Starting phenix.real_space_refine on Thu Mar 5 10:51:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n65_24195/03_2026/7n65_24195.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n65_24195/03_2026/7n65_24195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n65_24195/03_2026/7n65_24195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n65_24195/03_2026/7n65_24195.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n65_24195/03_2026/7n65_24195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n65_24195/03_2026/7n65_24195.map" } resolution = 4.15 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= 1.000 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 117 5.16 5 C 13365 2.51 5 N 3471 2.21 5 O 4572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21525 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3522 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 425} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1056 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1015 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "D" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 778 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "E" Number of atoms: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3522 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 425} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1056 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1015 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "H" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 778 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "I" Number of atoms: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3522 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 425} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "J" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1056 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1015 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 778 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: 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: "V" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "W" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "k" 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "n" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 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: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 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: "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: 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: "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: 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: "0" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "1" 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: "2" 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: "3" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "4" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "5" 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: "6" 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: "7" 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: "8" 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: "9" 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: "AA" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.74, per 1000 atoms: 0.27 Number of scatterers: 21525 At special positions: 0 Unit cell: (162, 163.35, 141.75, 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 117 16.00 O 4572 8.00 N 3471 7.00 C 13365 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.23 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.02 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.04 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.04 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.02 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=1.80 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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=18, symmetry=0 Links applied ALPHA1-2 " MAN 0 4 " - " MAN 0 5 " " MAN 4 4 " - " MAN 4 5 " " MAN S 4 " - " MAN S 5 " " MAN W 4 " - " MAN W 5 " " MAN j 4 " - " MAN j 5 " " MAN n 4 " - " MAN n 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " MAN 0 6 " - " MAN 0 7 " " BMA 2 3 " - " MAN 2 4 " " BMA 3 3 " - " MAN 3 7 " " MAN 3 4 " - " MAN 3 5 " " BMA 4 3 " - " MAN 4 4 " " MAN 4 6 " - " MAN 4 7 " " BMA S 3 " - " MAN S 4 " " MAN S 6 " - " MAN S 7 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 7 " " MAN V 4 " - " MAN V 5 " " BMA W 3 " - " MAN W 4 " " MAN W 6 " - " MAN W 7 " " BMA j 3 " - " MAN j 4 " " MAN j 6 " - " MAN j 7 " " BMA l 3 " - " MAN l 4 " " BMA m 3 " - " MAN m 7 " " MAN m 4 " - " MAN m 5 " " BMA n 3 " - " MAN n 4 " " MAN n 6 " - " MAN n 7 " ALPHA1-6 " BMA 0 3 " - " MAN 0 6 " " BMA 2 3 " - " MAN 2 5 " " BMA 3 3 " - " MAN 3 4 " " MAN 3 4 " - " MAN 3 6 " " BMA 4 3 " - " MAN 4 6 " " MAN 