Starting phenix.real_space_refine on Sat Oct 11 18:49:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bnl_44729/10_2025/9bnl_44729.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bnl_44729/10_2025/9bnl_44729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bnl_44729/10_2025/9bnl_44729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bnl_44729/10_2025/9bnl_44729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bnl_44729/10_2025/9bnl_44729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bnl_44729/10_2025/9bnl_44729.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.015 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 103 5.16 5 C 10479 2.51 5 N 2734 2.21 5 O 3433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16749 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3472 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "B" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 970 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3452 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Chain: "E" Number of atoms: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3452 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Chain: "F" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 970 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "G" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 970 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1031 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "D" 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: "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: "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: 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: "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: 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: "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: 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: "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: 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: "Z" 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: "a" 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: "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: 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: "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: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "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: 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: "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: 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: "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: 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: "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: 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: "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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "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: 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: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASN L 92 " occ=0.98 ... (6 atoms not shown) pdb=" ND2 ASN L 92 " occ=0.98 Time building chain proxies: 4.31, per 1000 atoms: 0.26 Number of scatterers: 16749 At special positions: 0 Unit cell: (124.5, 126.16, 154.38, 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 103 16.00 O 3433 8.00 N 2734 7.00 C 10479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=1.98 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 218 " - pdb=" SG CYS A 247 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.00 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.01 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " 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=2.03 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 G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=1.79 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 u 4 " - " MAN u 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA h 3 " - " MAN h 4 " " BMA u 3 " - " MAN u 4 " ALPHA1-6 " BMA h 3 " - " MAN h 5 " " BMA u 3 " - " MAN u 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " 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 X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " 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 n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 601 " - " ASN A 386 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 88 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 625 " " NAG C 601 " - " ASN C 339 " " NAG C 602 " - " ASN C 386 " " NAG C 603 " - " ASN C 448 " " NAG C 604 " - " ASN C 88 " " NAG C 605 " - " ASN C 133 " " NAG D 1 " - " ASN A 156 " " NAG E 601 " - " ASN E 339 " " NAG E 602 " - " ASN E 386 " " NAG E 603 " - " ASN E 448 " " NAG E 604 " - " ASN E 465 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 625 " " NAG F 703 " - " ASN F 637 " " NAG G 701 " - " ASN G 637 " " NAG G 702 " - " ASN G 625 " " NAG G 703 " - " ASN G 611 " " NAG I 1 " - " ASN A 241 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 276 " " NAG M 1 " - " ASN A 465 " " NAG N 1 " - " ASN A 392 " " NAG O 1 " - " ASN A 363 " " NAG P 1 " - " ASN A 332 " " NAG Q 1 " - " ASN A 301 " " NAG R 1 " - " ASN A 133 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 197 " " NAG U 1 " - " ASN A 160 " " NAG V 1 " - " ASN A 448 " " NAG W 1 " - " ASN B 611 " " NAG X 1 " - " ASN C 156 " " NAG Y 1 " - " ASN C 241 " " NAG Z 1 " - " ASN C 234 " " NAG a 1 " - " ASN C 276 " " NAG b 1 " - " ASN C 465 " " NAG c 1 " - " ASN C 363 " " NAG d 1 " - " ASN C 332 " " NAG e 1 " - " ASN C 301 " " NAG f 1 " - " ASN C 262 " " NAG g 1 " - " ASN C 197 " " NAG h 1 " - " ASN C 160 " " NAG i 1 " - " ASN C 392 " " NAG j 1 " - " ASN E 156 " " NAG k 1 " - " ASN E 88 " " NAG l 1 " - " ASN E 241 " " NAG m 1 " - " ASN E 276 " " NAG n 1 " - " ASN E 392 " " NAG o 1 " - " ASN E 363 " " NAG p 1 " - " ASN E 332 " " NAG q 1 " - " ASN E 301 " " NAG r 1 " - " ASN E 133 " " NAG s 1 " - " ASN E 262 " " NAG t 1 " - " ASN E 197 " " NAG u 1 " - " ASN E 160 " " NAG v 1 " - " ASN E 234 " Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 727.