Starting phenix.real_space_refine on Mon Aug 25 20:16:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9db3_46714/08_2025/9db3_46714.cif Found real_map, /net/cci-nas-00/data/ceres_data/9db3_46714/08_2025/9db3_46714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9db3_46714/08_2025/9db3_46714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9db3_46714/08_2025/9db3_46714.map" model { file = "/net/cci-nas-00/data/ceres_data/9db3_46714/08_2025/9db3_46714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9db3_46714/08_2025/9db3_46714.cif" } resolution = 2.3 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= -0.000 sd= 0.075 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 147 5.16 5 C 18729 2.51 5 N 4722 2.21 5 O 5868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29466 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 9064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1240, 9064 Classifications: {'peptide': 1240} Incomplete info: {'truncation_to_alanine': 205} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1197} Chain breaks: 6 Unresolved non-hydrogen bonds: 585 Unresolved non-hydrogen angles: 752 Unresolved non-hydrogen dihedrals: 448 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'ASN:plan1': 13, 'ARG:plan': 8, 'GLN:plan1': 6, 'ASP:plan': 32, 'GLU:plan': 22, 'TYR:plan': 5, 'HIS:plan': 3, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 352 Chain: "B" Number of atoms: 9064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1240, 9064 Classifications: {'peptide': 1240} Incomplete info: {'truncation_to_alanine': 205} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1197} Chain breaks: 6 Unresolved non-hydrogen bonds: 585 Unresolved non-hydrogen angles: 752 Unresolved non-hydrogen dihedrals: 448 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'ASN:plan1': 13, 'ARG:plan': 8, 'GLN:plan1': 6, 'ASP:plan': 32, 'GLU:plan': 22, 'TYR:plan': 5, 'HIS:plan': 3, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 352 Chain: "C" Number of atoms: 9064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1240, 9064 Classifications: {'peptide': 1240} Incomplete info: {'truncation_to_alanine': 205} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1197} Chain breaks: 6 Unresolved non-hydrogen bonds: 585 Unresolved non-hydrogen angles: 752 Unresolved non-hydrogen dihedrals: 448 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'ASN:plan1': 13, 'ARG:plan': 8, 'GLN:plan1': 6, 'ASP:plan': 32, 'GLU:plan': 22, 'TYR:plan': 5, 'HIS:plan': 3, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 352 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: "T" 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: "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: 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: "h" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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: 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: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 250 Unusual residues: {'NAG': 14, 'PAM': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 232 Unusual residues: {'NAG': 14, 'PAM': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 214 Unusual residues: {'NAG': 14, 'PAM': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Time building chain proxies: 9.04, per 1000 atoms: 0.31 Number of scatterers: 29466 At special positions: 0 Unit cell: (180.36, 195.474, 160.208, 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 147 16.00 O 5868 8.00 N 4722 7.00 C 18729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 68 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 260 " distance=2.03 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 450 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 405 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 498 " distance=2.03 Simple disulfide: pdb=" SG CYS A 573 " - pdb=" SG CYS A 632 " distance=2.03 Simple disulfide: pdb=" SG CYS A 587 " - pdb=" SG CYS A 600 " distance=2.03 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 642 " distance=2.03 Simple disulfide: pdb=" SG CYS A 691 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 803 " - pdb=" SG CYS A 815 " distance=2.05 Simple disulfide: pdb=" SG CYS A 866 " - pdb=" SG CYS A 888 " distance=2.03 Simple disulfide: pdb=" SG CYS A 871 " - pdb=" SG CYS A 877 " distance=2.03 Simple disulfide: pdb=" SG CYS A 989 " - pdb=" SG CYS A1000 " distance=2.03 Simple disulfide: pdb=" SG CYS A1192 " - pdb=" SG CYS A1203 " distance=2.03 Simple disulfide: pdb=" SG CYS A1242 " - pdb=" SG CYS A1293 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 68 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 160 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 260 " distance=2.03 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 450 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 405 " distance=2.03 Simple disulfide: pdb=" SG CYS B 489 " - pdb=" SG CYS B 498 " distance=2.03 Simple disulfide: pdb=" SG CYS B 573 " - pdb=" SG CYS B 632 " distance=2.03 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 600 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 642 " distance=2.03 Simple disulfide: pdb=" SG CYS B 691 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 803 " - pdb=" SG CYS B 815 " distance=2.05 Simple disulfide: pdb=" SG CYS B 866 " - pdb=" SG CYS B 888 " distance=2.03 Simple disulfide: pdb=" SG CYS B 871 " - pdb=" SG CYS B 877 " distance=2.03 Simple disulfide: pdb=" SG CYS B 989 " - pdb=" SG CYS B1000 " distance=2.03 Simple disulfide: pdb=" SG CYS B1192 " - pdb=" SG CYS B1203 " distance=2.03 Simple disulfide: pdb=" SG CYS B1242 " - pdb=" SG CYS B1293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 68 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 160 " distance=2.03 Simple disulfide: pdb=" SG CYS C 254 " - pdb=" SG CYS C 260 " distance=2.03 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 450 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 405 " distance=2.03 Simple disulfide: pdb=" SG CYS C 489 " - pdb=" SG CYS C 498 " distance=2.03 Simple disulfide: pdb=" SG CYS C 573 " - pdb=" SG CYS C 632 " distance=2.03 Simple disulfide: pdb=" SG CYS C 587 " - pdb=" SG CYS C 600 " distance=2.03 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 642 " distance=2.03 Simple disulfide: pdb=" SG CYS C 691 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 803 " - pdb=" SG CYS C 815 " distance=2.05 Simple disulfide: pdb=" SG CYS C 866 " - pdb=" SG CYS C 888 " distance=2.03 Simple disulfide: pdb=" SG CYS C 871 " - pdb=" SG CYS C 877 " distance=2.03 Simple disulfide: pdb=" SG CYS C 989 " - pdb=" SG CYS C1000 " distance=2.03 Simple disulfide: pdb=" SG CYS C1192 " - pdb=" SG CYS C1203 " distance=2.03 Simple disulfide: pdb=" SG CYS C1242 " - pdb=" SG CYS C1293 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA L 3 " - " MAN L 4 " " BMA S 3 " - " MAN S 4 " " BMA Z 3 " - " MAN Z 4 " " BMA g 3 " - " MAN g 4 " " BMA n 3 " - " MAN n 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA L 3 " - " MAN L 5 " " BMA S 3 " - " MAN S 5 " " BMA Z 3 " - " MAN Z 5 " " BMA g 3 " - " MAN g 5 " " BMA n 3 " - " MAN n 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " 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 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 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 T 2 " - " BMA T 3 " " 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 X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " 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 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 n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " NAG-ASN " NAG A1501 " - " ASN A 29 " " NAG A1502 " - " ASN A 236 " " NAG A1503 " - " ASN A 380 " " NAG A1504 " - " ASN A 537 " " NAG A1505 " - " ASN A 67 " " NAG A1506 " - " ASN A 567 " " NAG A1507 " - " ASN A 243 " " NAG A1508 " - " ASN A 410 " " NAG A1509 " - " ASN A 521 " " NAG A1510 " - " ASN A 339 " " NAG A1511 " - " ASN A 95 " " NAG A1512 " - " ASN A 176 " " NAG A1515 " - " ASN A 785 " " NAG A1516 " - " ASN A 709 " " NAG B1501 " - " ASN B 29 " " NAG B1502 " - " ASN B 236 " " NAG B1503 " - " ASN B 380 " " NAG B1504 " - " ASN B 537 " " NAG B1505 " - " ASN B 67 " " NAG B1506 " - " ASN B 567 " " NAG B1507 " - " ASN B 243 " " NAG B1508 " - " ASN B 410 " " NAG B1509 " - " ASN B 521 " " NAG B1510 " - " ASN B 339 " " NAG B1511 " - " ASN B 95 " " NAG B1512 " - " ASN B 176 " " NAG B1514 " - " ASN B 785 " " NAG B1515 " - " ASN B 709 " " NAG C1501 " - " ASN C 29 " " NAG C1502 " - " ASN C 236 " " NAG C1503 " - " ASN C 380 " " NAG C1504 " - " ASN C 537 " " NAG C1505 " - " ASN C 67 " " NAG C1506 " - " ASN C 567 " " NAG C1507 " - " ASN C 243 " " NAG C1508 " - " ASN C 410 " " NAG C1509 " - " ASN C 521 " " NAG C1510 " - " ASN C 339 " " NAG C1511 " - " ASN C 95 " " NAG C1512 " - " ASN C 176 " " NAG C1514 " - " ASN C 785 " " NAG C1515 " - " ASN C 709 " " NAG D 1 " - " ASN A 367 " " NAG E 1 " - " ASN A 290 " " NAG F 1 " - " ASN A 350 " " NAG G 1 " - " ASN A 559 " " NAG