4 6 " - " MAN 4 8 " " BMA S 3 " - " MAN S 6 " " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 4 " " MAN V 4 " - " MAN V 6 " " BMA W 3 " - " MAN W 6 " " MAN W 6 " - " MAN W 8 " " BMA j 3 " - " MAN j 6 " " BMA l 3 " - " MAN l 5 " " BMA m 3 " - " MAN m 4 " " MAN m 4 " - " MAN m 6 " " BMA n 3 " - " MAN n 6 " " MAN n 6 " - " MAN n 8 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " 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 k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAGAA 1 " - " NAGAA 2 " NAG-ASN " NAG 0 1 " - " ASN I 262 " " NAG 1 1 " - " ASN I 276 " " NAG 2 1 " - " ASN I 295 " " NAG 3 1 " - " ASN I 301 " " NAG 4 1 " - " ASN I 332 " " NAG 5 1 " - " ASN I 355 " " NAG 6 1 " - " ASN I 363 " " NAG 7 1 " - " ASN I 386 " " NAG 8 1 " - " ASN I 392 " " NAG 9 1 " - " ASN I 448 " " NAG A 601 " - " ASN A 339 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG E 601 " - " ASN E 339 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG I 601 " - " ASN I 339 " " NAG J 701 " - " ASN J 618 " " NAG J 702 " - " ASN J 637 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 133 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 160 " " NAG Q 1 " - " ASN A 197 " " NAG R 1 " - " ASN A 234 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 276 " " NAG U 1 " - " ASN A 295 " " NAG V 1 " - " ASN A 301 " " NAG W 1 " - " ASN A 332 " " NAG X 1 " - " ASN A 355 " " NAG Y 1 " - " ASN A 363 " " NAG Z 1 " - " ASN A 386 " " NAG a 1 " - " ASN A 392 " " NAG b 1 " - " ASN A 448 " " NAG c 1 " - " ASN B 611 " " NAG d 1 " - " ASN E 88 " " NAG e 1 " - " ASN E 133 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 160 " " NAG h 1 " - " ASN E 197 " " NAG i 1 " - " ASN E 234 " " NAG j 1 " - " ASN E 262 " " NAG k 1 " - " ASN E 276 " " NAG l 1 " - " ASN E 295 " " NAG m 1 " - " ASN E 301 " " NAG n 1 " - " ASN E 332 " " NAG o 1 " - " ASN E 355 " " NAG p 1 " - " ASN E 363 " " NAG q 1 " - " ASN E 386 " " NAG r 1 " - " ASN E 392 " " NAG s 1 " - " ASN E 448 " " NAG t 1 " - " ASN F 611 " " NAG u 1 " - " ASN I 88 " " NAG v 1 " - " ASN I 133 " " NAG w 1 " - " ASN I 156 " " NAG x 1 " - " ASN I 160 " " NAG y 1 " - " ASN I 197 " " NAG z 1 " - " ASN I 234 " " NAGAA 1 " - " ASN J 611 " Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.1 seconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4518 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 39 sheets defined 20.8% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.905A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.151A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.663A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 596 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.656A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 655 removed outlier: 3.540A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 662 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.577A pdb=" N ARG C 31 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 100 through 104 removed outlier: 4.516A pdb=" N LEU C 103 " --> pdb=" O ALA C 100 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL C 104 " --> pdb=" O TYR C 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 100 through 104' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 351 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.905A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 484 removed outlier: 4.152A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.662A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 596 Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.657A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 655 removed outlier: 3.540A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 662 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.578A pdb=" N ARG G 31 " --> pdb=" O GLY G 28 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 100 through 104 removed outlier: 4.515A pdb=" N LEU G 103 " --> pdb=" O ALA G 100 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL G 104 " --> pdb=" O TYR G 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 100 through 104' Processing helix chain 'I' and resid 99 through 117 Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 351 Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 387 through 391 Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.905A pdb=" N GLN I 428 " --> pdb=" O ASN I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 474 through 484 removed outlier: 4.152A pdb=" N ASN I 478 " --> pdb=" O ASP I 474 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 537 through 543 removed outlier: 3.662A pdb=" N ALA J 541 " --> pdb=" O LEU J 537 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 571 through 596 Processing helix chain 'J' and resid 619 through 624 Processing helix chain 'J' and resid 627 through 636 removed outlier: 3.657A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 