Starting phenix.real_space_refine on Sat Jun 14 23:18:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bnp_44733/06_2025/9bnp_44733.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bnp_44733/06_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_44733/06_2025/9bnp_44733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bnp_44733/06_2025/9bnp_44733.map" model { file = "/net/cci-nas-00/data/ceres_data/9bnp_44733/06_2025/9bnp_44733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bnp_44733/06_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-5710/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: 10.87, per 1000 atoms: 0.66 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: 4.96 Conformation dependent library (CDL) restraints added in 2.1 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: 1.74 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: 4.96 Time building geometry restraints manager: 5.74 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: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 39.030 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.970 ------------------------------------------------------------------------------- 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 : 1.726 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: 0.3065 time to fit residues: 87.9229 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 : 1.874 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.067730 restraints weight = 40579.658| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.95 r_work: 0.2978 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- 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 82.158 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 2.00892 ( 12) link_BETA1-4 : bond 0.00485 ( 43) link_BETA1-4 : angle 1.81498 ( 129) link_ALPHA1-2 : bond 0.01328 ( 2) link_ALPHA1-2 : angle 3.26825 ( 6) link_ALPHA1-3 : bond 0.01031 ( 4) link_ALPHA1-3 : angle 2.36684 ( 12) hydrogen bonds : bond 0.04238 ( 485) hydrogen bonds : angle 5.20610 ( 1305) SS BOND : bond 0.00193 ( 38) SS BOND : angle 0.92329 ( 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 : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6862 (tmtt) cc_final: 0.6253 (tptt) REVERT: A 271 MET cc_start: 0.7880 (mmm) cc_final: 0.7552 (mmt) REVERT: B 542 ARG cc_start: 0.9023 (ptm160) cc_final: 0.8683 (ptm160) REVERT: B 633 LYS cc_start: 0.9321 (mptt) cc_final: 0.8998 (mptt) REVERT: E 169 LYS cc_start: 0.8585 (mttt) cc_final: 0.8364 (mttt) REVERT: F 543 ASN cc_start: 0.9147 (m-40) cc_final: 0.8896 (m110) REVERT: F 584 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8598 (mt-10) REVERT: F 588 ARG cc_start: 0.8045 (mtt-85) cc_final: 0.7751 (ttm110) REVERT: F 621 GLU cc_start: 0.8633 (tp30) cc_final: 0.8424 (tp30) REVERT: F 647 GLU cc_start: 0.8585 (tt0) cc_final: 0.8187 (tt0) REVERT: H 43 LYS cc_start: 0.9035 (ptpp) cc_final: 0.8802 (ptpp) REVERT: I 161 MET cc_start: 0.9054 (tpt) cc_final: 0.8576 (tpt) REVERT: I 173 TYR cc_start: 0.8989 (p90) cc_final: 0.8573 (p90) REVERT: I 188 ASN cc_start: 0.7848 (p0) cc_final: 0.7609 (p0) REVERT: J 535 MET cc_start: 0.9265 (mmt) cc_final: 0.9058 (mpp) REVERT: J 624 ASP cc_start: 0.8697 (m-30) cc_final: 0.8134 (m-30) REVERT: J 632 ASP cc_start: 0.9310 (t0) cc_final: 0.9053 (t0) REVERT: J 657 GLU cc_start: 0.8086 (tp30) cc_final: 0.7737 (tt0) REVERT: L 17 ASP cc_start: 0.7243 (t0) cc_final: 0.6948 (t0) outliers start: 15 outliers final: 6 residues processed: 178 average time/residue: 0.3070 time to fit residues: 83.7863 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 : 1.771 ------------------------------------------------------------------------------- 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: 0.8980 chunk 108 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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** H 102 HIS I 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.080292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.059674 restraints weight = 41177.579| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 4.03 r_work: 0.2782 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16996 Z= 0.215 Angle : 0.679 10.897 23270 Z= 0.320 Chirality : 0.047 0.400 2886 Planarity : 0.004 0.040 2767 Dihedral : 8.924 69.749 4250 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.24 % Allowed : 8.15 % Favored : 90.61 % 