0.8106 (tp30) cc_final: 0.7775 (tt0) REVERT: L 79 GLN cc_start: 0.7776 (mm110) cc_final: 0.7465 (mm110) REVERT: L 82 ASP cc_start: 0.6080 (m-30) cc_final: 0.5818 (m-30) REVERT: L 100 GLN cc_start: 0.8937 (mp10) cc_final: 0.8676 (mp-120) outliers start: 23 outliers final: 14 residues processed: 185 average time/residue: 0.2931 time to fit residues: 81.0967 Evaluate side-chains 172 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 22 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 70 ASP 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 150 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 H 102 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.079470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.058773 restraints weight = 41638.151| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.06 r_work: 0.2762 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 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 = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16996 Z= 0.210 Angle : 0.644 11.042 23270 Z= 0.301 Chirality : 0.045 0.402 2886 Planarity : 0.003 0.036 2767 Dihedral : 7.860 58.326 4250 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.54 % Allowed : 10.22 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.20), residues: 1879 helix: 1.55 (0.27), residues: 406 sheet: -0.40 (0.22), residues: 538 loop : -0.48 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 112 HIS 0.003 0.001 HIS E 105 PHE 0.016 0.002 PHE H 58 TYR 0.018 0.001 TYR H 56 ARG 0.004 0.000 ARG A 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 54) link_NAG-ASN : angle 2.25052 ( 162) link_ALPHA1-6 : bond 0.00834 ( 4) link_ALPHA1-6 : angle 2.22766 ( 12) link_BETA1-4 : bond 0.00350 ( 43) link_BETA1-4 : angle 1.61269 ( 129) link_ALPHA1-2 : bond 0.01378 ( 2) link_ALPHA1-2 : angle 2.62373 ( 6) link_ALPHA1-3 : bond 0.01021 ( 4) link_ALPHA1-3 : angle 2.18387 ( 12) hydrogen bonds : bond 0.03786 ( 485) hydrogen bonds : angle 4.59567 ( 1305) SS BOND : bond 0.00278 ( 38) SS BOND : angle 1.42630 ( 76) covalent geometry : bond 0.00497 (16851) covalent geometry : angle 0.59783 (22873) *********************** 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 183 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9105 (tpt) cc_final: 0.8814 (tpt) REVERT: A 271 MET cc_start: 0.8263 (mmm) cc_final: 0.7978 (mmt) REVERT: A 475 MET cc_start: 0.8612 (tpp) cc_final: 0.8214 (tpp) REVERT: B 540 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7352 (mp-120) REVERT: B 542 ARG cc_start: 0.9088 (ptm160) cc_final: 0.8745 (ptm160) REVERT: B 632 ASP cc_start: 0.9266 (t0) cc_final: 0.9057 (t0) REVERT: B 633 LYS cc_start: 0.9396 (mptt) cc_final: 0.9070 (mptt) REVERT: E 169 LYS cc_start: 0.8610 (mttt) cc_final: 0.8373 (mtmm) REVERT: F 584 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8320 (mt-10) REVERT: F 588 ARG cc_start: 0.8183 (mtt-85) cc_final: 0.7851 (ttm110) REVERT: F 621 GLU cc_start: 0.8524 (tp30) cc_final: 0.8323 (tp30) REVERT: F 647 GLU cc_start: 0.8658 (tt0) cc_final: 0.8268 (tt0) REVERT: H 43 LYS cc_start: 0.9044 (ptpp) cc_final: 0.8601 (ptpp) REVERT: I 107 ASP cc_start: 0.8976 (t0) cc_final: 0.8701 (t0) REVERT: I 173 TYR cc_start: 0.9063 (p90) cc_final: 0.8762 (p90) REVERT: I 188 ASN cc_start: 0.7906 (p0) cc_final: 0.7593 (p0) REVERT: I 207 LYS cc_start: 0.8108 (tptt) cc_final: 0.7676 (tptp) REVERT: J 535 MET cc_start: 0.9286 (mmt) cc_final: 0.8936 (mpp) REVERT: J 632 ASP cc_start: 0.9425 (t0) cc_final: 0.9122 (t0) REVERT: J 633 LYS cc_start: 0.9548 (mmtp) cc_final: 0.9305 (mmmm) REVERT: J 657 GLU cc_start: 0.8090 (tp30) cc_final: 0.7741 (tt0) REVERT: L 79 GLN cc_start: 0.7730 (mm110) cc_final: 0.7368 (mm110) REVERT: L 82 ASP cc_start: 0.6231 (m-30) cc_final: 0.5980 (m-30) outliers start: 26 outliers final: 19 residues processed: 175 average time/residue: 0.2897 time to fit residues: 76.0971 Evaluate side-chains 175 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 574 LYS 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 443 ILE 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 I residue 244 THR Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 626 