655 removed outlier: 3.540A pdb=" N LEU J 645 " --> pdb=" O ILE J 641 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN J 650 " --> pdb=" O LEU J 646 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN J 651 " --> pdb=" O GLU J 647 " (cutoff:3.500A) Processing helix chain 'J' and resid 656 through 662 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.577A pdb=" N ARG K 31 " --> pdb=" O GLY K 28 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 32' Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'K' and resid 100 through 104 removed outlier: 4.516A pdb=" N LEU K 103 " --> pdb=" O ALA K 100 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL K 104 " --> pdb=" O TYR K 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 100 through 104' Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.592A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.619A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 176 removed outlier: 3.631A pdb=" N CYS A 131 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.557A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 309 removed outlier: 3.706A pdb=" N ASP A 321A" --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.234A pdb=" N GLY C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR C 94 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL C 124 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA C 92 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 97 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR C 34 " --> pdb=" O ASP C 50 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASP C 50 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 17 through 20 Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 4 Processing sheet with id=AB2, first strand: chain 'D' and resid 18 through 21 Processing sheet with id=AB3, first strand: chain 'D' and resid 47 through 48 Processing sheet with id=AB4, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AB5, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AB6, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.592A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AB8, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.618A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 170 through 176 removed outlier: 3.631A pdb=" N CYS E 131 " --> pdb=" O LYS E 189 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.558A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 309 removed outlier: 3.705A pdb=" N ASP E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE E 309 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ALA E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AC3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.234A pdb=" N GLY G 10 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR G 94 " --> pdb=" O THR G 122 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL G 124 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA G 92 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA G 97 " --> pdb=" O THR G 35 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR G 34 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASP G 50 " --> pdb=" O THR G 34 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 17 through 20 Processing sheet with id=AC5, first strand: chain 'H' and resid 3 through 4 Processing sheet with id=AC6, first strand: chain 'H' and resid 18 through 21 Processing sheet with id=AC7, first strand: chain 'H' and resid 47 through 48 Processing sheet with id=AC8, first strand: chain 'H' and resid 50 through 51 Processing sheet with id=AC9, first strand: chain 'I' and resid 35 through 40 Processing sheet with id=AD1, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.592A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 55 through 56 Processing sheet with id=AD3, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.618A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 170 through 176 removed outlier: 3.630A pdb=" N CYS I 131 " --> pdb=" O LYS I 189 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS I 189 " --> pdb=" O CYS I 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.558A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 259 through 261 current: chain 'I' and resid 284 through 309 removed outlier: 3.705A pdb=" N ASP I 321A" --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LYS I 305 " --> pdb=" O THR I 320 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N THR I 320 " --> pdb=" O LYS I 305 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE I 307 " --> pdb=" O TYR I 318 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N TYR I 318 " --> pdb=" O ILE I 307 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE I 309 " --> pdb=" O ALA I 316 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ALA I 316 " --> pdb=" O ILE I 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 315 through 323 