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3570 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 34 sheets defined 23.9% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.553A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.679A pdb=" N THR A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.603A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.842A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.234A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.864A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 removed outlier: 4.044A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 661 removed outlier: 4.667A pdb=" N GLN B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.649A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL C 127 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 386 through 390 removed outlier: 4.060A pdb=" N GLY C 389 " --> pdb=" O ASN C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.873A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.954A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 4.377A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 127 removed outlier: 3.772A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL E 127 " --> pdb=" O PRO E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.814A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.615A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.461A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.570A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU F 593 " --> pdb=" O ASP F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 635 through 661 removed outlier: 4.396A pdb=" N GLN F 640 " --> pdb=" O ASN F 636 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS F 658 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU F 659 " --> pdb=" O LYS F 655 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU F 660 " --> pdb=" O ASN F 656 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU F 661 " --> pdb=" O GLU F 657 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 537 through 544 removed outlier: 3.544A pdb=" N ALA G 541 " --> pdb=" O LEU G 537 " (cutoff:3.500A) Processing helix chain 'G' and resid 569 through 596 removed outlier: 3.579A pdb=" N LEU G 592 " --> pdb=" O ARG G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 618 through 625 Processing helix chain 'G' and resid 627 through 635 removed outlier: 3.591A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE G 635 " --> pdb=" O TRP G 631 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 661 removed outlier: 3.599A pdb=" N ARG G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.646A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.178A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.710A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.649A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.475A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.538A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N LYS A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.544A pdb=" N ILE A 294 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N GLU A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.967A pdb=" N VAL A 292 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ASN A 448 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N GLN A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR A 293 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR A 334 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS A 330 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.795A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N GLN A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ASN A 448 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 10.967A pdb=" N VAL A 292 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N GLU A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.544A pdb=" N ILE A 294 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N LYS A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 309 Processing sheet with id=AA9, first strand: chain 'C' and resid 495 through 499 Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.686A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.757A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB5, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.381A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 260 through 261 removed outlier: 10.389A pdb=" N LYS C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.674A pdb=" N ILE C 294 " --> pdb=" O LYS C 444 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N GLU C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.861A pdb=" N VAL C 292 " --> pdb=" O GLU C 446 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N ASN C 448 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N GLN C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 298 current: chain 'C' and resid 358 through 361 removed outlier: 3.718A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.365A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N GLN C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N ASN C 448 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 10.861A pdb=" N VAL C 292 " --> pdb=" O GLU C 446 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N GLU C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.674A pdb=" N ILE C 294 " --> pdb=" O LYS C 444 " (cutoff:3.500A) removed outlier: 10.389A pdb=" N LYS C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 443 through 456 current: chain 'C' and resid 413 through 418 Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 312 removed outlier: 6.687A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.559A pdb=" N CYS C 385 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.544A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.517A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AC6, first strand: chain 'E' and resid 154 through 162 Processing sheet with id=AC7, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.363A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.613A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N LYS E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.544A pdb=" N ILE E 294 " --> pdb=" O LYS