H 1 " - " ASN A 454 " " NAG I 1 " - " ASN A1299 " " NAG J 1 " - " ASN A1079 " " NAG K 1 " - " ASN A 210 " " NAG L 1 " - " ASN A1205 " " NAG M 1 " - " ASN A 730 " " NAG N 1 " - " ASN A 845 " " NAG O 1 " - " ASN A 824 " " NAG P 1 " - " ASN A 926 " " NAG Q 1 " - " ASN A 839 " " NAG R 1 " - " ASN B 367 " " NAG S 1 " - " ASN B 290 " " NAG T 1 " - " ASN B 350 " " NAG U 1 " - " ASN B 559 " " NAG V 1 " - " ASN B 454 " " NAG W 1 " - " ASN B1299 " " NAG X 1 " - " ASN B1079 " " NAG Y 1 " - " ASN B 210 " " NAG Z 1 " - " ASN B1205 " " NAG a 1 " - " ASN B 730 " " NAG b 1 " - " ASN B 845 " " NAG c 1 " - " ASN B 824 " " NAG d 1 " - " ASN B 926 " " NAG e 1 " - " ASN B 839 " " NAG f 1 " - " ASN C 367 " " NAG g 1 " - " ASN C 290 " " NAG h 1 " - " ASN C 350 " " NAG i 1 " - " ASN C 559 " " NAG j 1 " - " ASN C 454 " " NAG k 1 " - " ASN C1299 " " NAG l 1 " - " ASN C1079 " " NAG m 1 " - " ASN C 210 " " NAG n 1 " - " ASN C1205 " " NAG o 1 " - " ASN C 730 " " NAG p 1 " - " ASN C 845 " " NAG q 1 " - " ASN C 824 " " NAG r 1 " - " ASN C 926 " " NAG s 1 " - " ASN C 839 " Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6930 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 42 sheets defined 21.8% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 38 through 45 removed outlier: 3.902A pdb=" N PHE A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 removed outlier: 4.154A pdb=" N ILE A 159 " --> pdb=" O TRP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 Processing helix chain 'A' and resid 491 through 501 Processing helix chain 'A' and resid 618 through 622 Processing helix chain 'A' and resid 865 through 871 Processing helix chain 'A' and resid 874 through 882 Processing helix chain 'A' and resid 884 through 910 removed outlier: 3.647A pdb=" N CYS A 888 " --> pdb=" O TYR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 920 Processing helix chain 'A' and resid 921 through 926 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 950 Processing helix chain 'A' and resid 964 through 974 Processing helix chain 'A' and resid 997 through 1005 Processing helix chain 'A' and resid 1012 through 1029 Processing helix chain 'A' and resid 1030 through 1032 No H-bonds generated for 'chain 'A' and resid 1030 through 1032' Processing helix chain 'A' and resid 1043 through 1056 removed outlier: 3.504A pdb=" N ALA A1047 " --> pdb=" O PRO A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1086 removed outlier: 4.077A pdb=" N LEU A1069 " --> pdb=" O ASN A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1125 removed outlier: 3.603A pdb=" N ALA A1118 " --> pdb=" O THR A1114 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A1119 " --> pdb=" O GLN A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1128 No H-bonds generated for 'chain 'A' and resid 1126 through 1128' Processing helix chain 'A' and resid 1136 through 1144 Processing helix chain 'A' and resid 1145 through 1193 removed outlier: 3.723A pdb=" N ALA A1151 " --> pdb=" O PRO A1147 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A1155 " --> pdb=" O ALA A1151 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A1156 " --> pdb=" O GLN A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1285 No H-bonds generated for 'chain 'A' and resid 1283 through 1285' Processing helix chain 'B' and resid 38 through 45 removed outlier: 3.902A pdb=" N PHE B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 removed outlier: 4.155A pdb=" N ILE B 159 " --> pdb=" O TRP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 262 Processing helix chain 'B' and resid 491 through 501 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 865 through 871 Processing helix chain 'B' and resid 874 through 882 Processing helix chain 'B' and resid 884 through 910 removed outlier: 3.647A pdb=" N CYS B 888 " --> pdb=" O TYR B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 920 Processing helix chain 'B' and resid 921 through 926 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 950 Processing helix chain 'B' and resid 964 through 974 Processing helix chain 'B' and resid 997 through 1005 Processing helix chain 'B' and resid 1012 through 1029 Processing helix chain 'B' and resid 1030 through 1032 No H-bonds generated for 'chain 'B' and resid 1030 through 1032' Processing helix chain 'B' and resid 1043 through 1056 removed outlier: 3.504A pdb=" N ALA B1047 " --> pdb=" O PRO B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1065 through 1086 removed outlier: 4.077A pdb=" N LEU B1069 " --> pdb=" O ASN B1065 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1125 removed outlier: 3.603A pdb=" N ALA B1118 " --> pdb=" O THR B1114 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU B1119 " --> pdb=" O GLN B1115 " (cutoff:3.500A) Processing helix chain 'B' and resid 1126 through 1128 No H-bonds generated for 'chain 'B' and resid 1126 through 1128' Processing helix chain 'B' and resid 1136 through 1144 Processing helix chain 'B' and resid 1145 through 1193 removed outlier: 3.724A pdb=" N ALA B1151 " --> pdb=" O PRO B1147 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG B1155 " --> pdb=" O ALA B1151 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B1156 " --> pdb=" O GLN B1152 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1285 No H-bonds generated for 'chain 'B' and resid 1283 through 1285' Processing helix chain 'C' and resid 38 through 45 removed outlier: 3.902A pdb=" N PHE C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 removed outlier: 4.154A pdb=" N ILE C 159 " --> pdb=" O TRP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 Processing helix chain 'C' and resid 491 through 501 Processing helix chain 'C' and resid 618 through 622 Processing helix chain 'C' and resid 865 through 871 Processing helix chain 'C' and resid 874 through 882 Processing helix chain 'C' and resid 884 through 910 removed outlier: 3.647A pdb=" N CYS C 888 " --> pdb=" O TYR C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 920 Processing helix chain 'C' and resid 921 through 926 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 950 Processing helix chain 'C' and resid 964 through 974 Processing helix chain 'C' and resid 997 through 1005 Processing helix chain 'C' and resid 1012 through 1029 Processing helix chain 'C' and resid 1030 through 1032 No H-bonds generated for 'chain 'C' and resid 1030 through 1032' Processing helix chain 'C' and resid 1043 through 1056 removed outlier: 3.503A pdb=" N ALA C1047 " --> pdb=" O PRO C1043 " (cutoff:3.500A) Processing helix chain 'C' and resid 1065 through 1086 removed outlier: 4.077A pdb=" N LEU C1069 " --> pdb=" O ASN C1065 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1125 removed outlier: 3.603A pdb=" N ALA C1118 " --> pdb=" O THR C1114 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU C1119 " --> pdb=" O GLN C1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 1126 through 1128 No H-bonds generated for 'chain 'C' and resid 1126 through 1128' Processing helix chain 'C' and resid 1136 through 1144 Processing helix chain 'C' and resid 1145 through 1193 removed outlier: 3.723A pdb=" N ALA C1151 " --> pdb=" O PRO C1147 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG C1155 " --> pdb=" O ALA C1151 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU C1156 " --> pdb=" O GLN C1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1285 No H-bonds generated for 'chain 'C' and resid 1283 through 1285' Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 58 removed outlier: 4.282A pdb=" N TYR A 239 " --> pdb=" O CYS A 254 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 80 removed outlier: 7.173A pdb=" N ALA A 76 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR A 215 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N PHE A 208 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N GLU A 112 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASN A 210 " --> pdb=" O HIS A 110 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS A 110 " --> pdb=" O ASN A 210 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 106 " --> pdb=" O MET A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 197 through 202 removed outlier: 3.687A pdb=" N ASP A 89 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 296 through 313 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 296 through 313 current: chain 'A' and resid 426 through 430 removed outlier: 3.905A pdb=" N HIS A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N PHE A 435 " --> pdb=" O PHE A 442 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 440 through 444 current: chain 'A' and resid 483 through 488 Processing sheet with id=AA6, first strand: chain 'A' and resid 318 through 324 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 318 through 324 current: chain 'A' and resid 373 through 379 removed outlier: 7.525A pdb=" N CYS A 405 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N TYR A 416 " --> pdb=" O CYS A 405 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 407 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 508 through 