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 181 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 176 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.078009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.057220 restraints weight = 41839.019| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 4.05 r_work: 0.2726 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 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 = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 16996 Z= 0.247 Angle : 0.667 12.008 23270 Z= 0.315 Chirality : 0.046 0.414 2886 Planarity : 0.004 0.039 2767 Dihedral : 7.814 58.778 4250 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.36 % Allowed : 10.40 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1879 helix: 1.46 (0.27), residues: 404 sheet: -0.40 (0.22), residues: 530 loop : -0.58 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 112 HIS 0.004 0.001 HIS A 330 PHE 0.016 0.002 PHE H 58 TYR 0.016 0.001 TYR L 49 ARG 0.004 0.000 ARG A 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 54) link_NAG-ASN : angle 2.35110 ( 162) link_ALPHA1-6 : bond 0.00847 ( 4) link_ALPHA1-6 : angle 2.24161 ( 12) link_BETA1-4 : bond 0.00336 ( 43) link_BETA1-4 : angle 1.58506 ( 129) link_ALPHA1-2 : bond 0.01491 ( 2) link_ALPHA1-2 : angle 2.63927 ( 6) link_ALPHA1-3 : bond 0.01000 ( 4) link_ALPHA1-3 : angle 2.28013 ( 12) hydrogen bonds : bond 0.03953 ( 485) hydrogen bonds : angle 4.68490 ( 1305) SS BOND : bond 0.00334 ( 38) SS BOND : angle 1.26286 ( 76) covalent geometry : bond 0.00583 (16851) covalent geometry : angle 0.62237 (22873) *********************** 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 200 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9117 (tpt) cc_final: 0.8911 (tpt) REVERT: A 205 CYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7302 (m) REVERT: A 207 LYS cc_start: 0.7718 (tmtt) cc_final: 0.7148 (tptt) REVERT: A 376 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8424 (m-10) REVERT: A 475 MET cc_start: 0.8596 (tpp) cc_final: 0.8196 (tpp) REVERT: A 484 TYR cc_start: 0.8746 (p90) cc_final: 0.8368 (p90) REVERT: B 540 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7413 (mp-120) REVERT: B 542 ARG cc_start: 0.9101 (ptm160) cc_final: 0.8743 (ptm160) REVERT: B 543 ASN cc_start: 0.8875 (m-40) cc_final: 0.8654 (m-40) REVERT: B 632 ASP cc_start: 0.9259 (t0) cc_final: 0.9030 (t0) REVERT: B 633 LYS cc_start: 0.9392 (mptt) cc_final: 0.9066 (mptt) REVERT: E 475 MET cc_start: 0.7127 (mpp) cc_final: 0.6511 (mmm) REVERT: F 584 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8291 (mt-10) REVERT: F 588 ARG cc_start: 0.8224 (mtt-85) cc_final: 0.7887 (ttm110) REVERT: F 647 GLU cc_start: 0.8675 (tt0) cc_final: 0.8275 (tt0) REVERT: I 107 ASP cc_start: 0.9012 (t0) cc_final: 0.8668 (t0) REVERT: I 173 TYR cc_start: 0.9054 (p90) cc_final: 0.8807 (p90) REVERT: J 535 MET cc_start: 0.9293 (mmt) cc_final: 0.8906 (mpp) REVERT: J 630 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8486 (pm20) REVERT: J 632 ASP cc_start: 0.9438 (t0) cc_final: 0.9143 (t0) REVERT: J 633 LYS cc_start: 0.9565 (mmtp) cc_final: 0.9317 (mmmm) REVERT: J 657 GLU cc_start: 0.8097 (tp30) cc_final: 0.7760 (tt0) REVERT: L 50 LYS cc_start: 0.8871 (tppp) cc_final: 0.8636 (tppp) REVERT: L 79 GLN cc_start: 0.7687 (mm110) cc_final: 0.7265 (mm110) outliers start: 40 outliers final: 24 residues processed: 191 average time/residue: 0.2860 time to fit residues: 82.8252 Evaluate side-chains 184 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLN 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 205 CYS Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 615 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 I residue 244 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 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 Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.078703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.058258 restraints weight = 41491.050| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 4.00 r_work: 0.2750 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 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 = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16996 Z= 0.171 Angle : 0.625 11.870 23270 Z= 0.290 Chirality : 0.045 0.410 2886 Planarity : 0.003 0.039 2767 Dihedral : 7.580 58.527 4250 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.07 % Allowed : 11.28 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.20), residues: 1879 helix: 1.59 (0.27), residues: 404 sheet: -0.41 (0.22), residues: 531 loop : -0.55 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 112 HIS 0.003 0.001 HIS E 105 PHE 0.014 0.001 PHE H 58 TYR 0.021 0.001 TYR H 56 ARG 0.003 0.000 ARG A 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 54) link_NAG-ASN : angle 2.24271 ( 162) link_ALPHA1-6 : bond 0.00832 ( 4) link_ALPHA1-6 : angle 1.99616 ( 12) link_BETA1-4 : bond 0.00351 ( 43) link_BETA1-4 : angle 1.52010 ( 129) link_ALPHA1-2 : bond 0.01548 ( 2) link_ALPHA1-2 : angle 2.58779 ( 6) link_ALPHA1-3 : bond 0.00976 ( 4) link_ALPHA1-3 : angle 2.07101 ( 12) hydrogen bonds : bond 0.03650 ( 485) hydrogen bonds : angle 4.58311 ( 1305) SS BOND : bond 0.00263 ( 38) SS BOND : angle 0.94562 ( 76) covalent geometry : bond 0.00400 (16851) covalent geometry : angle 0.58274 (22873) *********************** 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 202 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9125 (tpt) cc_final: 0.8918 (tpt) REVERT: A 205 CYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7427 (m) REVERT: A 207 LYS cc_start: 0.7790 (tmtt) cc_final: 0.7378 (tptt) REVERT: A 475 MET cc_start: 0.8595 (tpp) cc_final: 0.8140 (tpp) REVERT: A 484 TYR cc_start: 0.8718 (p90) cc_final: 0.8324 (p90) REVERT: B 540 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7384 (mp-120) REVERT: B 542 ARG cc_start: 0.9093 (ptm160) cc_final: 0.8762 (ptm160) REVERT: B 632 ASP cc_start: 0.9193 (t0) cc_final: 0.8898 (t0) REVERT: B 633 LYS cc_start: 0.9391 (mptt) cc_final: 0.9039 (mptt) REVERT: E 475 MET cc_start: 0.7113 (mpp) cc_final: 0.6530 (mmm) REVERT: F 543 ASN cc_start: 0.8904 (m-40) cc_final: 0.8701 (m-40) REVERT: F 584 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8271 (mt-10) REVERT: F 588 ARG cc_start: 0.8225 (mtt-85) cc_final: 0.7898 (ttm110) REVERT: F 647 GLU cc_start: 0.8652 (tt0) cc_final: 0.8234 (tt0) REVERT: I 161 MET cc_start: 0.9158 (tpt) cc_final: 0.8826 (tpt) REVERT: I 173 TYR cc_start: 0.9053 (p90) cc_final: 0.8801 (p90) REVERT: J 535 MET cc_start: 0.9277 (mmt) cc_final: 0.8862 (mpp) REVERT: J 630 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8507 (pm20) REVERT: J 632 ASP cc_start: 0.9394 (t0) cc_final: 0.9124 (t0) REVERT: J 633 LYS cc_start: 0.9569 (mmtp) cc_final: 0.9316 (mmmm) REVERT: J 657 GLU cc_start: 0.8097 (tp30) cc_final: 0.7705 (tt0) REVERT: L 79 GLN cc_start: 0.7584 (mm110) cc_final: 0.7211 (mm110) outliers start: 35 outliers final: 25 residues processed: 192 average time/residue: 0.2886 time to fit residues: 84.6647 Evaluate side-chains 187 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 205 CYS 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 126 CYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 599 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 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 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 75 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 121 optimal weight: 0.0670 chunk 58 optimal weight: 8.9990 chunk 134 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 174 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 114 optimal weight: 0.0870 chunk 5 optimal weight: 3.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.081123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.060639 restraints weight = 40819.207| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 4.03 r_work: 0.2807 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16996 Z= 0.098 Angle : 0.584 11.413 23270 Z= 0.271 Chirality : 0.044 0.400 2886 Planarity : 0.003 0.037 2767 Dihedral : 7.199 59.590 4250 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.71 % Allowed : 11.