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: -0.14 (0.19), residues: 1879 helix: 1.42 (0.27), residues: 406 sheet: -0.43 (0.22), residues: 507 loop : -0.48 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 479 HIS 0.005 0.001 HIS E 330 PHE 0.018 0.002 PHE E 233 TYR 0.014 0.002 TYR L 49 ARG 0.004 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 54) link_NAG-ASN : angle 2.31925 ( 162) link_ALPHA1-6 : bond 0.00718 ( 4) link_ALPHA1-6 : angle 2.33346 ( 12) link_BETA1-4 : bond 0.00383 ( 43) link_BETA1-4 : angle 1.81603 ( 129) link_ALPHA1-2 : bond 0.01171 ( 2) link_ALPHA1-2 : angle 2.37385 ( 6) link_ALPHA1-3 : bond 0.00936 ( 4) link_ALPHA1-3 : angle 2.02396 ( 12) hydrogen bonds : bond 0.04262 ( 485) hydrogen bonds : angle 4.83155 ( 1305) SS BOND : bond 0.00247 ( 38) SS BOND : angle 1.04955 ( 76) covalent geometry : bond 0.00508 (16851) covalent geometry : angle 0.63455 (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 187 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.7210 (tmtt) cc_final: 0.6562 (tptt) REVERT: A 271 MET cc_start: 0.8170 (mmm) cc_final: 0.7864 (mmt) REVERT: A 475 MET cc_start: 0.8514 (tpp) cc_final: 0.8209 (tpp) REVERT: B 540 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7368 (mp-120) REVERT: B 542 ARG cc_start: 0.9080 (ptm160) cc_final: 0.8735 (ptm160) REVERT: E 169 LYS cc_start: 0.8626 (mttt) cc_final: 0.8379 (mttt) REVERT: F 543 ASN cc_start: 0.9148 (m-40) cc_final: 0.8946 (m110) REVERT: F 584 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8427 (mt-10) REVERT: F 588 ARG cc_start: 0.8136 (mtt-85) cc_final: 0.7792 (ttm110) REVERT: F 621 GLU cc_start: 0.8692 (tp30) cc_final: 0.8377 (tp30) REVERT: F 625 ASN cc_start: 0.8488 (t0) cc_final: 0.8213 (t0) REVERT: F 647 GLU cc_start: 0.8665 (tt0) cc_final: 0.8260 (tt0) REVERT: H 43 LYS cc_start: 0.9018 (ptpp) cc_final: 0.8776 (ptpp) REVERT: H 83 ARG cc_start: 0.8243 (mtm-85) cc_final: 0.7893 (mtt90) REVERT: I 173 TYR cc_start: 0.9030 (p90) cc_final: 0.8656 (p90) REVERT: I 188 ASN cc_start: 0.7780 (p0) cc_final: 0.7516 (p0) REVERT: J 535 MET cc_start: 0.9307 (mmt) cc_final: 0.9003 (mpp) REVERT: J 624 ASP cc_start: 0.8939 (m-30) cc_final: 0.8524 (m-30) REVERT: J 632 ASP cc_start: 0.9436 (t0) cc_final: 0.9131 (t0) REVERT: J 633 LYS cc_start: 0.9498 (mmtp) cc_final: 0.9010 (mmtm) REVERT: J 657 GLU cc_start: 0.8094 (tp30) cc_final: 0.7752 (tt0) REVERT: L 100 GLN cc_start: 0.8916 (mp10) cc_final: 0.8686 (mp-120) REVERT: L 105 GLU cc_start: 0.4538 (OUTLIER) cc_final: 0.4129 (tp30) outliers start: 21 outliers final: 14 residues processed: 178 average time/residue: 0.3113 time to fit residues: 83.0018 Evaluate side-chains 167 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 1.953 ------------------------------------------------------------------------------- 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: 10.0000 chunk 117 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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** J 540 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.080018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.059608 restraints weight = 40918.330| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 4.00 r_work: 0.2782 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2073 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= 0.177 Angle : 0.621 11.425 23270 Z= 0.288 Chirality : 0.045 0.402 2886 Planarity : 0.003 0.035 2767 Dihedral : 8.079 58.521 4250 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.65 % Allowed : 9.39 % Favored : 88.95 % 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: 1.45 (0.27), residues: 402 sheet: -0.44 (0.22), residues: 541 loop : -0.45 (0.21), residues: 936 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 0.016 0.001 PHE H 58 TYR 0.011 0.001 TYR I 318 ARG 0.003 0.000 ARG J 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 54) link_NAG-ASN : angle 2.23998 ( 162) link_ALPHA1-6 : bond 0.00817 ( 4) link_ALPHA1-6 : angle 2.26518 ( 12) link_BETA1-4 : bond 0.00419 ( 43) link_BETA1-4 : angle 1.61821 ( 129) link_ALPHA1-2 : bond 0.01516 ( 2) link_ALPHA1-2 : angle 2.69337 ( 6) link_ALPHA1-3 : bond 0.01056 ( 4) link_ALPHA1-3 : angle 2.29084 ( 12) hydrogen bonds : bond 0.03759 ( 485) hydrogen bonds : angle 4.66140 ( 1305) SS BOND : bond 0.00257 ( 38) SS BOND : angle 0.90905 ( 76) covalent geometry : bond 0.00416 (16851) covalent geometry : angle 0.57593 (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 195 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9077 (tpt) cc_final: 0.8788 (tpt) REVERT: A 207 LYS cc_start: 0.7413 (tmtt) cc_final: 0.6562 (tptt) REVERT: A 271 MET cc_start: 0.8198 (mmm) cc_final: 0.7902 (mmt) REVERT: A 475 MET cc_start: 0.8593 (tpp) cc_final: 0.8191 (tpp) REVERT: B 542 ARG cc_start: 0.9072 (ptm160) cc_final: 0.8715 (ptm160) REVERT: B 633 LYS cc_start: 0.9410 (mptt) cc_final: 0.9100 (mptt) REVERT: E 169 LYS cc_start: 0.8595 (mttt) cc_final: 0.8322 (mtmm) REVERT: F 543 ASN cc_start: 0.9130 (m-40) cc_final: 0.8914 (m110) REVERT: F 584 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8336 (mt-10) REVERT: F 588 ARG cc_start: 0.8174 (mtt-85) cc_final: 0.7832 (ttm110) REVERT: F 621 GLU cc_start: 0.8607 (tp30) cc_final: 0.8151 (tp30) REVERT: F 625 ASN cc_start: 0.8441 (t0) cc_final: 0.7970 (t0) REVERT: F 647 GLU cc_start: 0.8643 (tt0) cc_final: 0.8253 (tt0) REVERT: H 43 LYS cc_start: 0.9014 (ptpp) cc_final: 0.8754 (ptpp) REVERT: I 173 TYR cc_start: 0.9052 (p90) cc_final: 0.8750 (p90) REVERT: I 188 ASN cc_start: 0.7834 (p0) cc_final: 0.7552 (p0) REVERT: I 207 LYS cc_start: 0.8067 (tptt) cc_final: 0.7589 (tptp) REVERT: J 535 MET cc_start: 0.9289 (mmt) cc_final: 0.8944 (mpp) REVERT: J 632 ASP cc_start: 0.9397 (t0) cc_final: 0.9102 (t0) REVERT: J 633 LYS cc_start: 0.9533 (mmtp) cc_final: 0.9049 (mmtm) REVERT: J 657 GLU cc_start: 0.8091 (tp30) cc_final: 0.7750 (tt0) REVERT: L 79 GLN cc_start: 0.7847 (mm110) cc_final: 0.7532 (mm110) REVERT: L 82 ASP cc_start: 0.6181 (m-30) cc_final: 0.5903 (m-30) REVERT: L 100 GLN cc_start: 0.8983 (mp10) cc_final: 0.8697 (mp-120) outliers start: 28 outliers final: 17 residues processed: 184 average time/residue: 0.3230 time to fit residues: 89.8972 Evaluate side-chains 176 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 2.227 ------------------------------------------------------------------------------- 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 599 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 660 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 87 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 150 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.078961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.058425 restraints weight = 41538.574| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 4.02 r_work: 0.2755 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 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 = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16996 Z= 0.210 Angle : 0.644 11.457 23270 Z= 0.301 Chirality : 0.045 0.406 2886 Planarity : 0.003 0.036 2767 Dihedral : 7.935 58.398 4250 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.30 % Allowed : 10.51 % Favored : 88.19 % 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: 1.50 (0.27), residues: 405 sheet: -0.43 (0.22), residues: 531 loop : -0.49 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 112 HIS 0.003 0.001 HIS E 105 PHE 0.016 0.002 PHE H 58 TYR 0.019 0.002 TYR H 56 ARG 0.004 0.000 ARG A 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 54) link_NAG-ASN : angle 2.27369 ( 162) link_ALPHA1-6 : bond 0.00836 ( 4) link_ALPHA1-6 : angle 2.26113 ( 12) link_BETA1-4 : bond 0.00341 ( 43) link_BETA1-4 : angle 1.60634 ( 129) link_ALPHA1-2 : bond 0.01392 ( 2) link_ALPHA1-2 : angle 2.60896 ( 6) link_ALPHA1-3 : bond 0.01010 ( 4) link_ALPHA1-3 : angle 2.16181 ( 12) hydrogen bonds : bond 0.03814 ( 485) hydrogen bonds : angle 4.66294 ( 1305) SS BOND : bond 0.00289 ( 38) SS BOND : angle 1.33904 ( 76) covalent geometry : bond 0.00495 (16851) covalent geometry : angle 0.59789 (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 177 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9098 (tpt) cc_final: 0.8853 (tpt) REVERT: A 475 MET cc_start: 0.8628 (tpp) cc_final: 0.8209 (tpp) REVERT: B 540 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7405 (mp-120) REVERT: B 542 ARG cc_start: 0.9092 (ptm160) cc_final: 0.8751 (ptm160) REVERT: B 632 ASP cc_start: 0.9281 (t0) cc_final: 0.9071 (t0) REVERT: B 633 LYS cc_start: 0.9395 (mptt) cc_final: 0.9062 (mptt) REVERT: E 169 LYS cc_start: 0.8573 (mttt) cc_final: 0.8325 (mtmm) REVERT: E 475 MET cc_start: 0.7257 (mpp) cc_final: 0.6545 (mmm) REVERT: F 543 ASN cc_start: 0.9137 (m-40) cc_final: 0.8884 (m110) REVERT: F 584 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8300 (mt-10) REVERT: F 588 ARG cc_start: 0.8200 (mtt-85) cc_final: 0.7868 (ttm110) REVERT: F 621 GLU cc_start: 0.8622 (tp30) cc_final: 0.8140 (tp30) REVERT: F 625 ASN cc_start: 0.8542 (t0) cc_final: 0.8003 (t0) REVERT: F 647 GLU cc_start: 0.8670 (tt0) cc_final: 0.8274 (tt0) REVERT: I 173 TYR cc_start: 0.9073 (p90) cc_final: 0.8767 (p90) REVERT: I 188 ASN cc_start: 0.7907 (p0) cc_final: 0.7602 (p0) REVERT: I 207 LYS cc_start: 0.8044 (tptt) cc_final: 0.7583 (tptp) REVERT: J 535 MET cc_start: 0.9293 (mmt) cc_final: 0.8925 (mpp) REVERT: J 630 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8519 (pm20) REVERT: J 632 ASP cc_start: 0.9422 (t0) cc_final: 0.9126 (t0) REVERT: J 633 LYS cc_start: 0.9553 (mmtp) cc_final: 0.9310 (mmmm) REVERT: J 657 GLU cc_start: 0.8105 (tp30) cc_final: 0.7751 (tt0) REVERT: L 79 GLN cc_start: 0.7743 (mm110) cc_final: 0.7347 (mm110) REVERT: L 82 ASP cc_start: 0.6304 (m-30) cc_final: 0.6038 (m-30) outliers start: 22 outliers final: 15 residues processed: 170 average time/residue: 0.2976 time to fit residues: 75.9465 Evaluate side-chains 171 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 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: 0.9990 chunk 154 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.079581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.058907 restraints weight = 41403.261| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 4.04 r_work: 0.2765 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 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 = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16996 Z= 0.160 Angle : 0.606 11.508 23270 Z= 0.282 Chirality : 0.044 0.405 2886 Planarity : 0.003 0.036 2767 Dihedral : 7.672 57.850 4250 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.83 % Allowed : 10.75 % Favored : 87.42 % 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: -0.04 (0.20), residues: 1879 helix: 1.61 (0.27), residues: 405 sheet: -0.43 (0.22), residues: 540 loop : -0.43 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 112 HIS 0.003 0.001 HIS E 105 PHE 0.016 0.001 PHE H 58 TYR 0.012 0.001 TYR F 638 ARG 0.003 0.000 ARG A 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 54) link_NAG-ASN : angle 2.21452 ( 162) link_ALPHA1-6 : bond 0.00791 ( 4) link_ALPHA1-6 : angle 2.07766 ( 12) link_BETA1-4 : bond 0.00353 ( 43) link_BETA1-4 : angle 1.53170 ( 129) link_ALPHA1-2 : bond 0.01437 ( 2) link_ALPHA1-2 : angle 2.62026 ( 6) link_ALPHA1-3 : bond 0.01074 ( 4) link_ALPHA1-3 : angle 2.09818 ( 12) hydrogen bonds : bond 0.03588 ( 485) hydrogen bonds : angle 4.57476 ( 1305) SS BOND : bond 0.00260 ( 38) SS BOND : angle 0.95826 ( 76) covalent geometry : bond 0.00375 (16851) covalent geometry : angle 0.56279 (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 198 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9105 (tpt) cc_final: 0.8862 (tpt) REVERT: A 207 LYS cc_start: 0.7573 (tmtt) cc_final: 0.7093 (tptt) REVERT: A 376 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8526 (m-10) REVERT: A 475 MET cc_start: 0.8620 (tpp) cc_final: 0.8186 (tpp) REVERT: B 540 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7385 (mp-120) REVERT: B 542 ARG cc_start: 0.9082 (ptm160) cc_final: 0.8738 (ptm160) REVERT: B 632 ASP cc_start: 0.9256 (t0) cc_final: 0.9015 (t0) REVERT: B 633 LYS cc_start: 0.9400 (mptt) cc_final: 0.9076 (mptt) REVERT: E 475 MET cc_start: 0.7119 (mpp) cc_final: 0.6503 (mmm) REVERT: F 543 ASN cc_start: 0.9125 (m-40) cc_final: 0.8866 (m110) REVERT: F 584 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8284 (mt-10) REVERT: F 588 ARG cc_start: 0.8199 (mtt-85) cc_final: 0.7864 (ttm110) REVERT: F 647 GLU cc_start: 0.8660 (tt0) cc_final: 0.8264 (tt0) REVERT: I 107 ASP cc_start: 0.8953 (t0) cc_final: 0.8657 (t0) REVERT: I 173 TYR cc_start: 0.9055 (p90) cc_final: 0.8808 (p90) REVERT: I 188 ASN cc_start: 0.7876 (p0) cc_final: 0.7589 (p0) REVERT: J 535 MET cc_start: 0.9261 (mmt) cc_final: 0.8904 (mpp) REVERT: J 630 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8511 (pm20) REVERT: J 632 ASP cc_start: 0.9389 (t0) cc_final: 0.9100 (t0) REVERT: J 633 LYS cc_start: 0.9555 (mmtp) cc_final: 0.9306 (mmmm) REVERT: J 657 GLU cc_start: 0.8107 (tp30) cc_final: 0.7747 (tt0) REVERT: L 50 LYS cc_start: 0.8791 (tppp) cc_final: 0.8524 (tppp) REVERT: L 79 GLN cc_start: 0.7696 (mm110) cc_final: 0.7293 (mm110) REVERT: L 82 ASP cc_start: 0.6228 (m-30) cc_final: 