513 removed outlier: 3.850A pdb=" N GLY A 757 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS A 771 " --> pdb=" O SER A 782 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 521 through 525 removed outlier: 6.474A pdb=" N ASN A 521 " --> pdb=" O ASP A 693 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ASN A 695 " --> pdb=" O ASN A 521 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER A 523 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU A 726 " --> pdb=" O VAL A 739 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 533 through 546 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 552 through 554 current: chain 'A' and resid 598 through 599 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 598 through 599 current: chain 'A' and resid 654 through 672 Processing sheet with id=AB1, first strand: chain 'A' and resid 807 through 809 Processing sheet with id=AB2, first strand: chain 'A' and resid 838 through 843 removed outlier: 5.956A pdb=" N THR A1236 " --> pdb=" O ARG A1263 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG A1263 " --> pdb=" O THR A1236 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU A1261 " --> pdb=" O TRP A1238 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 846 through 856 removed outlier: 7.096A pdb=" N GLY A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA A1215 " --> pdb=" O GLY A1219 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A1221 " --> pdb=" O ALA A1213 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA A1213 " --> pdb=" O ILE A1221 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE A1223 " --> pdb=" O SER A1211 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER A1211 " --> pdb=" O PHE A1223 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A1225 " --> pdb=" O LEU A1209 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A1207 " --> pdb=" O LEU A1227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 862 through 864 Processing sheet with id=AB5, first strand: chain 'A' and resid 1287 through 1290 Processing sheet with id=AB6, first strand: chain 'B' and resid 25 through 29 Processing sheet with id=AB7, first strand: chain 'B' and resid 54 through 58 removed outlier: 4.282A pdb=" N TYR B 239 " --> pdb=" O CYS B 254 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 76 through 80 removed outlier: 7.174A pdb=" N ALA B 76 " --> pdb=" O TYR B 215 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR B 215 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N PHE B 208 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N GLU B 112 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASN B 210 " --> pdb=" O HIS B 110 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS B 110 " --> pdb=" O ASN B 210 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 106 " --> pdb=" O MET B 214 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 197 through 202 removed outlier: 3.687A pdb=" N ASP B 89 " --> pdb=" O VAL B 230 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 296 through 313 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 296 through 313 current: chain 'B' and resid 426 through 430 removed outlier: 3.906A pdb=" N HIS B 434 " --> pdb=" O SER B 430 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE B 435 " --> pdb=" O PHE B 442 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 440 through 444 current: chain 'B' and resid 483 through 488 Processing sheet with id=AC2, first strand: chain 'B' and resid 318 through 324 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 318 through 324 current: chain 'B' and resid 373 through 379 removed outlier: 7.525A pdb=" N CYS B 405 " --> pdb=" O TYR B 416 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N TYR B 416 " --> pdb=" O CYS B 405 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL B 407 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 508 through 513 removed outlier: 3.849A pdb=" N GLY B 757 " --> pdb=" O ALA B 749 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS B 771 " --> pdb=" O SER B 782 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 521 through 525 removed outlier: 6.474A pdb=" N ASN B 521 " --> pdb=" O ASP B 693 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ASN B 695 " --> pdb=" O ASN B 521 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER B 523 " --> pdb=" O ASN B 695 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU B 726 " --> pdb=" O VAL B 739 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 533 through 546 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 552 through 554 current: chain 'B' and resid 598 through 599 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 598 through 599 current: chain 'B' and resid 654 through 672 Processing sheet with id=AC6, first strand: chain 'B' and resid 807 through 809 Processing sheet with id=AC7, first strand: chain 'B' and resid 838 through 843 removed outlier: 5.956A pdb=" N THR B1236 " --> pdb=" O ARG B1263 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG B1263 " --> pdb=" O THR B1236 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU B1261 " --> pdb=" O TRP B1238 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 846 through 856 removed outlier: 7.097A pdb=" N GLY B1219 " --> pdb=" O ALA B1215 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA B1215 " --> pdb=" O GLY B1219 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE B1221 " --> pdb=" O ALA B1213 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA B1213 " --> pdb=" O ILE B1221 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE B1223 " --> pdb=" O SER B1211 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER B1211 " --> pdb=" O PHE B1223 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR B1225 " --> pdb=" O LEU B1209 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR B1207 " --> pdb=" O LEU B1227 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 862 through 864 Processing sheet with id=AD1, first strand: chain 'B' and resid 1287 through 1290 Processing sheet with id=AD2, first strand: chain 'C' and resid 25 through 29 Processing sheet with id=AD3, first strand: chain 'C' and resid 54 through 58 removed outlier: 4.282A pdb=" N TYR C 239 " --> pdb=" O CYS C 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 76 through 80 removed outlier: 7.173A pdb=" N ALA C 76 " --> pdb=" O TYR C 215 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR C 215 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N PHE C 208 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N GLU C 112 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASN C 210 " --> pdb=" O HIS C 110 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS C 110 " --> pdb=" O ASN C 210 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU C 106 " --> pdb=" O MET C 214 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 197 through 202 removed outlier: 3.686A pdb=" N ASP C 89 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 296 through 313 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 296 through 313 current: chain 'C' and resid 426 through 430 removed outlier: 3.905A pdb=" N HIS C 434 " --> pdb=" O SER C 430 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N PHE C 435 " --> pdb=" O PHE C 442 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 440 through 444 current: chain 'C' and resid 482 through 488 Processing sheet with id=AD7, first strand: chain 'C' and resid 318 through 324 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 318 through 324 current: chain 'C' and resid 373 through 379 removed outlier: 7.525A pdb=" N CYS C 405 " --> pdb=" O TYR C 416 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TYR C 416 " --> pdb=" O CYS C 405 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL C 407 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 508 through 513 removed outlier: 3.850A pdb=" N GLY C 757 " --> pdb=" O ALA C 749 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS C 771 " --> pdb=" O SER C 782 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 521 through 525 removed outlier: 6.474A pdb=" N ASN C 521 " --> pdb=" O ASP C 693 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ASN C 695 " --> pdb=" O ASN C 521 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER C 523 " --> pdb=" O ASN C 695 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU C 726 " --> pdb=" O VAL C 739 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 533 through 546 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 552 through 554 current: chain 'C' and resid 598 through 599 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 598 through 599 current: chain 'C' and resid 654 through 672 Processing sheet with id=AE2, first strand: chain 'C' and resid 807 through 809 Processing sheet with id=AE3, first strand: chain 'C' and resid 838 through 843 removed outlier: 5.956A pdb=" N THR C1236 " --> pdb=" O ARG C1263 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG C1263 " --> pdb=" O THR C1236 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU C1261 " --> pdb=" O TRP C1238 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 846 through 856 removed outlier: 7.095A pdb=" N GLY C1219 " --> pdb=" O ALA C1215 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA C1215 " --> pdb=" O GLY C1219 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE C1221 " --> pdb=" O ALA C1213 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA C1213 " --> pdb=" O ILE C1221 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE C1223 " --> pdb=" O SER C1211 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER C1211 " --> pdb=" O PHE C1223 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR C1225 " --> pdb=" O LEU C1209 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR C1207 " --> pdb=" O LEU C1227 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 862 through 864 Processing sheet with id=AE6, first strand: chain 'C' and resid 1287 through 1290 981 hydrogen bonds defined for protein. 