E 444 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N GLU E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.805A pdb=" N VAL E 292 " --> pdb=" O GLU E 446 " (cutoff:3.500A) removed outlier: 9.429A pdb=" N ASN E 448 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 10.012A pdb=" N GLN E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR E 293 " --> pdb=" O THR E 334 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR E 334 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.660A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.012A pdb=" N GLN E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.429A pdb=" N ASN E 448 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 10.805A pdb=" N VAL E 292 " --> pdb=" O GLU E 446 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N GLU E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.544A pdb=" N ILE E 294 " --> pdb=" O LYS E 444 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N LYS E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU E 466 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AD4, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.058A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.818A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU L 47 " --> pdb=" O TRP L 35 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.094A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1551 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5016 1.34 - 1.47: 4442 1.47 - 1.59: 7479 1.59 - 1.72: 1 1.72 - 1.84: 134 Bond restraints: 17072 Sorted by residual: bond pdb=" N GLY A 237 " pdb=" CA GLY A 237 " ideal model delta sigma weight residual 1.447 1.476 -0.029 9.20e-03 1.18e+04 9.91e+00 bond pdb=" N ILE C 359 " pdb=" CA ILE C 359 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.20e-02 6.94e+03 8.47e+00 bond pdb=" N ILE A 184 " pdb=" CA ILE A 184 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 7.99e+00 bond pdb=" C MET H 82C" pdb=" N ASP H 83 " ideal model delta sigma weight residual 1.331 1.375 -0.044 1.59e-02 3.96e+03 7.72e+00 bond pdb=" N LEU A 52 " pdb=" CA LEU A 52 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.70e+00 ... (remaining 17067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 22741 2.74 - 5.48: 419 5.48 - 8.21: 19 8.21 - 10.95: 1 10.95 - 13.69: 2 Bond angle restraints: 23182 Sorted by residual: angle pdb=" C CYS C 54 " pdb=" CA CYS C 54 " pdb=" CB CYS C 54 " ideal model delta sigma weight residual 109.76 98.68 11.08 1.99e+00 2.53e-01 3.10e+01 angle pdb=" CB MET F 530 " pdb=" CG MET F 530 " pdb=" SD MET F 530 " ideal model delta sigma weight residual 112.70 126.39 -13.69 3.00e+00 1.11e-01 2.08e+01 angle pdb=" N ASN E 302 " pdb=" CA ASN E 302 " pdb=" C ASN E 302 " ideal model delta sigma weight residual 110.91 115.98 -5.07 1.17e+00 7.31e-01 1.88e+01 angle pdb=" N CYS A 378 " pdb=" CA CYS A 378 " pdb=" C CYS A 378 " ideal model delta sigma weight residual 109.15 115.25 -6.10 1.44e+00 4.82e-01 1.79e+01 angle pdb=" N ASN A 234 " pdb=" CA ASN A 234 " pdb=" C ASN A 234 " ideal model delta sigma weight residual 113.20 108.16 5.04 1.21e+00 6.83e-01 1.73e+01 ... (remaining 23177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.04: 10944 21.04 - 42.07: 625 42.07 - 63.11: 166 63.11 - 84.14: 39 84.14 - 105.18: 9 Dihedral angle restraints: 11783 sinusoidal: 6262 harmonic: 5521 Sorted by residual: dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -159.70 73.70 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.41 -57.41 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 143.52 -50.52 1 1.00e+01 1.00e-02 3.50e+01 ... (remaining 11780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2526 0.065 - 0.131: 366 0.131 - 0.196: 57 0.196 - 0.261: 11 0.261 - 0.327: 2 Chirality restraints: 2962 Sorted by residual: chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.35e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.37e+01 chirality pdb=" CA CYS C 54 " pdb=" N CYS C 54 " pdb=" C CYS C 54 " pdb=" CB CYS C 54 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 2959 not shown) Planarity restraints: 2831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " 0.091 2.00e-02 2.50e+03 7.45e-02 6.93e+01 pdb=" C7 NAG J 1 " -0.022 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " 0.068 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " -0.119 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 192 " 0.216 9.50e-02 1.11e+02 9.67e-02 5.80e+00 pdb=" NE ARG A 192 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 192 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 192 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 192 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 211 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO C 212 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 212 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 212 " 0.029 5.00e-02 4.00e+02 ... (remaining 2828 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 994 2.73 - 3.27: 17100 3.27 - 3.82: 26207 3.82 - 4.36: 31302 4.36 - 4.90: 53853 Nonbonded interactions: 129456 Sorted by model distance: nonbonded pdb=" O LEU E 369 " pdb=" OG1 THR E 373 " model vdw 2.191 3.040 nonbonded pdb=" O ILE F 535 " pdb=" ND2 ASN G 651 " model vdw 2.192 3.120 nonbonded pdb=" OG SER A 199 " pdb=" O GLY A 431 " model vdw 2.242 3.040 nonbonded pdb=" CD2 HIS A 85 " pdb=" OD1 ASP A 87 " model vdw 2.312 3.260 nonbonded pdb=" O3 NAG d 2 " pdb=" O5 BMA d 3 " model vdw 2.317 3.040 ... (remaining 129451 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 185 or resid 188 through 603)) selection = (chain 'C' and (resid 33 through 135 or resid 152 through 603)) selection = (chain 'E' and (resid 33 through 135 or resid 152 through 603)) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 520 through 702) selection = (chain 'G' and resid 520 through 702) } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain 'J' selection = chain 'P' selection = chain 'S' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'f' selection = chain 'j' selection = chain 'l' selection = chain 'p' selection = chain 's' } 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=0.98 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.760 