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1879 helix: 1.63 (0.27), residues: 411 sheet: -0.21 (0.23), residues: 529 loop : -0.42 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 32 HIS 0.002 0.001 HIS E 105 PHE 0.011 0.001 PHE H 58 TYR 0.010 0.001 TYR A 484 ARG 0.003 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 54) link_NAG-ASN : angle 2.07027 ( 162) link_ALPHA1-6 : bond 0.00868 ( 4) link_ALPHA1-6 : angle 1.64006 ( 12) link_BETA1-4 : bond 0.00415 ( 43) link_BETA1-4 : angle 1.40323 ( 129) link_ALPHA1-2 : bond 0.01612 ( 2) link_ALPHA1-2 : angle 2.62890 ( 6) link_ALPHA1-3 : bond 0.01047 ( 4) link_ALPHA1-3 : angle 1.77078 ( 12) hydrogen bonds : bond 0.03157 ( 485) hydrogen bonds : angle 4.37952 ( 1305) SS BOND : bond 0.00262 ( 38) SS BOND : angle 0.77973 ( 76) covalent geometry : bond 0.00213 (16851) covalent geometry : angle 0.54620 (22873) *********************** 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 194 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9093 (tpt) cc_final: 0.8865 (tpt) REVERT: A 205 CYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7469 (m) REVERT: A 475 MET cc_start: 0.8552 (tpp) cc_final: 0.8080 (tpp) REVERT: A 484 TYR cc_start: 0.8511 (p90) cc_final: 0.8071 (p90) REVERT: B 540 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7295 (mp-120) REVERT: B 542 ARG cc_start: 0.9049 (ptm160) cc_final: 0.8713 (ptm160) REVERT: B 632 ASP cc_start: 0.9142 (t0) cc_final: 0.8825 (t0) REVERT: B 633 LYS cc_start: 0.9371 (mptt) cc_final: 0.9047 (mptt) REVERT: E 475 MET cc_start: 0.7048 (mpp) cc_final: 0.6522 (mmm) REVERT: F 584 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8231 (mt-10) REVERT: F 588 ARG cc_start: 0.8167 (mtt-85) cc_final: 0.7844 (ttm110) REVERT: F 633 LYS cc_start: 0.9166 (ttmm) cc_final: 0.8889 (mtmt) REVERT: F 647 GLU cc_start: 0.8635 (tt0) cc_final: 0.8251 (tt0) REVERT: H 43 LYS cc_start: 0.9034 (ptpp) cc_final: 0.8629 (ptpp) REVERT: I 173 TYR cc_start: 0.9020 (p90) cc_final: 0.8762 (p90) REVERT: I 188 ASN cc_start: 0.7713 (p0) cc_final: 0.7456 (p0) REVERT: J 535 MET cc_start: 0.9203 (mmt) cc_final: 0.8820 (mpp) REVERT: J 630 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8530 (pm20) REVERT: J 632 ASP cc_start: 0.9341 (t0) cc_final: 0.9078 (t0) REVERT: J 633 LYS cc_start: 0.9567 (mmtp) cc_final: 0.9307 (mmmm) REVERT: J 657 GLU cc_start: 0.8121 (tp30) cc_final: 0.7745 (tt0) REVERT: L 45 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7961 (ttmm) REVERT: L 70 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7739 (t0) outliers start: 29 outliers final: 17 residues processed: 185 average time/residue: 0.2742 time to fit residues: 76.8673 Evaluate side-chains 181 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 205 CYS 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 E residue 126 CYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 615 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 626 MET Chi-restraints excluded: chain J residue 630 GLN 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 70 ASP 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 106 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 65 optimal weight: 0.0570 chunk 99 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 151 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.080881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.060387 restraints weight = 40945.063| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 4.03 r_work: 0.2801 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16996 Z= 0.107 Angle : 0.581 11.896 23270 Z= 0.269 Chirality : 0.043 0.394 2886 Planarity : 0.003 0.036 2767 Dihedral : 7.092 56.504 4250 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.42 % Allowed : 12.