2727 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: 6.79 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 4555 1.31 - 1.44: 8743 1.44 - 1.57: 16450 1.57 - 1.70: 0 1.70 - 1.84: 192 Bond restraints: 29940 Sorted by residual: bond pdb=" C PHE C 453 " pdb=" O PHE C 453 " ideal model delta sigma weight residual 1.234 1.173 0.062 1.20e-02 6.94e+03 2.63e+01 bond pdb=" C PHE A 453 " pdb=" O PHE A 453 " ideal model delta sigma weight residual 1.234 1.173 0.061 1.20e-02 6.94e+03 2.59e+01 bond pdb=" C PHE B 453 " pdb=" O PHE B 453 " ideal model delta sigma weight residual 1.234 1.173 0.061 1.20e-02 6.94e+03 2.59e+01 bond pdb=" C PRO C 805 " pdb=" O PRO C 805 " ideal model delta sigma weight residual 1.233 1.175 0.058 1.16e-02 7.43e+03 2.47e+01 bond pdb=" C PRO A 805 " pdb=" O PRO A 805 " ideal model delta sigma weight residual 1.233 1.176 0.057 1.16e-02 7.43e+03 2.41e+01 ... (remaining 29935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 39820 1.99 - 3.98: 896 3.98 - 5.97: 174 5.97 - 7.96: 18 7.96 - 9.95: 12 Bond angle restraints: 40920 Sorted by residual: angle pdb=" C ILE C 806 " pdb=" N ILE C 807 " pdb=" CA ILE C 807 " ideal model delta sigma weight residual 122.99 113.84 9.15 1.39e+00 5.18e-01 4.34e+01 angle pdb=" C ILE A 806 " pdb=" N ILE A 807 " pdb=" CA ILE A 807 " ideal model delta sigma weight residual 122.99 113.84 9.15 1.39e+00 5.18e-01 4.33e+01 angle pdb=" C ILE B 806 " pdb=" N ILE B 807 " pdb=" CA ILE B 807 " ideal model delta sigma weight residual 122.99 113.86 9.13 1.39e+00 5.18e-01 4.32e+01 angle pdb=" C ASP B 752 " pdb=" CA ASP B 752 " pdb=" CB ASP B 752 " ideal model delta sigma weight residual 111.73 120.57 -8.84 1.42e+00 4.96e-01 3.87e+01 angle pdb=" C ASP A 752 " pdb=" CA ASP A 752 " pdb=" CB ASP A 752 " ideal model delta sigma weight residual 111.73 120.55 -8.82 1.42e+00 4.96e-01 3.86e+01 ... (remaining 40915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.35: 18539 21.35 - 42.69: 582 42.69 - 64.04: 103 64.04 - 85.39: 96 85.39 - 106.74: 57 Dihedral angle restraints: 19377 sinusoidal: 8559 harmonic: 10818 Sorted by residual: dihedral pdb=" CB CYS B 324 " pdb=" SG CYS B 324 " pdb=" SG CYS B 450 " pdb=" CB CYS B 450 " ideal model delta sinusoidal sigma weight residual -86.00 -26.10 -59.90 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS C 324 " pdb=" SG CYS C 324 " pdb=" SG CYS C 450 " pdb=" CB CYS C 450 " ideal model delta sinusoidal sigma weight residual -86.00 -26.10 -59.90 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS A 324 " pdb=" SG CYS A 324 " pdb=" SG CYS A 450 " pdb=" CB CYS A 450 " ideal model delta sinusoidal sigma weight residual -86.00 -26.10 -59.90 1 1.00e+01 1.00e-02 4.78e+01 ... (remaining 19374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 4998 0.118 - 0.236: 168 0.236 - 0.354: 27 0.354 - 0.472: 3 0.472 - 0.590: 9 Chirality restraints: 5205 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 -1.81 -0.59 2.00e-02 2.50e+03 8.69e+02 chirality pdb=" C1 BMA X 3 " pdb=" O4 NAG X 2 " pdb=" C2 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-02 2.50e+03 8.69e+02 chirality pdb=" C1 BMA l 3 " pdb=" O4 NAG l 2 " pdb=" C2 BMA l 3 " pdb=" O5 BMA l 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-02 2.50e+03 8.69e+02 ... (remaining 5202 not shown) Planarity restraints: 5130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 PAM B1516 " 0.222 2.00e-02 2.50e+03 1.67e-01 2.80e+02 pdb=" C11 PAM B1516 " -0.082 2.00e-02 2.50e+03 pdb=" C8 PAM B1516 " 0.082 2.00e-02 2.50e+03 pdb=" C9 PAM B1516 " -0.222 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PAM A1517 " 0.222 2.00e-02 2.50e+03 1.67e-01 2.80e+02 pdb=" C11 PAM A1517 " -0.082 2.00e-02 2.50e+03 pdb=" C8 PAM A1517 " 0.082 2.00e-02 2.50e+03 pdb=" C9 PAM A1517 " -0.222 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PAM A1514 " 0.222 2.00e-02 2.50e+03 1.67e-01 2.79e+02 pdb=" C11 PAM A1514 " -0.082 2.00e-02 2.50e+03 pdb=" C8 PAM A1514 " 0.082 2.00e-02 2.50e+03 pdb=" C9 PAM A1514 " -0.222 2.00e-02 2.50e+03 ... (remaining 5127 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1625 2.74 - 3.28: 26891 3.28 - 3.82: 48105 3.82 - 4.36: 57587 4.36 - 4.90: 98546 Nonbonded interactions: 232754 Sorted by model distance: nonbonded pdb=" OD1 ASN C 380 " pdb=" OH TYR C 389 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASN A 380 " pdb=" OH TYR A 389 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASN B 380 " pdb=" OH TYR B 389 " model vdw 2.199 3.040 nonbonded pdb=" O LYS B 103 " pdb=" OH TYR B 229 " model vdw 2.240 3.040 nonbonded pdb=" O LYS C 103 " pdb=" OH TYR C 229 " model vdw 2.240 3.040 ... (remaining 232749 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 18 through 1513 or resid 1515)) selection = (chain 'B' and (resid 18 through 1513 or resid 1515)) selection = (chain 'C' and (resid 18 through 1513 or resid 1515)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'S' selection = chain 'Z' selection = chain 'g' selection = chain 'n' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'T' selection = chain 'X' selection = chain 'h' selection = chain 'l' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 31.780 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 0.219 30141 Z= 0.344 Angle : 0.779 15.672 41472 Z= 0.454 Chirality : 0.058 0.590 5205 Planarity : 0.008 0.229 5046 Dihedral : 13.472 106.737 12294 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.31 % Favored : 98.61 % Rotamer: Outliers : 0.81 % Allowed : 7.15 % Favored : 92.04 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.38 % 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: 0.92 (0.14), residues: 3678 helix: 2.44 (0.20), residues: 741 sheet: 0.62 (0.16), residues: 1086 loop : -0.09 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 649 TYR 0.018 0.001 TYR A1022 PHE 0.011 0.001 PHE B 325 TRP 0.008 0.001 TRP A 464 HIS 0.003 0.001 HIS C1224 Details of bonding type rmsd covalent geometry : bond 0.00466 (29940) covalent geometry : angle 0.69692 (40920) SS BOND : bond 0.00478 ( 51) SS BOND : angle 0.99007 ( 102) hydrogen bonds : bond 0.11371 ( 981) hydrogen bonds : angle 5.17438 ( 2727) link_ALPHA1-3 : bond 0.15931 ( 6) link_ALPHA1-3 : angle 6.63401 ( 18) link_ALPHA1-6 : bond 0.01246 ( 6) link_ALPHA1-6 : angle 9.50580 ( 18) link_BETA1-4 : bond 0.02163 ( 54) link_BETA1-4 : angle 3.45886 ( 162) link_NAG-ASN : bond 0.00666 ( 84) link_NAG-ASN : angle 1.80765 ( 252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 272 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.7813 (tt0) cc_final: 0.7534 (tt0) REVERT: A 231 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.6543 (p90) REVERT: A 359 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8626 (mtm) REVERT: A 549 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.7382 (t80) REVERT: A 584 HIS cc_start: 0.7776 (t70) cc_final: 0.7523 (t70) REVERT: A 649 ARG cc_start: 0.8563 (ttm-80) cc_final: 0.8252 (ttp-110) REVERT: A 822 PHE cc_start: 0.7973 (m-80) cc_final: 0.6708 (t80) REVERT: A 1117 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7327 (tm-30) REVERT: B 184 GLU cc_start: 0.7751 (tt0) cc_final: 0.7502 (tt0) REVERT: B 201 TRP cc_start: 0.7471 (m-90) cc_final: 0.6921 (m100) REVERT: B 230 VAL cc_start: 0.6686 (OUTLIER) cc_final: 0.6385 (m) REVERT: B 549 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.6566 (t80) REVERT: B 1019 MET cc_start: 0.8833 (tpp) cc_final: 0.8433 (tpp) REVERT: B 1117 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7509 (tm-30) REVERT: C 184 GLU cc_start: 0.7826 (tt0) cc_final: 0.7531 (tt0) REVERT: C 201 TRP cc_start: 0.7232 (m-90) cc_final: 0.6749 (m100) REVERT: C 214 MET cc_start: 0.6341 (ttp) cc_final: 0.5882 (ttp) REVERT: C 231 TYR cc_start: 0.7337 (OUTLIER) cc_final: 0.6725 (p90) REVERT: C 272 VAL cc_start: 0.8038 (t) cc_final: 0.7690 (p) REVERT: C 526 LEU cc_start: 0.8815 (mt) cc_final: 0.8564 (mp) REVERT: C 649 ARG cc_start: 0.8532 (ttm-80) cc_final: 0.8302 (ttm170) REVERT: C 1016 ASP cc_start: 0.8030 (m-30) cc_final: 0.7644 (t0) REVERT: C 1117 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7238 (tm-30) REVERT: C 1258 