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 : 0.005 0.242 17226 Z= 0.261 Angle : 0.987 17.959 23610 Z= 0.507 Chirality : 0.050 0.327 2962 Planarity : 0.005 0.097 2771 Dihedral : 13.613 105.178 8111 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.19), residues: 1864 helix: 0.25 (0.26), residues: 401 sheet: -0.67 (0.22), residues: 496 loop : -1.47 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 273 TYR 0.008 0.001 TYR E 217 PHE 0.029 0.002 PHE L 83 TRP 0.020 0.001 TRP F 628 HIS 0.008 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00438 (17072) covalent geometry : angle 0.87106 (23182) SS BOND : bond 0.04301 ( 34) SS BOND : angle 3.54481 ( 68) hydrogen bonds : bond 0.22800 ( 556) hydrogen bonds : angle 8.31119 ( 1551) link_ALPHA1-2 : bond 0.00929 ( 1) link_ALPHA1-2 : angle 3.66988 ( 3) link_ALPHA1-3 : bond 0.01413 ( 3) link_ALPHA1-3 : angle 3.91508 ( 9) link_ALPHA1-6 : bond 0.01979 ( 2) link_ALPHA1-6 : angle 3.51430 ( 6) link_BETA1-4 : bond 0.01505 ( 54) link_BETA1-4 : angle 4.55657 ( 162) link_NAG-ASN : bond 0.00362 ( 60) link_NAG-ASN : angle 2.26916 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 647 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8405 (mt-10) REVERT: B 654 GLU cc_start: 0.9442 (mm-30) cc_final: 0.8372 (mp0) REVERT: C 95 MET cc_start: 0.7649 (ptp) cc_final: 0.7332 (ptp) REVERT: C 195 ASN cc_start: 0.8057 (m110) cc_final: 0.7814 (m110) REVERT: C 434 MET cc_start: 0.8799 (tpp) cc_final: 0.8067 (tpp) REVERT: F 642 ILE cc_start: 0.9630 (mt) cc_final: 0.9416 (mt) REVERT: H 36 TRP cc_start: 0.8005 (m100) cc_final: 0.7356 (m100) REVERT: H 82 ASN cc_start: 0.9285 (m-40) cc_final: 0.8685 (t0) REVERT: H 82 MET cc_start: 0.8374 (mmm) cc_final: 0.7750 (mmm) REVERT: H 100 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8094 (mm-30) REVERT: H 100 MET cc_start: 0.8340 (tpp) cc_final: 0.8067 (tpp) REVERT: H 105 GLN cc_start: 0.8750 (pt0) cc_final: 0.8484 (pt0) REVERT: H 108 ARG cc_start: 0.8515 (mmt90) cc_final: 0.8026 (tpt-90) REVERT: L 17 ASP cc_start: 0.9106 (t0) cc_final: 0.8815 (p0) REVERT: L 87 TYR cc_start: 0.8238 (m-80) cc_final: 0.7802 (m-10) REVERT: L 105 ASP cc_start: 0.8363 (t0) cc_final: 0.7994 (p0) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1220 time to fit residues: 21.8937 Evaluate side-chains 75 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS A 377 ASN A 425 ASN E 246 GLN E 249 HIS ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.045962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.036272 restraints weight = 107291.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.037575 restraints weight = 55265.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.038420 restraints weight = 37474.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.038955 restraints weight = 29508.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.039286 restraints weight = 25419.279| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17226 Z= 0.166 Angle : 0.741 17.110 23610 Z= 0.341 Chirality : 0.048 0.409 2962 Planarity : 0.004 0.043 2771 Dihedral : 9.189 69.764 4516 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.18 % Allowed : 9.40 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.19), residues: 1864 helix: 0.98 (0.26), residues: 408 sheet: -0.59 (0.22), residues: 520 loop : -1.26 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 192 TYR 0.014 0.001 TYR C 352 PHE 0.012 0.002 PHE C 353 TRP 0.014 0.001 TRP B 631 HIS 0.005 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00360 (17072) covalent geometry : angle 0.66616 (23182) SS BOND : bond 0.00342 ( 34) SS BOND : angle 1.08379 ( 68) hydrogen bonds : bond 0.05428 ( 556) hydrogen bonds : angle 5.79460 ( 1551) link_ALPHA1-2 : bond 0.00495 ( 1) link_ALPHA1-2 : angle 2.87569 ( 3) link_ALPHA1-3 : bond 0.01127 ( 3) link_ALPHA1-3 : angle 2.54845 ( 9) link_ALPHA1-6 : bond 0.00953 ( 2) link_ALPHA1-6 : angle 1.43594 ( 6) link_BETA1-4 : bond 0.00979 ( 54) link_BETA1-4 : angle 3.25932 ( 162) link_NAG-ASN : bond 0.00313 ( 60) link_NAG-ASN : angle 2.09408 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.8845 (p) REVERT: A 479 TRP cc_start: 0.8786 (m-90) cc_final: 0.8573 (m-90) REVERT: B 647 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8188 (mt-10) REVERT: C 95 MET cc_start: 0.8135 (ptp) cc_final: 0.7868 (ptp) REVERT: C 161 MET cc_start: 0.8577 (tpt) cc_final: 0.8253 (tpt) REVERT: C 195 ASN cc_start: 0.8151 (m110) cc_final: 0.7922 (m110) REVERT: C 434 MET cc_start: 0.8733 (tpp) cc_final: 0.8328 (tpp) REVERT: E 492 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8533 (tt0) REVERT: F 642 ILE cc_start: 0.9745 (mt) cc_final: 0.9530 (mt) REVERT: F 652 GLN cc_start: 0.8959 (tp40) cc_final: 0.8658 (tp-100) REVERT: G 590 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8761 (tm-30) REVERT: G 654 GLU cc_start: 0.8948 (tp30) cc_final: 0.8656 (tp30) REVERT: H 36 TRP cc_start: 0.8328 (m100) cc_final: 0.7776 (m100) REVERT: H 46 GLU cc_start: 0.8715 (tt0) cc_final: 0.8312 (tt0) REVERT: H 82 MET cc_start: 0.8482 (mmm) cc_final: 0.7924 (mmm) REVERT: H 100 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8059 (mm-30) REVERT: H 105 GLN cc_start: 0.8707 (pt0) cc_final: 0.8465 (pt0) REVERT: H 108 ARG cc_start: 0.8598 (mmt90) cc_final: 0.8076 (tpt-90) REVERT: L 4 MET cc_start: 0.8862 (tpp) cc_final: 0.8582 (tpp) REVERT: L 105 ASP cc_start: 0.8501 (t0) cc_final: 0.8148 (p0) outliers start: 20 outliers final: 6 residues processed: 99 average time/residue: 0.1258 time to fit residues: 20.1882 Evaluate side-chains 80 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 492 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 2 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 153 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 129 optimal weight: 0.0570 chunk 24 optimal weight: 7.9990 overall best weight: 2.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 377 ASN G 650 GLN H 105 GLN L 3 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.044774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.034972 restraints weight = 109201.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.036227 restraints weight = 55579.