0.5975 (m-30) outliers start: 31 outliers final: 22 residues processed: 191 average time/residue: 0.2963 time to fit residues: 85.6847 Evaluate side-chains 183 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 1.775 ------------------------------------------------------------------------------- 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 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 368 ASP Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 164 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.079985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.059297 restraints weight = 41404.357| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 4.05 r_work: 0.2771 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16996 Z= 0.136 Angle : 0.595 11.925 23270 Z= 0.276 Chirality : 0.044 0.403 2886 Planarity : 0.003 0.036 2767 Dihedral : 7.439 57.708 4250 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.95 % Allowed : 11.16 % Favored : 86.89 % 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: 0.01 (0.20), residues: 1879 helix: 1.68 (0.27), residues: 405 sheet: -0.39 (0.22), residues: 531 loop : -0.41 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 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 0.00276 ( 54) link_NAG-ASN : angle 2.16331 ( 162) link_ALPHA1-6 : bond 0.00843 ( 4) link_ALPHA1-6 : angle 1.92727 ( 12) link_BETA1-4 : bond 0.00369 ( 43) link_BETA1-4 : angle 1.48735 ( 129) link_ALPHA1-2 : bond 0.01510 ( 2) link_ALPHA1-2 : angle 2.62965 ( 6) link_ALPHA1-3 : bond 0.01042 ( 4) link_ALPHA1-3 : angle 1.99073 ( 12) hydrogen bonds : bond 0.03447 ( 485) hydrogen bonds : angle 4.49371 ( 1305) SS BOND : bond 0.00224 ( 38) SS BOND : angle 0.85242 ( 76) covalent geometry : bond 0.00317 (16851) covalent geometry : angle 0.55366 (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 199 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9102 (tpt) cc_final: 0.8855 (tpt) REVERT: A 207 LYS cc_start: 0.7629 (tmtt) cc_final: 0.7154 (tptt) REVERT: A 376 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8548 (m-10) REVERT: A 475 MET cc_start: 0.8602 (tpp) cc_final: 0.8163 (tpp) REVERT: B 540 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7336 (mp-120) REVERT: B 542 ARG cc_start: 0.9063 (ptm160) cc_final: 0.8726 (ptm160) REVERT: B 632 ASP cc_start: 0.9205 (t0) cc_final: 0.8904 (t0) REVERT: B 633 LYS cc_start: 0.9393 (mptt) cc_final: 0.9042 (mptt) REVERT: E 475 MET cc_start: 0.7089 (mpp) cc_final: 0.6545 (mmm) REVERT: F 543 ASN cc_start: 0.9120 (m-40) cc_final: 0.8855 (m110) REVERT: F 584 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8263 (mt-10) REVERT: F 588 ARG cc_start: 0.8169 (mtt-85) cc_final: 0.7836 (ttm110) REVERT: F 647 GLU cc_start: 0.8650 (tt0) cc_final: 0.8251 (tt0) REVERT: H 43 LYS cc_start: 0.9105 (ptpp) cc_final: 0.8779 (ptpp) REVERT: I 107 ASP cc_start: 0.8934 (t0) cc_final: 0.8663 (t0) REVERT: I 161 MET cc_start: 0.9161 (tpt) cc_final: 0.8813 (tpt) REVERT: I 173 TYR cc_start: 0.9053 (p90) cc_final: 0.8804 (p90) REVERT: J 535 MET cc_start: 0.9258 (mmt) cc_final: 0.8917 (mpp) REVERT: J 630 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8519 (pm20) REVERT: J 632 ASP cc_start: 0.9377 (t0) cc_final: 0.9096 (t0) REVERT: J 633 LYS cc_start: 0.9559 (mmtp) cc_final: 0.9308 (mmmm) REVERT: J 657 GLU cc_start: 0.8077 (tp30) cc_final: 0.7710 (tt0) REVERT: L 50 LYS cc_start: 0.8766 (tppp) cc_final: 0.8540 (tppp) REVERT: L 79 GLN cc_start: 0.7601 (mm110) cc_final: 0.7212 (mm110) REVERT: L 82 ASP cc_start: 0.6183 (m-30) cc_final: 0.5956 (m-30) outliers start: 33 outliers final: 23 residues processed: 189 average time/residue: 0.3464 time to fit residues: 102.6303 Evaluate side-chains 188 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 2.147 ------------------------------------------------------------------------------- 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 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 368 ASP Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 75 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.079907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.059325 restraints weight = 41039.630| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 4.03 r_work: 0.2774 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2539 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= 0.141 Angle : 0.596 11.562 23270 Z= 0.276 