GLN cc_start: 0.8979 (mt0) cc_final: 0.8648 (mm-40) outliers start: 21 outliers final: 6 residues processed: 284 average time/residue: 0.5916 time to fit residues: 202.9332 Evaluate side-chains 241 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 229 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 549 TYR Chi-restraints excluded: chain C residue 231 TYR Chi-restraints excluded: chain C residue 359 MET Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 549 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.0770 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 334 ASN A 653 ASN A 903 ASN A1067 GLN A1082 GLN A1183 GLN A1198 GLN B 27 GLN B 266 ASN B 334 ASN B 653 ASN B 903 ASN B1067 GLN B1082 GLN B1183 GLN C 27 GLN C 334 ASN C 653 ASN C 903 ASN C1067 GLN C1183 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.161574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.121878 restraints weight = 28269.261| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.31 r_work: 0.3177 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30141 Z= 0.191 Angle : 0.661 11.115 41472 Z= 0.336 Chirality : 0.047 0.309 5205 Planarity : 0.005 0.062 5046 Dihedral : 9.252 74.163 7168 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.27 % Allowed : 7.00 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.61 (0.13), residues: 3678 helix: 2.25 (0.19), residues: 741 sheet: 0.60 (0.16), residues: 1026 loop : -0.43 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 346 TYR 0.026 0.002 TYR B1022 PHE 0.019 0.002 PHE B 325 TRP 0.008 0.002 TRP B 432 HIS 0.011 0.002 HIS A1224 Details of bonding type rmsd covalent geometry : bond 0.00414 (29940) covalent geometry : angle 0.61850 (40920) SS BOND : bond 0.00773 ( 51) SS BOND : angle 1.29896 ( 102) hydrogen bonds : bond 0.07695 ( 981) hydrogen bonds : angle 4.86279 ( 2727) link_ALPHA1-3 : bond 0.00858 ( 6) link_ALPHA1-3 : angle 1.38943 ( 18) link_ALPHA1-6 : bond 0.00680 ( 6) link_ALPHA1-6 : angle 1.47857 ( 18) link_BETA1-4 : bond 0.00962 ( 54) link_BETA1-4 : angle 2.61960 ( 162) link_NAG-ASN : bond 0.00305 ( 84) link_NAG-ASN : angle 2.09437 ( 252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.7950 (tt0) cc_final: 0.7747 (tt0) REVERT: A 231 TYR cc_start: 0.7465 (p90) cc_final: 0.7034 (p90) REVERT: A 549 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.7305 (t80) REVERT: A 584 HIS cc_start: 0.8261 (t70) cc_final: 0.8055 (t70) REVERT: A 649 ARG cc_start: 0.8904 (ttm-80) cc_final: 0.8695 (ttp-170) REVERT: A 1117 GLN cc_start: 0.8647 (mm-40) cc_final: 0.7856 (tm-30) REVERT: B 184 GLU cc_start: 0.7992 (tt0) cc_final: 0.7350 (tm-30) REVERT: B 201 TRP cc_start: 0.7707 (m-90) cc_final: 0.7179 (m100) REVERT: B 230 VAL cc_start: 0.6345 (OUTLIER) cc_final: 0.6070 (m) REVERT: B 426 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8464 (tt0) REVERT: B 549 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.6529 (t80) REVERT: B 907 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8595 (t70) REVERT: B 1019 MET cc_start: 0.9027 (tpp) cc_final: 0.8647 (tpp) REVERT: B 1117 GLN cc_start: 0.8594 (mm-40) cc_final: 0.7893 (tm-30) REVERT: B 1276 MET cc_start: 0.9210 (mtp) cc_final: 0.8847 (mtm) REVERT: C 184 GLU cc_start: 0.8045 (tt0) cc_final: 0.7792 (tt0) REVERT: C 201 TRP cc_start: 0.7450 (m-90) cc_final: 0.6972 (m100) REVERT: C 214 MET cc_start: 0.6465 (ttp) cc_final: 0.6011 (ttp) REVERT: C 231 TYR cc_start: 0.7428 (p90) cc_final: 0.6867 (p90) REVERT: C 272 VAL cc_start: 0.8011 (OUTLIER) cc_final: 0.7726 (p) REVERT: C 522 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8721 (tttp) REVERT: C 1109 GLN cc_start: 0.8948 (tp-100) cc_final: 0.8731 (tp-100) REVERT: C 1117 GLN cc_start: 0.8527 (mm-40) cc_final: 0.7724 (tm-30) REVERT: C 1258 GLN cc_start: 0.9230 (mt0) cc_final: 0.9023 (mm-40) outliers start: 33 outliers final: 17 residues processed: 251 average time/residue: 0.6325 time to fit residues: 189.2981 Evaluate side-chains 241 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 549 TYR Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 1298 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 522 LYS Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 907 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 169 optimal weight: 0.6980 chunk 175 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 235 optimal weight: 2.9990 chunk 3 optimal weight: 0.0770 chunk 14 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 300 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN A 653 ASN A1067 GLN A1198 GLN B 200 ASN B 653 ASN B1067 GLN C 200 ASN C 653 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.162302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.122729 restraints weight = 28265.362| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.35 r_work: 0.3192 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30141 Z= 0.139 Angle : 0.575 10.547 41472 Z= 0.291 Chirality : 0.045 0.305 5205 Planarity : 0.004 0.041 5046 Dihedral : 7.879 66.293 7153 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.38 % Allowed : 7.46 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.61 (0.13), residues: 3678 helix: 2.37 (0.19), residues: 732 sheet: 0.55 (0.16), residues: 1029 loop : -0.44 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1174 TYR 0.020 0.002 TYR C1022 PHE 0.015 0.001 PHE B 107 TRP 0.008 0.001 TRP B 432 HIS 0.006 0.001 HIS A1224 Details of bonding type rmsd covalent geometry : bond 0.00289 (29940) covalent geometry : angle 0.53259 (40920) SS BOND : bond 0.00547 ( 51) SS BOND : angle 1.20996 ( 102) hydrogen bonds : bond 0.06584 ( 981) hydrogen bonds : angle 4.69751 ( 2727) link_ALPHA1-3 : bond 0.00960 ( 6) link_ALPHA1-3 : angle 1.33916 ( 18) link_ALPHA1-6 : bond 0.00703 ( 6) link_ALPHA1-6 : angle 1.38488 ( 18) link_BETA1-4 : bond 0.00871 ( 54) link_BETA1-4 : angle 2.43799 ( 162) link_NAG-ASN : bond 0.00307 ( 84) link_NAG-ASN : angle 1.90600 ( 252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.7929 (tt0) cc_final: 0.7727 (tt0) REVERT: A 231 TYR cc_start: 0.7516 (p90) cc_final: 0.7065 (p90) REVERT: A 549 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.7134 (t80) REVERT: A 1117 GLN cc_start: 0.8557 (mm-40) cc_final: 0.7783 (tm-30) REVERT: B 184 GLU cc_start: 0.7964 (tt0) cc_final: 0.7346 (tm-30) REVERT: B 201 TRP cc_start: 0.7699 (m-90) cc_final: 0.7203 (m100) REVERT: B 426 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8501 (tt0) REVERT: B 549 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6434 (t80) REVERT: B 907 ASP cc_start: 0.8760 (OUTLIER) cc_final: 0.8508 (t70) REVERT: B 1019 MET cc_start: 0.9006 (tpp) cc_final: 0.8585 (tpp) REVERT: B 1117 GLN cc_start: 0.8544 (mm-40) cc_final: 0.7831 (tm130) REVERT: C 184 GLU cc_start: 0.8031 (tt0) cc_final: 0.7775 (tt0) REVERT: C 201 TRP cc_start: 0.7415 (m-90) cc_final: 0.7017 (m100) REVERT: C 231 TYR cc_start: 0.7384 (p90) cc_final: 0.6857 (p90) REVERT: C 272 VAL cc_start: 0.8015 (OUTLIER) cc_final: 0.7743 (p) REVERT: C 1109 GLN cc_start: 0.8953 (tp-100) cc_final: 0.8734 (tp-100) REVERT: C 1117 GLN cc_start: 0.8471 (mm-40) cc_final: 0.7640 (tm-30) REVERT: C 1258 GLN cc_start: 0.9213 (mt0) cc_final: 0.9007 (mm-40) outliers start: 36 outliers final: 20 residues processed: 247 average time/residue: 0.6334 time to fit residues: 185.2413 Evaluate side-chains 241 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 549 TYR Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 1298 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 907 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 338 optimal weight: 0.3980 chunk 17 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 267 optimal weight: 10.0000 chunk 302 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 329 optimal weight: 0.9990 chunk 312 optimal weight: 0.8980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 ASN A1067 GLN A1129 ASN B 653 ASN B1067 GLN C 653 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.161578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.122105 restraints weight = 27950.226| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.29 r_work: 0.3180 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30141 Z= 0.153 Angle : 0.612 12.973 41472 Z= 0.309 Chirality : 0.046 0.359 5205 Planarity : 0.004 0.044 5046 Dihedral : 7.632 64.358 7152 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.58 % Allowed : 7.54 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 (0.13), residues: 3678 helix: 2.34 (0.19), residues: 729 sheet: 0.51 (0.16), residues: 1029 loop : -0.50 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 346 TYR 0.021 0.002 TYR C1022 PHE 0.016 0.002 PHE B 325 TRP 0.010 0.001 TRP B 432 HIS 0.007 0.001 HIS A1224 Details of bonding type rmsd covalent geometry : bond 0.00325 (29940) covalent geometry : angle 0.56487 (40920) SS BOND : bond 0.00618 ( 51) SS BOND : angle 1.56773 ( 102) hydrogen bonds : bond 0.06985 ( 981) hydrogen bonds : angle 4.76626 ( 2727) link_ALPHA1-3 : bond 0.00968 ( 6) link_ALPHA1-3 : angle 1.39960 ( 18) link_ALPHA1-6 : bond 0.00721 ( 