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.037081 restraints weight = 37932.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.037607 restraints weight = 29820.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.037947 restraints weight = 25743.616| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17226 Z= 0.186 Angle : 0.694 16.794 23610 Z= 0.316 Chirality : 0.046 0.394 2962 Planarity : 0.004 0.042 2771 Dihedral : 8.773 67.068 4516 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.24 % Allowed : 9.99 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.19), residues: 1864 helix: 1.34 (0.26), residues: 399 sheet: -0.38 (0.22), residues: 493 loop : -1.10 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 18 TYR 0.008 0.001 TYR E 217 PHE 0.011 0.002 PHE C 353 TRP 0.018 0.001 TRP B 628 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00408 (17072) covalent geometry : angle 0.62532 (23182) SS BOND : bond 0.00329 ( 34) SS BOND : angle 0.92615 ( 68) hydrogen bonds : bond 0.04437 ( 556) hydrogen bonds : angle 5.19354 ( 1551) link_ALPHA1-2 : bond 0.00718 ( 1) link_ALPHA1-2 : angle 3.08157 ( 3) link_ALPHA1-3 : bond 0.00950 ( 3) link_ALPHA1-3 : angle 2.66942 ( 9) link_ALPHA1-6 : bond 0.00789 ( 2) link_ALPHA1-6 : angle 1.37730 ( 6) link_BETA1-4 : bond 0.00897 ( 54) link_BETA1-4 : angle 2.94429 ( 162) link_NAG-ASN : bond 0.00292 ( 60) link_NAG-ASN : angle 2.00821 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 THR cc_start: 0.9372 (OUTLIER) cc_final: 0.9008 (p) REVERT: B 647 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8262 (mt-10) REVERT: E 95 MET cc_start: 0.9270 (ppp) cc_final: 0.8057 (ppp) REVERT: F 648 GLU cc_start: 0.9158 (pt0) cc_final: 0.8860 (pp20) REVERT: F 652 GLN cc_start: 0.8993 (tp40) cc_final: 0.8671 (tp40) REVERT: G 650 GLN cc_start: 0.9555 (OUTLIER) cc_final: 0.9123 (tt0) REVERT: H 34 MET cc_start: 0.9134 (tpp) cc_final: 0.8660 (mmm) REVERT: H 100 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8131 (mm-30) REVERT: H 105 GLN cc_start: 0.8655 (pt0) cc_final: 0.8424 (pt0) REVERT: H 108 ARG cc_start: 0.8647 (mmt90) cc_final: 0.8121 (tpt-90) REVERT: L 105 ASP cc_start: 0.8568 (t0) cc_final: 0.8221 (p0) outliers start: 21 outliers final: 10 residues processed: 90 average time/residue: 0.1243 time to fit residues: 18.2715 Evaluate side-chains 75 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain F residue 585 HIS Chi-restraints excluded: chain G residue 650 GLN Chi-restraints excluded: chain H residue 78 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 31 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN C 99 ASN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.044999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.035213 restraints weight = 106429.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.036512 restraints weight = 54910.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.037277 restraints weight = 36962.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.037864 restraints weight = 29657.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.038188 restraints weight = 25273.143| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17226 Z= 0.138 Angle : 0.648 16.981 23610 Z= 0.293 Chirality : 0.045 0.409 2962 Planarity : 0.003 0.037 2771 Dihedral : 8.574 64.139 4516 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.83 % Allowed : 11.41 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.19), residues: 1864 helix: 1.40 (0.26), residues: 402 sheet: -0.35 (0.22), residues: 517 loop : -1.11 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 350 TYR 0.006 0.001 TYR L 49 PHE 0.011 0.001 PHE L 98 TRP 0.011 0.001 TRP H 103 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00300 (17072) covalent geometry : angle 0.58085 (23182) SS BOND : bond 0.00283 ( 34) SS BOND : angle 0.77589 ( 68) hydrogen bonds : bond 0.03956 ( 556) hydrogen bonds : angle 4.96297 ( 1551) link_ALPHA1-2 : bond 0.00537 ( 1) link_ALPHA1-2 : angle 2.79130 ( 3) link_ALPHA1-3 : bond 0.00890 ( 3) link_ALPHA1-3 : angle 2.61854 ( 9) link_ALPHA1-6 : bond 0.00867 ( 2) link_ALPHA1-6 : angle 1.33591 ( 6) link_BETA1-4 : bond 0.00962 ( 54) link_BETA1-4 : angle 2.83313 ( 162) link_NAG-ASN : bond 0.00218 ( 60) link_NAG-ASN : angle 1.88804 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 THR cc_start: 0.9366 (OUTLIER) cc_final: 0.9010 (p) REVERT: B 636 ASN cc_start: 0.9603 (t0) cc_final: 0.9216 (p0) REVERT: B 647 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8300 (mt-10) REVERT: E 95 MET cc_start: 0.9285 (ppp) cc_final: 0.7937 (ppp) REVERT: E 475 MET cc_start: 0.9390 (tpt) cc_final: 0.9178 (tpp) REVERT: F 648 GLU cc_start: 0.9153 (pt0) cc_final: 0.8863 (pp20) REVERT: F 652 GLN cc_start: 0.9017 (tp40) cc_final: 0.8744 (tp40) REVERT: G 657 GLU cc_start: 0.9042 (tt0) cc_final: 0.8796 (pp20) REVERT: H 34 MET cc_start: 0.9168 (tpp) cc_final: 0.8736 (mmm) REVERT: H 46 GLU cc_start: 0.8898 (tt0) cc_final: 0.8490 (tt0) REVERT: H 100 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7959 (tp30) REVERT: H 105 GLN cc_start: 0.8649 (pt0) cc_final: 0.8416 (pt0) REVERT: H 108 ARG cc_start: 0.8672 (mmt90) cc_final: 0.8160 (tpt-90) REVERT: L 105 ASP cc_start: 0.8601 (t0) cc_final: 0.8246 (p0) outliers start: 14 outliers final: 6 residues processed: 82 average time/residue: 0.1321 time to fit residues: 17.5399 Evaluate side-chains 73 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain H residue 78 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 118 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 HIS ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS G 650 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.044801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.035023 restraints weight = 106825.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.036268 restraints weight = 54444.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.037121 restraints weight = 37101.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.037650 restraints weight = 29160.