current: chain 'I' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 381 through 385 current: chain 'I' and resid 465 through 470 Processing sheet with id=AD7, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.233A pdb=" N GLY K 10 " --> pdb=" O THR K 125 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR K 94 " --> pdb=" O THR K 122 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL K 124 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA K 92 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA K 97 " --> pdb=" O THR K 35 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR K 34 " --> pdb=" O ASP K 50 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASP K 50 " --> pdb=" O THR K 34 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 17 through 20 Processing sheet with id=AD9, first strand: chain 'L' and resid 3 through 4 Processing sheet with id=AE1, first strand: chain 'L' and resid 18 through 21 Processing sheet with id=AE2, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AE3, first strand: chain 'L' and resid 50 through 51 516 hydrogen bonds defined for protein. 1341 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3418 1.32 - 1.44: 6285 1.44 - 1.57: 12047 1.57 - 1.69: 15 1.69 - 1.82: 156 Bond restraints: 21921 Sorted by residual: bond pdb=" C CYS I 218 " pdb=" N ALA I 219 " ideal model delta sigma weight residual 1.335 1.190 0.145 3.59e-02 7.76e+02 1.63e+01 bond pdb=" C CYS A 218 " pdb=" N ALA A 219 " ideal model delta sigma weight residual 1.335 1.190 0.145 3.59e-02 7.76e+02 1.63e+01 bond pdb=" C CYS E 218 " pdb=" N ALA E 219 " ideal model delta sigma weight residual 1.335 1.191 0.144 3.59e-02 7.76e+02 1.61e+01 bond pdb=" C5 BMA V 3 " pdb=" C6 BMA V 3 " ideal model delta sigma weight residual 1.526 1.455 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C5 BMA 3 3 " pdb=" C6 BMA 3 3 " ideal model delta sigma weight residual 1.526 1.456 0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 21916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 28733 3.27 - 6.53: 898 6.53 - 9.80: 129 9.80 - 13.06: 18 13.06 - 16.33: 3 Bond angle restraints: 29781 Sorted by residual: angle pdb=" N ALA E 70 " pdb=" CA ALA E 70 " pdb=" C ALA E 70 " ideal model delta sigma weight residual 114.75 104.06 10.69 1.26e+00 6.30e-01 7.19e+01 angle pdb=" N ALA A 70 " pdb=" CA ALA A 70 " pdb=" C ALA A 70 " ideal model delta sigma weight residual 114.75 104.11 10.64 1.26e+00 6.30e-01 7.14e+01 angle pdb=" N ALA I 70 " pdb=" CA ALA I 70 " pdb=" C ALA I 70 " ideal model delta sigma weight residual 114.75 104.11 10.64 1.26e+00 6.30e-01 7.13e+01 angle pdb=" N LYS E 65 " pdb=" CA LYS E 65 " pdb=" C LYS E 65 " ideal model delta sigma weight residual 110.80 127.13 -16.33 2.13e+00 2.20e-01 5.87e+01 angle pdb=" N LYS A 65 " pdb=" CA LYS A 65 " pdb=" C LYS A 65 " ideal model delta sigma weight residual 110.80 127.10 -16.30 2.13e+00 2.20e-01 5.86e+01 ... (remaining 29776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.62: 14045 23.62 - 47.23: 1002 47.23 - 70.85: 202 70.85 - 94.46: 186 94.46 - 118.08: 102 Dihedral angle restraints: 15537 sinusoidal: 8508 harmonic: 7029 Sorted by residual: dihedral pdb=" CA CYS E 501 " pdb=" C CYS E 501 " pdb=" N LYS E 502 " pdb=" CA LYS E 502 " ideal model delta harmonic sigma weight residual -180.00 -131.54 -48.46 0 5.00e+00 4.00e-02 9.39e+01 dihedral pdb=" CA CYS I 501 " pdb=" C CYS I 501 " pdb=" N LYS I 502 " pdb=" CA LYS I 502 " ideal model delta harmonic sigma weight residual -180.00 -131.55 -48.45 0 5.00e+00 4.00e-02 9.39e+01 dihedral pdb=" CA CYS A 501 " pdb=" C CYS A 501 " pdb=" N LYS A 502 " pdb=" CA LYS A 502 " ideal model delta harmonic sigma weight residual 180.00 -131.55 -48.45 0 5.00e+00 4.00e-02 9.39e+01 ... (remaining 15534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3578 0.104 - 0.208: 256 0.208 - 0.311: 54 0.311 - 0.415: 9 0.415 - 0.519: 12 Chirality restraints: 3909 Sorted by residual: chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 8.86e+00 chirality pdb=" C1 NAG 3 2 " pdb=" O4 NAG 3 1 " pdb=" C2 NAG 3 2 " pdb=" O5 NAG 3 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 8.57e+00 chirality pdb=" C1 NAG m 2 " pdb=" O4 NAG m 1 " pdb=" C2 NAG m 2 " pdb=" O5 NAG m 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 8.47e+00 ... (remaining 3906 not shown) Planarity restraints: 3591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 205 " -0.062 5.00e-02 4.00e+02 9.35e-02 1.40e+01 pdb=" N PRO A 206 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS I 205 " -0.062 5.00e-02 4.00e+02 9.33e-02 1.39e+01 pdb=" N PRO I 206 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO I 206 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO I 206 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 205 " 0.062 5.00e-02 4.00e+02 9.33e-02 1.39e+01 pdb=" N PRO E 206 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO E 206 