6) link_ALPHA1-6 : angle 1.55177 ( 18) link_BETA1-4 : bond 0.00815 ( 54) link_BETA1-4 : angle 2.44149 ( 162) link_NAG-ASN : bond 0.00308 ( 84) link_NAG-ASN : angle 2.18731 ( 252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7409 (tmm-80) REVERT: A 184 GLU cc_start: 0.7956 (tt0) cc_final: 0.7753 (tt0) REVERT: A 201 TRP cc_start: 0.7631 (m-90) cc_final: 0.7044 (m100) REVERT: A 231 TYR cc_start: 0.7552 (p90) cc_final: 0.7167 (p90) REVERT: A 549 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.7102 (t80) REVERT: A 876 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8270 (mtt180) REVERT: A 1117 GLN cc_start: 0.8589 (mm-40) cc_final: 0.7815 (tm-30) REVERT: B 184 GLU cc_start: 0.7987 (tt0) cc_final: 0.7397 (tm-30) REVERT: B 201 TRP cc_start: 0.7714 (m-90) cc_final: 0.7214 (m100) REVERT: B 426 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8500 (tt0) REVERT: B 549 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.6355 (t80) REVERT: B 893 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8822 (tt0) REVERT: B 907 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8569 (t70) REVERT: B 1019 MET cc_start: 0.9061 (tpp) cc_final: 0.8703 (tpp) REVERT: B 1117 GLN cc_start: 0.8585 (mm-40) cc_final: 0.7859 (tm130) REVERT: C 184 GLU cc_start: 0.8028 (tt0) cc_final: 0.7774 (tt0) REVERT: C 201 TRP cc_start: 0.7457 (m-90) cc_final: 0.7051 (m100) REVERT: C 214 MET cc_start: 0.6453 (ttp) cc_final: 0.6016 (ttp) REVERT: C 231 TYR cc_start: 0.7440 (p90) cc_final: 0.6954 (p90) REVERT: C 272 VAL cc_start: 0.8027 (OUTLIER) cc_final: 0.7768 (p) REVERT: C 1109 GLN cc_start: 0.8956 (tp-100) cc_final: 0.8745 (tp-100) REVERT: C 1117 GLN cc_start: 0.8540 (mm-40) cc_final: 0.7686 (tm-30) REVERT: C 1258 GLN cc_start: 0.9217 (mt0) cc_final: 0.9001 (mm-40) outliers start: 41 outliers final: 24 residues processed: 241 average time/residue: 0.5392 time to fit residues: 154.1563 Evaluate side-chains 238 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 876 ARG Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 549 TYR Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 1298 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 848 ILE Chi-restraints excluded: chain C residue 907 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 247 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 210 optimal weight: 0.8980 chunk 327 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 98 optimal weight: 0.0270 chunk 101 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 334 ASN A 653 ASN A1067 GLN B 653 ASN B1067 GLN C 653 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.163467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124086 restraints weight = 28347.042| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.34 r_work: 0.3213 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 30141 Z= 0.115 Angle : 0.555 13.155 41472 Z= 0.277 Chirality : 0.044 0.207 5205 Planarity : 0.003 0.041 5046 Dihedral : 7.084 61.387 7152 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.35 % Allowed : 7.84 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.66 (0.14), residues: 3678 helix: 2.54 (0.19), residues: 729 sheet: 0.59 (0.16), residues: 1044 loop : -0.47 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1174 TYR 0.022 0.001 TYR C 784 PHE 0.015 0.001 PHE A 107 TRP 0.008 0.001 TRP B 432 HIS 0.004 0.001 HIS A1224 Details of bonding type rmsd covalent geometry : bond 0.00231 (29940) covalent geometry : angle 0.50330 (40920) SS BOND : bond 0.00434 ( 51) SS BOND : angle 1.46393 ( 102) hydrogen bonds : bond 0.05901 ( 981) hydrogen bonds : angle 4.58352 ( 2727) link_ALPHA1-3 : bond 0.01066 ( 6) link_ALPHA1-3 : angle 1.39110 ( 18) link_ALPHA1-6 : bond 0.00859 ( 6) link_ALPHA1-6 : angle 1.51019 ( 18) link_BETA1-4 : bond 0.00801 ( 54) link_BETA1-4 : angle 2.27586 ( 162) link_NAG-ASN : bond 0.00301 ( 84) link_NAG-ASN : angle 2.25743 ( 252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.7929 (tt0) cc_final: 0.7708 (tt0) REVERT: A 201 TRP cc_start: 0.7633 (m-90) cc_final: 0.7050 (m100) REVERT: A 231 TYR cc_start: 0.7537 (p90) cc_final: 0.7154 (p90) REVERT: A 549 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.7037 (t80) REVERT: A 822 PHE cc_start: 0.8098 (m-80) cc_final: 0.6931 (t80) REVERT: A 876 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8260 (mtt180) REVERT: A 1117 GLN cc_start: 0.8521 (mm-40) cc_final: 0.7705 (tm-30) REVERT: B 184 GLU cc_start: 0.7955 (tt0) cc_final: 0.7373 (tm-30) REVERT: B 201 TRP cc_start: 0.7712 (m-90) cc_final: 0.7206 (m100) REVERT: B 426 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8485 (tt0) REVERT: B 549 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6333 (t80) REVERT: B 893 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8857 (tt0) REVERT: B 907 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8461 (t70) REVERT: B 1019 MET cc_start: 0.9041 (tpp) cc_final: 0.8623 (tpp) REVERT: B 1117 GLN cc_start: 0.8500 (mm-40) cc_final: 0.7762 (tm130) REVERT: C 184 GLU cc_start: 0.8011 (tt0) cc_final: 0.7769 (tt0) REVERT: C 201 TRP cc_start: 0.7454 (m-90) cc_final: 0.7049 (m100) REVERT: C 214 MET cc_start: 0.6454 (ttp) cc_final: 0.6046 (ttp) REVERT: C 231 TYR cc_start: 0.7445 (p90) cc_final: 0.6910 (p90) REVERT: C 272 VAL cc_start: 0.8061 (OUTLIER) cc_final: 0.7790 (p) REVERT: C 1109 GLN cc_start: 0.8943 (tp-100) cc_final: 0.8729 (tp-100) REVERT: C 1117 GLN cc_start: 0.8520 (mm-40) cc_final: 0.7633 (tm-30) REVERT: C 1258 GLN cc_start: 0.9203 (mt0) cc_final: 0.8975 (mm-40) outliers start: 35 outliers final: 22 residues processed: 229 average time/residue: 0.5954 time to fit residues: 162.2821 Evaluate side-chains 232 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 876 ARG Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 549 TYR Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 1298 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 848 ILE Chi-restraints excluded: chain C residue 907 ASP Chi-restraints excluded: chain C residue 1298 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 21 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 316 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 234 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 340 optimal weight: 7.9990 chunk 267 optimal weight: 9.9990 chunk 12 optimal weight: 30.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 653 ASN A1067 GLN B1067 GLN C 653 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.163578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.124597 restraints weight = 28075.007| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.24 r_work: 0.3228 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30141 Z= 0.138 Angle : 0.590 13.361 41472 Z= 0.297 Chirality : 0.045 0.195 5205 Planarity : 0.004 0.043 5046 Dihedral : 7.077 60.618 7152 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.42 % Allowed : 8.11 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.58 (0.14), residues: 3678 helix: 2.43 (0.19), residues: 729 sheet: 0.54 (0.16), residues: 1029 loop : -0.49 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.020 0.002 TYR C1022 PHE 0.016 0.001 PHE A 107 TRP 0.009 0.001 TRP B 432 HIS 0.006 0.001 HIS A1224 Details of bonding type rmsd covalent geometry : bond 0.00290 (29940) covalent geometry : angle 0.54370 (40920) SS BOND : bond 0.00589 ( 51) SS BOND : angle 1.60105 ( 102) hydrogen bonds : bond 0.06598 ( 981) hydrogen bonds : angle 4.68587 ( 2727) link_ALPHA1-3 : bond 0.01007 ( 6) link_ALPHA1-3 : angle 1.43498 ( 18) link_ALPHA1-6 : bond 0.00857 ( 6) link_ALPHA1-6 : angle 1.56123 ( 18) link_BETA1-4 : bond 0.00774 ( 54) link_BETA1-4 : angle 2.32827 ( 162) link_NAG-ASN : bond 0.00259 ( 84) link_NAG-ASN : angle 2.08850 ( 252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.7934 (tt0) cc_final: 0.7709 (tt0) REVERT: A 201 TRP cc_start: 0.7542 (m-90) cc_final: 0.7061 (m100) REVERT: A 231 TYR cc_start: 0.7569 (p90) cc_final: 0.7197 (p90) REVERT: A 549 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.6955 (t80) REVERT: A 876 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8295 (mtt180) REVERT: A 1117 GLN cc_start: 0.8554 (mm-40) cc_final: 0.7804 (tm-30) REVERT: B 184 GLU cc_start: 0.7968 (tt0) cc_final: 0.7390 (tm-30) REVERT: B 201 TRP cc_start: 0.7684 (m-90) cc_final: 0.7186 (m100) REVERT: B 426 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8434 (tt0) REVERT: B 549 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.6306 (t80) REVERT: B 893 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8768 (tt0) REVERT: B 907 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8497 (t70) REVERT: B 1019 MET cc_start: 0.9060 (tpp) cc_final: 0.8654 (tpp) REVERT: B 1117 GLN cc_start: 0.8553 (mm-40) cc_final: 0.7854 (tm130) REVERT: B 1268 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8156 (mtpp) REVERT: C 184 GLU cc_start: 0.8032 (tt0) cc_final: 0.7784 (tt0) REVERT: C 201 TRP cc_start: 0.7473 (m-90) cc_final: 0.7064 (m100) REVERT: C 231 TYR cc_start: 0.7462 (p90) cc_final: 0.6925 (p90) REVERT: C 272 