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1879 helix: 1.71 (0.27), residues: 408 sheet: -0.21 (0.23), residues: 531 loop : -0.41 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 479 HIS 0.002 0.000 HIS E 105 PHE 0.012 0.001 PHE H 58 TYR 0.019 0.001 TYR H 56 ARG 0.002 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 54) link_NAG-ASN : angle 2.05285 ( 162) link_ALPHA1-6 : bond 0.00863 ( 4) link_ALPHA1-6 : angle 1.61045 ( 12) link_BETA1-4 : bond 0.00400 ( 43) link_BETA1-4 : angle 1.40504 ( 129) link_ALPHA1-2 : bond 0.01564 ( 2) link_ALPHA1-2 : angle 2.59836 ( 6) link_ALPHA1-3 : bond 0.00970 ( 4) link_ALPHA1-3 : angle 1.84977 ( 12) hydrogen bonds : bond 0.03169 ( 485) hydrogen bonds : angle 4.31660 ( 1305) SS BOND : bond 0.00219 ( 38) SS BOND : angle 0.83478 ( 76) covalent geometry : bond 0.00244 (16851) covalent geometry : angle 0.54340 (22873) *********************** 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 188 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9124 (tpt) cc_final: 0.8876 (tpt) REVERT: A 205 CYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7631 (m) REVERT: A 475 MET cc_start: 0.8547 (tpp) cc_final: 0.8080 (tpp) REVERT: A 484 TYR cc_start: 0.8549 (p90) cc_final: 0.8093 (p90) REVERT: B 540 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7277 (mp-120) REVERT: B 542 ARG cc_start: 0.9041 (ptm160) cc_final: 0.8708 (ptm160) REVERT: B 632 ASP cc_start: 0.9141 (t0) cc_final: 0.8841 (t0) REVERT: B 633 LYS cc_start: 0.9376 (mptt) cc_final: 0.9054 (mptt) REVERT: E 191 TYR cc_start: 0.9003 (m-80) cc_final: 0.8537 (m-80) REVERT: E 475 MET cc_start: 0.7116 (mpp) cc_final: 0.6577 (mmm) REVERT: F 584 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8281 (mt-10) REVERT: F 588 ARG cc_start: 0.8161 (mtt-85) cc_final: 0.7841 (ttm110) REVERT: F 647 GLU cc_start: 0.8646 (tt0) cc_final: 0.8262 (tt0) REVERT: H 43 LYS cc_start: 0.9063 (ptpp) cc_final: 0.8656 (ptpp) REVERT: I 173 TYR cc_start: 0.9014 (p90) cc_final: 0.8763 (p90) REVERT: J 535 MET cc_start: 0.9189 (mmt) cc_final: 0.8857 (mpp) REVERT: J 630 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8529 (pm20) REVERT: J 632 ASP cc_start: 0.9350 (t0) cc_final: 0.9087 (t0) REVERT: J 633 LYS cc_start: 0.9566 (mmtp) cc_final: 0.9303 (mmmm) REVERT: J 657 GLU cc_start: 0.8113 (tp30) cc_final: 0.7737 (tt0) REVERT: L 45 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7961 (ttmm) REVERT: L 70 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7725 (t0) outliers start: 24 outliers final: 20 residues processed: 180 average time/residue: 0.2777 time to fit residues: 75.9746 Evaluate side-chains 183 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 CYS 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 E residue 126 CYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 615 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 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 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 70 ASP 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 85 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 27 optimal weight: 0.0980 chunk 110 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 chunk 71 optimal weight: 0.7980 chunk 169 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 352 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.081403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.060953 restraints weight = 41055.420| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 4.04 r_work: 0.2813 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16996 Z= 0.103 Angle : 0.578 12.053 23270 Z= 0.268 Chirality : 0.043 0.387 2886 Planarity : 0.003 0.039 2767 Dihedral : 6.946 55.807 4250 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.36 % Allowed : 12.46 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1879 helix: 1.71 (0.27), residues: 408 sheet: -0.14 (0.23), residues: 534 loop : -0.38 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 631 HIS 0.002 0.000 HIS E 105 PHE 0.012 0.001 PHE H 58 TYR 0.008 0.001 TYR A 484 ARG 0.002 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 54) link_NAG-ASN : angle 2.00593 ( 162) link_ALPHA1-6 : bond 0.00821 ( 4) link_ALPHA1-6 : angle 1.51427 ( 12) link_BETA1-4 : bond 0.00404 ( 43) link_BETA1-4 : angle 1.37483 ( 129) link_ALPHA1-2 : bond 0.01651 ( 2) link_ALPHA1-2 : angle 2.57638 ( 6) link_ALPHA1-3 : bond 0.00982 ( 4) link_ALPHA1-3 : angle 1.81131 ( 12) hydrogen bonds : bond 0.03122 ( 485) hydrogen bonds : angle 4.25192 ( 1305) SS BOND : bond 0.00206 ( 38) SS BOND : angle 0.79012 ( 76) covalent geometry : bond 0.00233 (16851) covalent geometry : angle 0.54185 (22873) ********************** 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 