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.038012 restraints weight = 25106.876| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17226 Z= 0.143 Angle : 0.637 16.961 23610 Z= 0.289 Chirality : 0.045 0.403 2962 Planarity : 0.003 0.038 2771 Dihedral : 8.461 61.780 4516 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.12 % Allowed : 11.88 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.19), residues: 1864 helix: 1.46 (0.26), residues: 402 sheet: -0.34 (0.22), residues: 537 loop : -1.06 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 469 TYR 0.008 0.001 TYR E 217 PHE 0.009 0.001 PHE A 210 TRP 0.012 0.001 TRP C 112 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00312 (17072) covalent geometry : angle 0.57342 (23182) SS BOND : bond 0.00267 ( 34) SS BOND : angle 0.73876 ( 68) hydrogen bonds : bond 0.03705 ( 556) hydrogen bonds : angle 4.80435 ( 1551) link_ALPHA1-2 : bond 0.00567 ( 1) link_ALPHA1-2 : angle 2.79799 ( 3) link_ALPHA1-3 : bond 0.00821 ( 3) link_ALPHA1-3 : angle 2.57944 ( 9) link_ALPHA1-6 : bond 0.00859 ( 2) link_ALPHA1-6 : angle 1.32737 ( 6) link_BETA1-4 : bond 0.00915 ( 54) link_BETA1-4 : angle 2.74043 ( 162) link_NAG-ASN : bond 0.00217 ( 60) link_NAG-ASN : angle 1.82628 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.8990 (p) REVERT: A 479 TRP cc_start: 0.8797 (m-90) cc_final: 0.8570 (m-90) REVERT: B 636 ASN cc_start: 0.9575 (t0) cc_final: 0.9274 (p0) REVERT: B 647 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8317 (mt-10) REVERT: E 475 MET cc_start: 0.9390 (tpt) cc_final: 0.9182 (tpp) REVERT: F 648 GLU cc_start: 0.9164 (pt0) cc_final: 0.8888 (pp20) REVERT: G 657 GLU cc_start: 0.9026 (tt0) cc_final: 0.8807 (pp20) REVERT: H 34 MET cc_start: 0.9218 (tpp) cc_final: 0.8809 (mmm) REVERT: H 46 GLU cc_start: 0.8935 (tt0) cc_final: 0.8624 (tt0) REVERT: H 100 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7906 (tp30) REVERT: H 108 ARG cc_start: 0.8688 (mmt90) cc_final: 0.8191 (tpt-90) REVERT: L 105 ASP cc_start: 0.8701 (t0) cc_final: 0.8278 (p0) outliers start: 19 outliers final: 12 residues processed: 87 average time/residue: 0.1307 time to fit residues: 18.2470 Evaluate side-chains 75 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 650 GLN Chi-restraints excluded: chain H residue 78 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 89 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 142 optimal weight: 0.5980 chunk 145 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.044917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.035102 restraints weight = 106959.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.036384 restraints weight = 55323.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.037222 restraints weight = 37355.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.037747 restraints weight = 29434.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.038103 restraints weight = 25390.902| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17226 Z= 0.138 Angle : 0.627 16.907 23610 Z= 0.284 Chirality : 0.044 0.401 2962 Planarity : 0.003 0.067 2771 Dihedral : 8.421 60.239 4516 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.42 % Allowed : 12.12 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.19), residues: 1864 helix: 1.57 (0.26), residues: 402 sheet: -0.30 (0.22), residues: 538 loop : -1.07 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 46 TYR 0.006 0.001 TYR E 217 PHE 0.009 0.001 PHE L 83 TRP 0.011 0.001 TRP A 112 HIS 0.003 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00303 (17072) covalent geometry : angle 0.56466 (23182) SS BOND : bond 0.00267 ( 34) SS BOND : angle 0.73414 ( 68) hydrogen bonds : bond 0.03621 ( 556) hydrogen bonds : angle 4.74264 ( 1551) link_ALPHA1-2 : bond 0.00545 ( 1) link_ALPHA1-2 : angle 2.71063 ( 3) link_ALPHA1-3 : bond 0.00804 ( 3) link_ALPHA1-3 : angle 2.57842 ( 9) link_ALPHA1-6 : bond 0.00873 ( 2) link_ALPHA1-6 : angle 1.31617 ( 6) link_BETA1-4 : bond 0.00907 ( 54) link_BETA1-4 : angle 2.69098 ( 162) link_NAG-ASN : bond 0.00212 ( 60) link_NAG-ASN : angle 1.78859 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 THR cc_start: 0.9361 (OUTLIER) cc_final: 0.8990 (p) REVERT: A 426 MET cc_start: 0.7538 (ptt) cc_final: 0.7301 (ptt) REVERT: B 647 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8323 (mt-10) REVERT: C 434 MET cc_start: 0.8450 (ttm) cc_final: 0.8157 (ttm) REVERT: E 95 MET cc_start: 0.9297 (ppp) cc_final: 0.7929 (ppp) REVERT: E 102 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8450 (tm-30) REVERT: F 648 GLU cc_start: 0.9168 (pt0) cc_final: 0.8895 (pp20) REVERT: G 657 GLU cc_start: 0.9087 (tt0) cc_final: 0.8854 (pp20) REVERT: H 34 MET cc_start: 0.9218 (tpp) cc_final: 0.8817 (mmm) REVERT: H 46 GLU cc_start: 0.8935 (tt0) cc_final: 0.8622 (tt0) REVERT: H 100 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7859 (tp30) REVERT: H 108 ARG cc_start: 0.8725 (mmt90) cc_final: 0.8320 (tpt-90) REVERT: L 105 ASP cc_start: 0.8731 (t0) cc_final: 0.8264 (p0) outliers start: 24 outliers final: 13 residues processed: 85 average time/residue: 0.1117 time to fit residues: 15.7499 Evaluate side-chains 74 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain L residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 133 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.045062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.035162 restraints weight = 102458.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.036429 restraints weight = 52628.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.037292 restraints weight = 35636.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.037776 restraints weight = 27883.