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7827 (p) REVERT: C 1109 GLN cc_start: 0.8938 (tp-100) cc_final: 0.8726 (tp-100) REVERT: C 1117 GLN cc_start: 0.8566 (mm-40) cc_final: 0.7701 (tm-30) outliers start: 37 outliers final: 22 residues processed: 231 average time/residue: 0.5786 time to fit residues: 158.6889 Evaluate side-chains 233 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 876 ARG Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 549 TYR Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 1268 LYS Chi-restraints excluded: chain B residue 1298 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 848 ILE Chi-restraints excluded: chain C residue 907 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 113 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 167 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 344 optimal weight: 4.9990 chunk 325 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 334 ASN A 577 ASN A 653 ASN A1067 GLN B 200 ASN B1067 GLN C 653 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.163763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.124911 restraints weight = 28267.701| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.22 r_work: 0.3232 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30141 Z= 0.130 Angle : 0.575 12.589 41472 Z= 0.289 Chirality : 0.044 0.205 5205 Planarity : 0.003 0.043 5046 Dihedral : 6.924 59.434 7152 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.58 % Allowed : 8.19 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.60 (0.14), residues: 3678 helix: 2.46 (0.19), residues: 729 sheet: 0.59 (0.16), residues: 1017 loop : -0.51 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1174 TYR 0.020 0.001 TYR C1022 PHE 0.015 0.001 PHE A 107 TRP 0.009 0.001 TRP B 432 HIS 0.005 0.001 HIS A1224 Details of bonding type rmsd covalent geometry : bond 0.00270 (29940) covalent geometry : angle 0.52763 (40920) SS BOND : bond 0.00556 ( 51) SS BOND : angle 1.50679 ( 102) hydrogen bonds : bond 0.06371 ( 981) hydrogen bonds : angle 4.65401 ( 2727) link_ALPHA1-3 : bond 0.01040 ( 6) link_ALPHA1-3 : angle 1.40458 ( 18) link_ALPHA1-6 : bond 0.00903 ( 6) link_ALPHA1-6 : angle 1.53712 ( 18) link_BETA1-4 : bond 0.00765 ( 54) link_BETA1-4 : angle 2.27868 ( 162) link_NAG-ASN : bond 0.00264 ( 84) link_NAG-ASN : angle 2.17438 ( 252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.7904 (tt0) cc_final: 0.7690 (tt0) REVERT: A 201 TRP cc_start: 0.7563 (m-90) cc_final: 0.7071 (m100) REVERT: A 231 TYR cc_start: 0.7610 (p90) cc_final: 0.7255 (p90) REVERT: A 549 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.6873 (t80) REVERT: A 822 PHE cc_start: 0.8115 (m-80) cc_final: 0.6988 (t80) REVERT: A 1117 GLN cc_start: 0.8565 (mm-40) cc_final: 0.7807 (tm-30) REVERT: B 184 GLU cc_start: 0.7944 (tt0) cc_final: 0.7385 (tm-30) REVERT: B 201 TRP cc_start: 0.7684 (m-90) cc_final: 0.7189 (m100) REVERT: B 426 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8419 (tt0) REVERT: B 549 TYR cc_start: 0.7517 (OUTLIER) cc_final: 0.6307 (t80) REVERT: B 893 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8766 (tt0) REVERT: B 907 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8484 (t70) REVERT: B 1019 MET cc_start: 0.9044 (tpp) cc_final: 0.8641 (tpp) REVERT: B 1117 GLN cc_start: 0.8519 (mm-40) cc_final: 0.7818 (tm130) REVERT: B 1268 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8144 (mtpp) REVERT: C 184 GLU cc_start: 0.8004 (tt0) cc_final: 0.7740 (tt0) REVERT: C 201 TRP cc_start: 0.7496 (m-90) cc_final: 0.7077 (m100) REVERT: C 231 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.6933 (p90) REVERT: C 272 VAL cc_start: 0.8024 (OUTLIER) cc_final: 0.7774 (p) REVERT: C 549 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.5768 (m-80) REVERT: C 1109 GLN cc_start: 0.8929 (tp-100) cc_final: 0.8719 (tp-100) REVERT: C 1117 GLN cc_start: 0.8552 (mm-40) cc_final: 0.7689 (tm-30) outliers start: 41 outliers final: 24 residues processed: 230 average time/residue: 0.6569 time to fit residues: 179.4876 Evaluate side-chains 233 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 549 TYR Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 1268 LYS Chi-restraints excluded: chain B residue 1298 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 231 TYR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 848 ILE Chi-restraints excluded: chain C residue 907 ASP Chi-restraints excluded: chain C residue 1268 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 254 optimal weight: 7.9990 chunk 201 optimal weight: 7.9990 chunk 240 optimal weight: 0.9990 chunk 330 optimal weight: 3.9990 chunk 311 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 chunk 246 optimal weight: 4.9990 chunk 262 optimal weight: 0.0010 chunk 266 optimal weight: 0.9980 chunk 241 optimal weight: 0.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 653 ASN A1067 GLN B 200 ASN B1067 GLN C 653 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.164468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.125728 restraints weight = 28180.546| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.22 r_work: 0.3244 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 30141 Z= 0.117 Angle : 0.546 11.150 41472 Z= 0.275 Chirality : 0.044 0.215 5205 Planarity : 0.003 0.042 5046 Dihedral : 6.587 56.726 7152 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.50 % Allowed : 8.27 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.63 (0.14), residues: 3678 helix: 2.55 (0.19), residues: 729 sheet: 0.62 (0.17), residues: 966 loop : -0.49 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1174 TYR 0.018 0.001 TYR C1022 PHE 0.015 0.001 PHE B 107 TRP 0.008 0.001 TRP C 432 HIS 0.004 0.001 HIS A1224 Details of bonding type rmsd covalent geometry : bond 0.00236 (29940) covalent geometry : angle 0.50191 (40920) SS BOND : bond 0.00505 ( 51) SS BOND : angle 1.35011 ( 102) hydrogen bonds : bond 0.05941 ( 981) hydrogen bonds : angle 4.57655 ( 2727) link_ALPHA1-3 : bond 0.01065 ( 6) link_ALPHA1-3 : angle 1.43339 ( 18) link_ALPHA1-6 : bond 0.00947 ( 6) link_ALPHA1-6 : angle 1.54140 ( 18) link_BETA1-4 : bond 0.00732 ( 54) link_BETA1-4 : angle 2.19381 ( 162) link_NAG-ASN : bond 0.00247 ( 84) link_NAG-ASN : angle 1.99909 ( 252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.7881 (tt0) cc_final: 0.7655 (tt0) REVERT: A 201 TRP cc_start: 0.7573 (m-90) cc_final: 0.7074 (m100) REVERT: A 231 TYR cc_start: 0.7596 (p90) cc_final: 0.7164 (p90) REVERT: A 549 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.6943 (t80) REVERT: A 822 PHE cc_start: 0.8088 (m-80) cc_final: 0.7008 (t80) REVERT: A 1117 GLN cc_start: 0.8557 (mm-40) cc_final: 0.7756 (tm-30) REVERT: B 184 GLU cc_start: 0.7936 (tt0) cc_final: 0.7311 (tm-30) REVERT: B 201 TRP cc_start: 0.7688 (m-90) cc_final: 0.7189 (m100) REVERT: B 426 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: B 549 TYR cc_start: 0.7497 (OUTLIER) cc_final: 0.6293 (t80) REVERT: B 893 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8786 (tt0) REVERT: B 907 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8464 (t70) REVERT: B 1019 MET cc_start: 0.9035 (tpp) cc_final: 0.8644 (tpp) REVERT: B 1117 GLN cc_start: 0.8492 (mm-40) cc_final: 0.7773 (tm-30) REVERT: B 1268 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8146 (mtpp) REVERT: C 184 GLU cc_start: 0.7973 (tt0) cc_final: 0.7735 (tt0) REVERT: C 201 TRP cc_start: 0.7485 (m-90) cc_final: 0.7053 (m100) REVERT: C 231 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.6944 (p90) REVERT: C 272 VAL cc_start: 0.8067 (OUTLIER) cc_final: 0.7807 (p) REVERT: C 549 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.5823 (m-80) REVERT: C 1109 GLN cc_start: 0.8936 (tp-100) cc_final: 0.8727 (tp-100) REVERT: C 1117 GLN cc_start: 0.8547 (mm-40) cc_final: 0.7685 (tm-30) outliers start: 39 outliers final: 24 residues processed: 231 average time/residue: 0.6171 time to fit residues: 169.3507 Evaluate side-chains 232 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 549 TYR Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 1268 LYS Chi-restraints excluded: chain B residue 1298 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 231 TYR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 848 ILE Chi-restraints excluded: chain C residue 907 ASP Chi-restraints excluded: chain C residue 1268 LYS Chi-restraints excluded: chain C residue 1298 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 98 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 221 optimal weight: 2.9990 chunk 60 optimal weight: 0.0370 chunk 139 optimal weight: 0.0470 chunk 243 optimal weight: 0.6980 chunk 231 optimal weight: 0.9980 chunk 262 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 334 ASN A 653 ASN A1067 GLN B1067 GLN C 653 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.165807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.127261 restraints weight = 28385.489| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.22 r_work: 0.3266 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 30141 Z= 0.102 Angle : 0.531 16.644 