188 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9119 (tpt) cc_final: 0.8826 (tpt) REVERT: A 205 CYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7591 (m) REVERT: A 475 MET cc_start: 0.8525 (tpp) cc_final: 0.8040 (tpp) REVERT: A 484 TYR cc_start: 0.8524 (p90) cc_final: 0.8144 (p90) REVERT: B 540 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7210 (mp-120) REVERT: B 542 ARG cc_start: 0.9049 (ptm160) cc_final: 0.8730 (ptm160) REVERT: B 632 ASP cc_start: 0.9139 (t0) cc_final: 0.8824 (t0) REVERT: B 633 LYS cc_start: 0.9367 (mptt) cc_final: 0.9050 (mptt) REVERT: E 191 TYR cc_start: 0.8942 (m-80) cc_final: 0.8504 (m-80) REVERT: E 475 MET cc_start: 0.7066 (mpp) cc_final: 0.6517 (mmm) REVERT: E 484 TYR cc_start: 0.9249 (p90) cc_final: 0.8891 (p90) REVERT: F 584 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8273 (mt-10) REVERT: F 588 ARG cc_start: 0.8163 (mtt-85) cc_final: 0.7851 (ttm110) REVERT: F 633 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8889 (mtmt) REVERT: F 647 GLU cc_start: 0.8642 (tt0) cc_final: 0.8262 (tt0) REVERT: H 43 LYS cc_start: 0.9060 (ptpp) cc_final: 0.8649 (ptpp) REVERT: I 173 TYR cc_start: 0.9004 (p90) cc_final: 0.8700 (p90) REVERT: J 535 MET cc_start: 0.9176 (mmt) cc_final: 0.8878 (mpp) REVERT: J 630 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8526 (pm20) REVERT: J 631 TRP cc_start: 0.8563 (t-100) cc_final: 0.8049 (t-100) REVERT: J 632 ASP cc_start: 0.9339 (t0) cc_final: 0.9087 (t0) REVERT: J 633 LYS cc_start: 0.9563 (mmtp) cc_final: 0.9304 (mmmm) REVERT: J 657 GLU cc_start: 0.8101 (tp30) cc_final: 0.7735 (tt0) REVERT: L 45 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7915 (ttmm) REVERT: L 70 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7699 (t0) outliers start: 23 outliers final: 18 residues processed: 179 average time/residue: 0.2904 time to fit residues: 79.2750 Evaluate side-chains 187 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 CYS 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 636 SER Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain F residue 544 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 135 THR Chi-restraints excluded: chain I residue 149 ILE 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 L residue 20 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 70 ASP 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 151 optimal weight: 0.0030 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 159 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 100 optimal weight: 0.4980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.081582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.061149 restraints weight = 41033.197| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 4.05 r_work: 0.2821 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 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 = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16996 Z= 0.100 Angle : 0.573 11.790 23270 Z= 0.266 Chirality : 0.043 0.383 2886 Planarity : 0.003 0.039 2767 Dihedral : 6.847 55.655 4250 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.65 % Allowed : 12.34 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.20), residues: 1879 helix: 1.75 (0.27), residues: 408 sheet: -0.10 (0.23), residues: 532 loop : -0.38 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 631 HIS 0.002 0.000 HIS E 105 PHE 0.011 0.001 PHE H 58 TYR 0.023 0.001 TYR H 56 ARG 0.002 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 54) link_NAG-ASN : angle 1.97953 ( 162) link_ALPHA1-6 : bond 0.00835 ( 4) link_ALPHA1-6 : angle 1.48907 ( 12) link_BETA1-4 : bond 0.00405 ( 43) link_BETA1-4 : angle 1.36471 ( 129) link_ALPHA1-2 : bond 0.01543 ( 2) link_ALPHA1-2 : angle 2.54863 ( 6) link_ALPHA1-3 : bond 0.00935 ( 4) link_ALPHA1-3 : angle 1.79206 ( 12) hydrogen bonds : bond 0.03053 ( 485) hydrogen bonds : angle 4.14790 ( 1305) SS BOND : bond 0.00192 ( 38) SS BOND : angle 0.78466 ( 76) covalent geometry : bond 0.00228 (16851) covalent geometry : angle 0.53781 (22873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7754.84 seconds wall clock time: 135 minutes 39.79 seconds (8139.79 seconds total)