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.038187 restraints weight = 24117.327| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17226 Z= 0.122 Angle : 0.616 17.002 23610 Z= 0.279 Chirality : 0.044 0.404 2962 Planarity : 0.003 0.036 2771 Dihedral : 8.315 57.806 4516 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.30 % Allowed : 12.53 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.19), residues: 1864 helix: 1.63 (0.26), residues: 402 sheet: -0.25 (0.22), residues: 538 loop : -1.04 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 46 TYR 0.007 0.001 TYR E 217 PHE 0.009 0.001 PHE E 382 TRP 0.011 0.001 TRP B 631 HIS 0.003 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00267 (17072) covalent geometry : angle 0.55654 (23182) SS BOND : bond 0.00245 ( 34) SS BOND : angle 0.66818 ( 68) hydrogen bonds : bond 0.03464 ( 556) hydrogen bonds : angle 4.65682 ( 1551) link_ALPHA1-2 : bond 0.00504 ( 1) link_ALPHA1-2 : angle 2.62943 ( 3) link_ALPHA1-3 : bond 0.00785 ( 3) link_ALPHA1-3 : angle 2.57677 ( 9) link_ALPHA1-6 : bond 0.00905 ( 2) link_ALPHA1-6 : angle 1.30335 ( 6) link_BETA1-4 : bond 0.00925 ( 54) link_BETA1-4 : angle 2.63666 ( 162) link_NAG-ASN : bond 0.00189 ( 60) link_NAG-ASN : angle 1.71870 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8921 (tp) REVERT: A 257 THR cc_start: 0.9351 (OUTLIER) cc_final: 0.8986 (p) REVERT: A 426 MET cc_start: 0.7503 (ptt) cc_final: 0.7237 (ptt) REVERT: A 479 TRP cc_start: 0.8780 (m-90) cc_final: 0.8567 (m-90) REVERT: B 647 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8319 (mt-10) REVERT: C 161 MET cc_start: 0.8750 (mmm) cc_final: 0.8515 (tpt) REVERT: C 434 MET cc_start: 0.8334 (ttm) cc_final: 0.7986 (ttm) REVERT: E 95 MET cc_start: 0.9293 (ppp) cc_final: 0.7842 (ppp) REVERT: E 102 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8437 (tm-30) REVERT: F 648 GLU cc_start: 0.9173 (pt0) cc_final: 0.8912 (pp20) REVERT: G 657 GLU cc_start: 0.9073 (tt0) cc_final: 0.8865 (pp20) REVERT: H 34 MET cc_start: 0.9203 (tpp) cc_final: 0.8288 (mmm) REVERT: H 46 GLU cc_start: 0.8931 (tt0) cc_final: 0.8619 (tt0) REVERT: H 100 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7787 (tp30) REVERT: H 108 ARG cc_start: 0.8737 (mmt90) cc_final: 0.8249 (tpt-90) REVERT: L 105 ASP cc_start: 0.8761 (t0) cc_final: 0.8307 (p0) REVERT: L 106 ILE cc_start: 0.7087 (mp) cc_final: 0.6856 (mp) outliers start: 22 outliers final: 14 residues processed: 88 average time/residue: 0.1193 time to fit residues: 17.3733 Evaluate side-chains 80 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain L residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 36 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN E 99 ASN E 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.043372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.033431 restraints weight = 108554.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.034629 restraints weight = 56686.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.035449 restraints weight = 38876.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.035979 restraints weight = 30806.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.036307 restraints weight = 26540.890| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 17226 Z= 0.313 Angle : 0.754 16.866 23610 Z= 0.345 Chirality : 0.046 0.407 2962 Planarity : 0.004 0.050 2771 Dihedral : 8.846 62.022 4516 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.42 % Allowed : 12.94 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.19), residues: 1864 helix: 1.40 (0.26), residues: 402 sheet: -0.34 (0.22), residues: 532 loop : -1.11 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 46 TYR 0.011 0.002 TYR A 40 PHE 0.014 0.002 PHE E 53 TRP 0.023 0.002 TRP A 112 HIS 0.005 0.001 HIS F 570 Details of bonding type rmsd covalent geometry : bond 0.00691 (17072) covalent geometry : angle 0.69698 (23182) SS BOND : bond 0.00423 ( 34) SS BOND : angle 1.05877 ( 68) hydrogen bonds : bond 0.03964 ( 556) hydrogen bonds : angle 4.90576 ( 1551) link_ALPHA1-2 : bond 0.00987 ( 1) link_ALPHA1-2 : angle 2.97983 ( 3) link_ALPHA1-3 : bond 0.00887 ( 3) link_ALPHA1-3 : angle 2.52641 ( 9) link_ALPHA1-6 : bond 0.00639 ( 2) link_ALPHA1-6 : angle 1.30924 ( 6) link_BETA1-4 : bond 0.00897 ( 54) link_BETA1-4 : angle 2.73685 ( 162) link_NAG-ASN : bond 0.00525 ( 60) link_NAG-ASN : angle 2.07933 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8900 (tp) REVERT: A 257 THR cc_start: 0.9419 (OUTLIER) cc_final: 0.9100 (p) REVERT: A 426 MET cc_start: 0.7844 (ptt) cc_final: 0.7618 (ptt) REVERT: B 647 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8300 (mt-10) REVERT: B 657 GLU cc_start: 0.9192 (tt0) cc_final: 0.8767 (tm-30) REVERT: C 161 MET cc_start: 0.8699 (mmm) cc_final: 0.8391 (tpt) REVERT: E 102 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8557 (tm-30) REVERT: G 657 GLU cc_start: 0.9082 (tt0) cc_final: 0.8857 (pp20) REVERT: H 46 GLU cc_start: 0.8953 (tt0) cc_final: 0.8612 (tt0) REVERT: H 100 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7756 (tp30) REVERT: H 108 ARG cc_start: 0.8743 (mmt90) cc_final: 0.8343 (tpt-90) REVERT: L 105 ASP cc_start: 0.8876 (t0) cc_final: 0.8363 (p0) outliers start: 24 outliers final: 19 residues processed: 82 average time/residue: 0.1162 time to fit residues: 16.1310 Evaluate side-chains 83 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 99 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 87 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 121 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.044842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.034903 restraints weight = 102457.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.036198 restraints weight = 52540.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.037054 restraints weight = 35246.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.037615 restraints weight = 27633.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.037955 restraints weight = 23630.459| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17226 Z= 0.113 Angle : 0.631 16.778 23610 Z= 0.287 Chirality : 0.045 0.404 2962 Planarity : 0.003 0.038 2771 Dihedral : 8.418 58.106 4516 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.36 % Allowed : 13.18 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.19), residues: 1864 helix: 1.63 (0.26), residues: 402 sheet: -0.28 (0.22), residues: 538 loop : -1.04 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 46 TYR 0.010 0.001 TYR H 100 PHE 0.011 0.001 PHE L 83 TRP 0.014 0.001 TRP A 112 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00241 (17072) covalent geometry : angle 0.57589 (23182) SS BOND : bond 0.00261 ( 34) SS BOND : angle 0.73814 ( 68) hydrogen bonds : bond 0.03510 ( 556) hydrogen bonds : angle 4.69041 ( 1551) link_ALPHA1-2 : bond 0.00562 ( 1) link_ALPHA1-2 : angle 2.61504 ( 3) link_ALPHA1-3 : bond 0.00719 ( 3) link_ALPHA1-3 : angle 2.66321 ( 