41472 Z= 0.264 Chirality : 0.043 0.224 5205 Planarity : 0.003 0.041 5046 Dihedral : 6.252 54.155 7152 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.23 % Allowed : 8.65 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.73 (0.14), residues: 3678 helix: 2.68 (0.19), residues: 729 sheet: 0.67 (0.17), residues: 975 loop : -0.44 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1174 TYR 0.035 0.001 TYR A 409 PHE 0.016 0.001 PHE A 107 TRP 0.008 0.001 TRP C 223 HIS 0.003 0.000 HIS B1208 Details of bonding type rmsd covalent geometry : bond 0.00197 (29940) covalent geometry : angle 0.48381 (40920) SS BOND : bond 0.00413 ( 51) SS BOND : angle 1.17123 ( 102) hydrogen bonds : bond 0.05322 ( 981) hydrogen bonds : angle 4.47809 ( 2727) link_ALPHA1-3 : bond 0.01124 ( 6) link_ALPHA1-3 : angle 1.46635 ( 18) link_ALPHA1-6 : bond 0.01003 ( 6) link_ALPHA1-6 : angle 1.53316 ( 18) link_BETA1-4 : bond 0.00724 ( 54) link_BETA1-4 : angle 2.09948 ( 162) link_NAG-ASN : bond 0.00270 ( 84) link_NAG-ASN : angle 2.17118 ( 252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 184 GLU cc_start: 0.7879 (tt0) cc_final: 0.7670 (tt0) REVERT: A 201 TRP cc_start: 0.7582 (m-90) cc_final: 0.7087 (m100) REVERT: A 231 TYR cc_start: 0.7586 (p90) cc_final: 0.7163 (p90) REVERT: A 426 GLU cc_start: 0.8635 (tt0) cc_final: 0.8362 (tt0) REVERT: A 549 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.6904 (t80) REVERT: A 822 PHE cc_start: 0.8057 (m-80) cc_final: 0.7019 (t80) REVERT: A 1117 GLN cc_start: 0.8523 (mm-40) cc_final: 0.7725 (tm-30) REVERT: B 184 GLU cc_start: 0.7929 (tt0) cc_final: 0.7318 (tm-30) REVERT: B 201 TRP cc_start: 0.7695 (m-90) cc_final: 0.7191 (m100) REVERT: B 549 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.6304 (t80) REVERT: B 893 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8780 (tt0) REVERT: B 907 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8442 (t70) REVERT: B 1019 MET cc_start: 0.9023 (tpp) cc_final: 0.8643 (tpp) REVERT: B 1117 GLN cc_start: 0.8456 (mm-40) cc_final: 0.7765 (tm130) REVERT: B 1268 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8111 (mtpp) REVERT: C 184 GLU cc_start: 0.7967 (tt0) cc_final: 0.7731 (tt0) REVERT: C 201 TRP cc_start: 0.7531 (m-90) cc_final: 0.7101 (m100) REVERT: C 214 MET cc_start: 0.6365 (ttp) cc_final: 0.5848 (ttp) REVERT: C 231 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.6884 (p90) REVERT: C 272 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7782 (p) REVERT: C 549 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.5834 (m-80) REVERT: C 1109 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8712 (tp-100) REVERT: C 1117 GLN cc_start: 0.8501 (mm-40) cc_final: 0.7614 (tm-30) outliers start: 32 outliers final: 21 residues processed: 221 average time/residue: 0.6530 time to fit residues: 171.1863 Evaluate side-chains 228 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 549 TYR Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 1268 LYS Chi-restraints excluded: chain B residue 1298 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 231 TYR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 848 ILE Chi-restraints excluded: chain C residue 907 ASP Chi-restraints excluded: chain C residue 1268 LYS Chi-restraints excluded: chain C residue 1298 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 196 optimal weight: 4.9990 chunk 148 optimal weight: 0.2980 chunk 132 optimal weight: 0.3980 chunk 270 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 353 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 264 optimal weight: 0.6980 chunk 306 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 ASN A1067 GLN B1067 GLN C 653 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.163541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.124781 restraints weight = 28003.773| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.18 r_work: 0.3231 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30141 Z= 0.139 Angle : 0.599 11.659 41472 Z= 0.299 Chirality : 0.045 0.318 5205 Planarity : 0.004 0.043 5046 Dihedral : 6.860 91.879 7152 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.35 % Allowed : 8.73 % Favored : 89.93 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.59 (0.14), residues: 3678 helix: 2.50 (0.19), residues: 729 sheet: 0.57 (0.17), residues: 954 loop : -0.49 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1174 TYR 0.034 0.002 TYR C 409 PHE 0.019 0.002 PHE A 107 TRP 0.009 0.001 TRP C 223 HIS 0.005 0.001 HIS A1224 Details of bonding type rmsd covalent geometry : bond 0.00292 (29940) covalent geometry : angle 0.55233 (40920) SS BOND : bond 0.00589 ( 51) SS BOND : angle 1.50507 ( 102) hydrogen bonds : bond 0.06557 ( 981) hydrogen bonds : angle 4.66477 ( 2727) link_ALPHA1-3 : bond 0.01004 ( 6) link_ALPHA1-3 : angle 1.46825 ( 18) link_ALPHA1-6 : bond 0.00907 ( 6) link_ALPHA1-6 : angle 1.59582 ( 18) link_BETA1-4 : bond 0.00689 ( 54) link_BETA1-4 : angle 2.22042 ( 162) link_NAG-ASN : bond 0.00263 ( 84) link_NAG-ASN : angle 2.25256 ( 252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7356 Ramachandran restraints generated. 3678 Oldfield, 0 Emsley, 3678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 184 GLU cc_start: 0.7893 (tt0) cc_final: 0.7673 (tt0) REVERT: A 201 TRP cc_start: 0.7624 (m-90) cc_final: 0.7122 (m100) REVERT: A 231 TYR cc_start: 0.7583 (p90) cc_final: 0.7222 (p90) REVERT: A 549 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.6834 (t80) REVERT: A 822 PHE cc_start: 0.8107 (m-80) cc_final: 0.7025 (t80) REVERT: A 1117 GLN cc_start: 0.8582 (mm-40) cc_final: 0.7803 (tm-30) REVERT: B 184 GLU cc_start: 0.7945 (tt0) cc_final: 0.7350 (tm-30) REVERT: B 201 TRP cc_start: 0.7738 (m-90) cc_final: 0.7235 (m100) REVERT: B 426 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8382 (tt0) REVERT: B 549 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.6296 (t80) REVERT: B 893 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8756 (tt0) REVERT: B 907 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8493 (t70) REVERT: B 1019 MET cc_start: 0.9047 (tpp) cc_final: 0.8690 (tpp) REVERT: B 1117 GLN cc_start: 0.8549 (mm-40) cc_final: 0.7849 (tm-30) REVERT: B 1268 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8142 (mtpp) REVERT: C 184 GLU cc_start: 0.8004 (tt0) cc_final: 0.7742 (tt0) REVERT: C 201 TRP cc_start: 0.7531 (m-90) cc_final: 0.7097 (m100) REVERT: C 214 MET cc_start: 0.6327 (ttp) cc_final: 0.5776 (ttp) REVERT: C 231 TYR cc_start: 0.7490 (OUTLIER) cc_final: 0.6983 (p90) REVERT: C 272 VAL cc_start: 0.8069 (OUTLIER) cc_final: 0.7807 (p) REVERT: C 549 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.5860 (m-80) REVERT: C 1109 GLN cc_start: 0.8948 (tp-100) cc_final: 0.8742 (tp-100) REVERT: C 1117 GLN cc_start: 0.8572 (mm-40) cc_final: 0.7718 (tm-30) outliers start: 35 outliers final: 20 residues processed: 223 average time/residue: 0.6201 time to fit residues: 164.8293 Evaluate side-chains 226 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 549 TYR Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 1268 LYS Chi-restraints excluded: chain B residue 1298 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 231 TYR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 848 ILE Chi-restraints excluded: chain C residue 1268 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 244 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 352 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 293 optimal weight: 0.6980 chunk 360 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 653 ASN A1067 GLN B1067 GLN C 653 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.164371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.125642 restraints weight = 28274.781| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.21 r_work: 0.3239 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30141 Z= 0.125 Angle : 0.613 22.053 41472 Z= 0.298 Chirality : 0.045 0.393 5205 Planarity : 0.003 0.042 5046 Dihedral : 7.204 106.679 7152 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.23 % Allowed : 8.88 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.58 (0.14), residues: 3678 helix: 2.54 (0.19), residues: 729 sheet: 0.53 (0.17), residues: 960 loop : -0.50 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1174 TYR 0.041 0.001 TYR C 784 PHE 0.018 0.001 PHE A 107 TRP 0.008 0.001 TRP B 432 HIS 0.005 0.001 HIS A1224 Details of bonding type rmsd covalent geometry : bond 0.00257 (29940) covalent geometry : angle 0.54136 (40920) SS BOND : bond 0.00517 ( 51) SS BOND : angle 1.41049 ( 102) hydrogen bonds : bond 0.06127 ( 981) hydrogen bonds : angle 4.60695 ( 2727) link_ALPHA1-3 : bond 0.01031 ( 6) link_ALPHA1-3 : angle 1.43442 ( 18) link_ALPHA1-6 : bond 0.00946 ( 6) link_ALPHA1-6 : angle 1.55001 ( 18) link_BETA1-4 : bond 0.00676 ( 54) link_BETA1-4 : angle 2.15680 ( 162) link_NAG-ASN : bond 0.00298 ( 84) link_NAG-ASN : angle 3.18495 ( 252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14848.18 seconds wall clock time: 252 minutes 15.00 seconds (15135.00 seconds total)