Chirality : 0.044 0.399 2886 Planarity : 0.003 0.037 2767 Dihedral : 7.316 57.972 4250 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.77 % Allowed : 11.40 % Favored : 86.83 % 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: 0.04 (0.20), residues: 1879 helix: 1.72 (0.27), residues: 404 sheet: -0.32 (0.22), residues: 529 loop : -0.43 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 112 HIS 0.003 0.001 HIS E 105 PHE 0.014 0.001 PHE H 58 TYR 0.015 0.001 TYR F 638 ARG 0.003 0.000 ARG A 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 54) link_NAG-ASN : angle 2.13442 ( 162) link_ALPHA1-6 : bond 0.00876 ( 4) link_ALPHA1-6 : angle 1.83485 ( 12) link_BETA1-4 : bond 0.00373 ( 43) link_BETA1-4 : angle 1.46481 ( 129) link_ALPHA1-2 : bond 0.01499 ( 2) link_ALPHA1-2 : angle 2.59043 ( 6) link_ALPHA1-3 : bond 0.00979 ( 4) link_ALPHA1-3 : angle 1.97245 ( 12) hydrogen bonds : bond 0.03386 ( 485) hydrogen bonds : angle 4.45418 ( 1305) SS BOND : bond 0.00287 ( 38) SS BOND : angle 0.88658 ( 76) covalent geometry : bond 0.00328 (16851) covalent geometry : angle 0.55527 (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 195 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9132 (tpt) cc_final: 0.8877 (tpt) REVERT: A 205 CYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7313 (m) REVERT: A 207 LYS cc_start: 0.7690 (tmtt) cc_final: 0.7228 (tptt) REVERT: A 376 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8533 (m-10) REVERT: A 475 MET cc_start: 0.8587 (tpp) cc_final: 0.8119 (tpp) REVERT: B 540 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7310 (mp-120) REVERT: B 542 ARG cc_start: 0.9070 (ptm160) cc_final: 0.8744 (ptm160) REVERT: B 632 ASP cc_start: 0.9209 (t0) cc_final: 0.8934 (t0) REVERT: B 633 LYS cc_start: 0.9392 (mptt) cc_final: 0.9059 (mptt) REVERT: E 475 MET cc_start: 0.7114 (mpp) cc_final: 0.6566 (mmm) REVERT: F 543 ASN cc_start: 0.9133 (m-40) cc_final: 0.8862 (m110) REVERT: F 584 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8267 (mt-10) REVERT: F 588 ARG cc_start: 0.8178 (mtt-85) cc_final: 0.7850 (ttm110) REVERT: F 633 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8885 (mtmt) REVERT: F 647 GLU cc_start: 0.8640 (tt0) cc_final: 0.8239 (tt0) REVERT: H 43 LYS cc_start: 0.9105 (ptpp) cc_final: 0.8786 (ptpp) REVERT: I 107 ASP cc_start: 0.8935 (t0) cc_final: 0.8727 (t0) REVERT: I 161 MET cc_start: 0.9152 (tpt) cc_final: 0.8797 (tpt) REVERT: I 173 TYR cc_start: 0.9059 (p90) cc_final: 0.8811 (p90) REVERT: I 188 ASN cc_start: 0.7742 (p0) cc_final: 0.7495 (p0) REVERT: I 207 LYS cc_start: 0.8101 (tptt) cc_final: 0.7706 (tptp) REVERT: J 535 MET cc_start: 0.9245 (mmt) cc_final: 0.8871 (mpp) REVERT: J 630 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8540 (pm20) REVERT: J 632 ASP cc_start: 0.9368 (t0) cc_final: 0.9092 (t0) REVERT: J 633 LYS cc_start: 0.9567 (mmtp) cc_final: 0.9309 (mmmm) REVERT: J 657 GLU cc_start: 0.8122 (tp30) cc_final: 0.7757 (tt0) REVERT: L 50 LYS cc_start: 0.8786 (tppp) cc_final: 0.8553 (tppp) outliers start: 30 outliers final: 22 residues processed: 185 average time/residue: 0.3885 time to fit residues: 111.2538 Evaluate side-chains 189 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 2.035 ------------------------------------------------------------------------------- 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 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 F residue 599 SER Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 87 PHE Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 106 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 167 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 151 optimal weight: 0.1980 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.080640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.060309 restraints weight = 40934.455| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 4.01 r_work: 0.2800 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 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 = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2533 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 : 0.578 11.663 23270 Z= 0.268 Chirality : 0.043 0.397 2886 Planarity : 0.003 0.037 2767 Dihedral : 7.111 56.371 4250 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.48 % Allowed : 11.87 % 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: 0.14 (0.20), residues: 1879 helix: 1.78 (0.27), residues: 405 sheet: -0.27 (0.22), residues: 532 loop : -0.36 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 112 HIS 0.002 0.000 HIS E 105 PHE 0.010 0.001 PHE H 58 TYR 0.020 0.001 TYR H 56 ARG 0.003 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 54) link_NAG-ASN : angle 2.05966 ( 162) link_ALPHA1-6 : bond 0.00838 ( 4) link_ALPHA1-6 : angle 1.66015 ( 12) link_BETA1-4 : bond 0.00393 ( 43) link_BETA1-4 : angle 1.40937 ( 129) link_ALPHA1-2 : bond 0.01556 ( 2) link_ALPHA1-2 : angle 2.57929 ( 6) link_ALPHA1-3 : bond 0.01002 ( 4) link_ALPHA1-3 : angle 1.84804 ( 12) hydrogen bonds : bond 0.03195 ( 485) hydrogen bonds : angle 4.36522 ( 1305) SS BOND : bond 0.00216 ( 38) SS BOND : angle 0.83683 ( 76) covalent geometry : bond 0.00243 (16851) covalent geometry : angle 0.53995 (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 196 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9136 (tpt) cc_final: 0.8859 (tpt) REVERT: A 205 CYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7528 (m) REVERT: A 475 MET cc_start: 0.8565 (tpp) cc_final: 0.8090 (tpp) REVERT: B 540 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7253 (mp-120) REVERT: B 542 ARG cc_start: 0.9055 (ptm160) cc_final: 0.8732 (ptm160) REVERT: B 632 ASP cc_start: 0.9196 (t0) cc_final: 0.8915 (t0) REVERT: B 633 LYS cc_start: 0.9389 (mptt) cc_final: 0.9060 (mptt) REVERT: E 191 TYR cc_start: 0.9023 (m-80) cc_final: 0.8571 (m-80) REVERT: E 475 MET cc_start: 0.7128 (mpp) cc_final: 0.6585 (mmm) REVERT: F 543 ASN cc_start: 0.9132 (m-40) cc_final: 0.8871 (m110) REVERT: F 584 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8264 (mt-10) REVERT: F 588 ARG cc_start: 0.8163 (mtt-85) cc_final: 0.7838 (ttm110) REVERT: F 633 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8888 (mtmt) REVERT: F 647 GLU cc_start: 0.8638 (tt0) cc_final: 0.8254 (tt0) REVERT: H 43 LYS cc_start: 0.9076 (ptpp) cc_final: 0.8649 (ptpp) REVERT: I 107 ASP cc_start: 0.8907 (t0) cc_final: 0.8663 (t0) REVERT: I 161 MET cc_start: 0.9137 (tpt) cc_final: 0.8850 (tpt) REVERT: I 173 TYR cc_start: 0.9012 (p90) cc_final: 0.8695 (p90) REVERT: I 188 ASN cc_start: 0.7713 (p0) cc_final: 0.7434 (p0) REVERT: I 191 TYR cc_start: 0.9203 (m-80) cc_final: 0.8918 (m-80) REVERT: I 207 LYS cc_start: 0.8102 (tptt) cc_final: 0.7694 (tptp) REVERT: J 535 MET cc_start: 0.9189 (mmt) cc_final: 0.8826 (mpp) REVERT: J 630 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8535 (pm20) REVERT: J 632 ASP cc_start: 0.9346 (t0) cc_final: 0.9082 (t0) REVERT: J 633 LYS cc_start: 0.9562 (mmtp) cc_final: 0.9302 (mmmm) REVERT: J 657 GLU cc_start: 0.8083 (tp30) cc_final: 0.7716 (tt0) REVERT: L 50 LYS cc_start: 0.8759 (tppp) cc_final: 0.8543 (tppp) outliers start: 25 outliers final: 20 residues processed: 187 average time/residue: 0.2944 time to fit residues: 83.4727 Evaluate side-chains 189 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 1.712 ------------------------------------------------------------------------------- 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 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 F residue 599 SER Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 626 MET 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 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: 0.9990 chunk 87 optimal weight: 3.9990 chunk 27 optimal weight: 0.0970 chunk 110 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.080512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.059979 restraints weight = 41137.130| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 4.04 r_work: 0.2799 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16996 Z= 0.125 Angle : 0.582 11.809 23270 Z= 0.269 Chirality : 0.043 0.393 2886 Planarity : 0.003 0.038 2767 Dihedral : 7.067 56.783 4250 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.65 % Allowed : 11.87 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.63 (0.27), residues: 414 sheet: -0.25 (0.22), residues: 532 loop : -0.35 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 112 HIS 0.003 0.001 HIS E 105 PHE 0.013 0.001 PHE H 58 TYR 0.015 0.001 TYR F 638 ARG 0.002 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 54) link_NAG-ASN : angle 2.06348 ( 162) link_ALPHA1-6 : bond 0.00823 ( 4) link_ALPHA1-6 : angle 1.64169 ( 12) link_BETA1-4 : bond 0.00380 ( 43) link_BETA1-4 : angle 1.41559 ( 129) link_ALPHA1-2 : bond 0.01532 ( 2) link_ALPHA1-2 : angle 2.56143 ( 6) link_ALPHA1-3 : bond 0.00937 ( 4) link_ALPHA1-3 : angle 1.88866 ( 12) hydrogen bonds : bond 0.03235 ( 485) hydrogen bonds : angle 4.34583 ( 1305) SS BOND : bond 0.00213 ( 38) SS BOND : angle 0.81980 ( 76) covalent geometry : bond 0.00291 (16851) covalent geometry : angle 0.54441 (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 191 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9152 (tpt) cc_final: 0.8862 (tpt) REVERT: A 205 CYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7564 (m) REVERT: A 475 MET cc_start: 0.8562 (tpp) cc_final: 0.8098 (tpp) REVERT: B 540 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7280 (mp-120) REVERT: B 542 ARG cc_start: 0.9065 (ptm160) cc_final: 0.8734 (ptm160) REVERT: B 632 ASP cc_start: 0.9176 (t0) cc_final: 0.8888 (t0) REVERT: B 633 LYS cc_start: 0.9377 (mptt) cc_final: 0.9056 (mptt) REVERT: E 475 MET cc_start: 0.7121 (mpp) cc_final: 0.6610 (mmm) REVERT: F 543 ASN cc_start: 0.9136 (m-40) cc_final: 0.8869 (m110) REVERT: F 584 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8288 (mt-10) REVERT: F 588 ARG cc_start: 0.8178 (mtt-85) cc_final: 0.7854 (ttm110) REVERT: F 633 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8889 (mtmt) REVERT: F 647 GLU cc_start: 0.8638 (tt0) cc_final: 0.8217 (tt0) REVERT: H 43 LYS cc_start: 0.9098 (ptpp) cc_final: 0.8776 (ptpp) REVERT: I 107 ASP cc_start: 0.8922 (t0) cc_final: 0.8681 (t0) REVERT: I 161 MET cc_start: 0.9156 (tpt) cc_final: 0.8837 (tpt) REVERT: I 173 TYR cc_start: 0.9044 (p90) cc_final: 0.8739 (p90) REVERT: I 188 ASN cc_start: 0.7749 (p0) cc_final: 0.7463 (p0) REVERT: I 191 TYR cc_start: 0.9221 (m-80) cc_final: 0.8894 (m-80) REVERT: J 535 MET cc_start: 0.9176 (mmt) cc_final: 0.8867 (mpp) REVERT: J 630 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8529 (pm20) REVERT: J 632 ASP cc_start: 0.9352 (t0) cc_final: 0.9080 (t0) REVERT: J 633 LYS cc_start: 0.9562 (mmtp) cc_final: 0.9299 (mmmm) REVERT: J 657 GLU cc_start: 0.8119 (tp30) cc_final: 0.7744 (tt0) REVERT: L 50 LYS cc_start: 0.8794 (tppp) cc_final: 0.8583 (tppp) REVERT: L 70 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7722 (t0) outliers start: 28 outliers final: 22 residues processed: 181 average time/residue: 0.2950 time to fit residues: 81.0577 Evaluate side-chains 190 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 1.920 ------------------------------------------------------------------------------- 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 52 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 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 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 151 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 159 optimal weight: 0.0370 chunk 138 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.080918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.060416 restraints weight = 41042.394| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 4.04 r_work: 0.2802 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 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 = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16996 Z= 0.111 Angle : 0.575 11.239 23270 Z= 0.266 Chirality : 0.043 0.388 2886 Planarity : 0.003 0.038 2767 Dihedral : 6.926 56.082 4250 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.71 % Allowed : 11.87 % Favored : 86.41 % 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: 0.19 (0.20), residues: 1879 helix: 1.67 (0.27), residues: 414 sheet: -0.16 (0.23), residues: 526 loop : -0.33 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 112 HIS 0.006 0.001 HIS A 66 PHE 0.011 0.001 PHE H 58 TYR 0.023 0.001 TYR H 56 ARG 0.003 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 54) link_NAG-ASN : angle 2.02325 ( 162) link_ALPHA1-6 : bond 0.00812 ( 4) link_ALPHA1-6 : angle 1.55213 ( 12) link_BETA1-4 : bond 0.00391 ( 43) link_BETA1-4 : angle 1.38557 ( 129) link_ALPHA1-2 : bond 0.01496 ( 2) link_ALPHA1-2 : angle 2.52762 ( 6) link_ALPHA1-3 : bond 0.00933 ( 4) link_ALPHA1-3 : angle 1.81872 ( 12) hydrogen bonds : bond 0.03143 ( 485) hydrogen bonds : angle 4.25934 ( 1305) SS BOND : bond 0.00201 ( 38) SS BOND : angle 0.78144 ( 76) covalent geometry : bond 0.00256 (16851) covalent geometry : angle 0.53836 (22873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8469.93 seconds wall clock time: 149 minutes 10.96 seconds (8950.96 seconds total)