9) link_ALPHA1-6 : bond 0.00917 ( 2) link_ALPHA1-6 : angle 1.29368 ( 6) link_BETA1-4 : bond 0.00935 ( 54) link_BETA1-4 : angle 2.57436 ( 162) link_NAG-ASN : bond 0.00194 ( 60) link_NAG-ASN : angle 1.68969 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8864 (tp) REVERT: A 426 MET cc_start: 0.7373 (ptt) cc_final: 0.7161 (ptt) REVERT: A 434 MET cc_start: 0.8809 (tpp) cc_final: 0.8537 (mmm) REVERT: B 647 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8300 (mt-10) REVERT: B 657 GLU cc_start: 0.9167 (tt0) cc_final: 0.8709 (tm-30) REVERT: E 161 MET cc_start: 0.8759 (tpt) cc_final: 0.8536 (tpt) REVERT: F 648 GLU cc_start: 0.9179 (pt0) cc_final: 0.8917 (pp20) REVERT: G 657 GLU cc_start: 0.9062 (tt0) cc_final: 0.8857 (pp20) REVERT: H 34 MET cc_start: 0.9146 (tpp) cc_final: 0.8310 (mmm) REVERT: H 46 GLU cc_start: 0.8980 (tt0) cc_final: 0.8573 (tt0) REVERT: H 82 MET cc_start: 0.8408 (mmm) cc_final: 0.8113 (mmm) REVERT: H 108 ARG cc_start: 0.8780 (mmt90) cc_final: 0.8305 (tpt-90) REVERT: L 18 ARG cc_start: 0.9140 (ttt90) cc_final: 0.8863 (tpp80) REVERT: L 97 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7909 (t) REVERT: L 105 ASP cc_start: 0.8866 (t0) cc_final: 0.8311 (p0) outliers start: 23 outliers final: 17 residues processed: 85 average time/residue: 0.1213 time to fit residues: 16.8263 Evaluate side-chains 80 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 4 optimal weight: 0.0870 chunk 10 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 48 optimal weight: 0.0270 chunk 78 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 overall best weight: 0.8818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.044995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.035085 restraints weight = 102407.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.036350 restraints weight = 52565.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.037224 restraints weight = 35519.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.037788 restraints weight = 27724.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.038140 restraints weight = 23666.067| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17226 Z= 0.113 Angle : 0.615 16.932 23610 Z= 0.281 Chirality : 0.044 0.401 2962 Planarity : 0.003 0.036 2771 Dihedral : 8.247 56.827 4516 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.30 % Allowed : 13.18 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.19), residues: 1864 helix: 1.64 (0.26), residues: 405 sheet: -0.21 (0.22), residues: 541 loop : -1.06 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 46 TYR 0.013 0.001 TYR H 100 PHE 0.011 0.001 PHE L 83 TRP 0.012 0.001 TRP B 631 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00243 (17072) covalent geometry : angle 0.56017 (23182) SS BOND : bond 0.00250 ( 34) SS BOND : angle 0.68033 ( 68) hydrogen bonds : bond 0.03348 ( 556) hydrogen bonds : angle 4.56255 ( 1551) link_ALPHA1-2 : bond 0.00467 ( 1) link_ALPHA1-2 : angle 2.59757 ( 3) link_ALPHA1-3 : bond 0.00744 ( 3) link_ALPHA1-3 : angle 2.52382 ( 9) link_ALPHA1-6 : bond 0.00913 ( 2) link_ALPHA1-6 : angle 1.30168 ( 6) link_BETA1-4 : bond 0.00924 ( 54) link_BETA1-4 : angle 2.54617 ( 162) link_NAG-ASN : bond 0.00214 ( 60) link_NAG-ASN : angle 1.63837 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8821 (tp) REVERT: A 434 MET cc_start: 0.8791 (tpp) cc_final: 0.8511 (mmm) REVERT: B 647 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8317 (mt-10) REVERT: E 95 MET cc_start: 0.9280 (ppp) cc_final: 0.7806 (ppp) REVERT: F 648 GLU cc_start: 0.9176 (pt0) cc_final: 0.8920 (pp20) REVERT: H 34 MET cc_start: 0.9123 (tpp) cc_final: 0.8807 (mmm) REVERT: H 46 GLU cc_start: 0.8983 (tt0) cc_final: 0.8639 (tt0) REVERT: H 82 MET cc_start: 0.8443 (mmm) cc_final: 0.7465 (mmm) REVERT: H 108 ARG cc_start: 0.8793 (mmt90) cc_final: 0.8341 (tpt-90) REVERT: L 18 ARG cc_start: 0.9127 (ttt90) cc_final: 0.8843 (tpp80) REVERT: L 97 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7878 (t) REVERT: L 105 ASP cc_start: 0.8841 (t0) cc_final: 0.8282 (p0) outliers start: 22 outliers final: 18 residues processed: 84 average time/residue: 0.1202 time to fit residues: 16.4849 Evaluate side-chains 82 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 155 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 70 optimal weight: 0.0020 chunk 96 optimal weight: 4.9990 overall best weight: 3.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 HIS E 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.043891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.034027 restraints weight = 107239.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.035281 restraints weight = 55506.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.036011 restraints weight = 37653.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.036595 restraints weight = 30377.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.036942 restraints weight = 25920.970| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17226 Z= 0.224 Angle : 0.687 16.966 23610 Z= 0.314 Chirality : 0.044 0.400 2962 Planarity : 0.004 0.046 2771 Dihedral : 8.559 58.502 4516 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.24 % Allowed : 13.18 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.19), residues: 1864 helix: 1.59 (0.26), residues: 402 sheet: -0.34 (0.22), residues: 552 loop : -1.02 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 46 TYR 0.009 0.001 TYR E 217 PHE 0.013 0.002 PHE L 83 TRP 0.026 0.002 TRP A 112 HIS 0.004 0.001 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00493 (17072) covalent geometry : angle 0.63207 (23182) SS BOND : bond 0.00356 ( 34) SS BOND : angle 0.94601 ( 68) hydrogen bonds : bond 0.03611 ( 556) hydrogen bonds : angle 4.68799 ( 1551) link_ALPHA1-2 : bond 0.00799 ( 1) link_ALPHA1-2 : angle 2.75515 ( 3) link_ALPHA1-3 : bond 0.00750 ( 3) link_ALPHA1-3 : angle 2.50106 ( 9) link_ALPHA1-6 : bond 0.00719 ( 2) link_ALPHA1-6 : angle 1.30105 ( 6) link_BETA1-4 : bond 0.00872 ( 54) link_BETA1-4 : angle 2.59957 ( 162) link_NAG-ASN : bond 0.00378 ( 60) link_NAG-ASN : angle 1.87310 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2412.32 seconds wall clock time: 42 minutes 59.94 seconds (2579.94 seconds total)