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 206 " 0.050 5.00e-02 4.00e+02 ... (remaining 3588 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 542 2.53 - 3.12: 19669 3.12 - 3.71: 33779 3.71 - 4.31: 47794 4.31 - 4.90: 72597 Nonbonded interactions: 174381 Sorted by model distance: nonbonded pdb=" OE2 GLU B 647 " pdb=" NH1 ARG F 542 " model vdw 1.935 3.120 nonbonded pdb=" O LEU C 27 " pdb=" O2 BMA V 3 " model vdw 2.001 2.432 nonbonded pdb=" O LEU G 27 " pdb=" O2 BMA m 3 " model vdw 2.005 2.432 nonbonded pdb=" OG SER I 274 " pdb=" O ASN I 283 " model vdw 2.091 3.040 nonbonded pdb=" OG SER A 274 " pdb=" O ASN A 283 " model vdw 2.092 3.040 ... (remaining 174376 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: 0.04 Found NCS groups: ncs_group { reference = (chain '0' and (resid 1 or resid 4 through 7)) selection = (chain '3' and (resid 1 or resid 4 through 7)) selection = (chain '4' and (resid 2 or resid 5 through 8)) selection = (chain 'S' and (resid 1 or resid 4 through 7)) selection = (chain 'V' and (resid 1 or resid 4 through 7)) selection = (chain 'W' and (resid 2 or resid 5 through 8)) selection = (chain 'j' and (resid 1 or resid 4 through 7)) selection = (chain 'm' and (resid 1 or resid 4 through 7)) selection = (chain 'n' and (resid 2 or resid 5 through 8)) } ncs_group { reference = chain '1' selection = chain '6' selection = chain '7' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'T' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'k' selection = chain 'p' selection = chain 'q' selection = chain 'u' selection = chain 'w' selection = chain 'x' } ncs_group { reference = chain '2' selection = chain 'U' selection = chain 'l' } ncs_group { reference = chain '5' selection = chain '8' selection = chain '9' selection = chain 'AA' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'X' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'h' selection = chain 'i' selection = chain 'o' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'v' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 22.820 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 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 : 0.012 0.228 22164 Z= 0.587 Angle : 1.461 16.325 30417 Z= 0.715 Chirality : 0.071 0.519 3909 Planarity : 0.007 0.093 3531 Dihedral : 20.892 118.077 10902 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 35.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 15.22 % Favored : 84.58 % Rotamer: Outliers : 4.29 % Allowed : 11.29 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -4.44 (0.14), residues: 2412 helix: -2.71 (0.20), residues: 375 sheet: -2.06 (0.21), residues: 579 loop : -3.58 (0.13), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 503 TYR 0.024 0.003 TYR L 93 PHE 0.024 0.004 PHE I 159 TRP 0.031 0.004 TRP F 610 HIS 0.006 0.002 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.01122 (21921) covalent geometry : angle 1.35835 (29781) SS BOND : bond 0.04920 ( 39) SS BOND : angle 3.76044 ( 78) hydrogen bonds : bond 0.17165 ( 516) hydrogen bonds : angle 9.08247 ( 1341) Misc. bond : bond 0.06805 ( 18) link_ALPHA1-2 : bond 0.00492 ( 6) link_ALPHA1-2 : angle 4.41462 ( 18) link_ALPHA1-3 : bond 0.00891 ( 21) link_ALPHA1-3 : angle 2.89203 ( 63) link_ALPHA1-6 : bond 0.01046 ( 18) link_ALPHA1-6 : angle 2.43265 ( 54) link_BETA1-4 : bond 0.01029 ( 81) link_BETA1-4 : angle 4.07511 ( 243) link_NAG-ASN : bond 0.01117 ( 60) link_NAG-ASN : angle 4.51469 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 305 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8120 (p0) REVERT: A 115 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8636 (t) REVERT: A 116 LEU cc_start: 0.8672 (mt) cc_final: 0.8288 (tp) REVERT: A 194 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8716 (mt) REVERT: A 377 ASN cc_start: 0.8323 (t0) cc_final: 0.7998 (t0) REVERT: B 545 LEU cc_start: 0.7295 (tp) cc_final: 0.6642 (tp) REVERT: B 624 ASP cc_start: 0.8366 (t70) cc_final: 0.7766 (t70) REVERT: B 626 MET cc_start: 0.6185 (ttm) cc_final: 0.4845 (mtt) REVERT: B 643 TYR cc_start: 0.8597 (m-10) cc_final: 0.8345 (m-80) REVERT: C 53 GLU cc_start: 0.7638 (pp20) cc_final: 0.7005 (pp20) REVERT: D 72 SER cc_start: 0.9083 (t) cc_final: 0.8745 (p) REVERT: D 88 TYR cc_start: 0.8482 (m-80) cc_final: 0.8226 (m-80) REVERT: E 116 LEU cc_start: 0.8714 (mt) cc_final: 0.8290 (tp) REVERT: E 251 ILE cc_start: 0.8609 (mt) cc_final: 0.8329 (mm) REVERT: E 377 ASN cc_start: 0.8236 (t0) cc_final: 0.8026 (t0) REVERT: E 391 PHE cc_start: 0.8215 (m-80) cc_final: 0.7675 (m-80) REVERT: G 53 GLU cc_start: 0.7411 (pp20) cc_final: 0.6704 (pp20) REVERT: H 81 GLN cc_start: 0.9195 (mm110) cc_final: 0.8740 (mm-40) REVERT: I 161 MET cc_start: 0.7763 (tpt) cc_final: 0.7401 (tpt) REVERT: I 194 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8543 (mt) REVERT: I 251 ILE cc_start: 0.8853 (mt) cc_final: 0.8460 (mm) REVERT: I 377 ASN cc_start: 0.8414 (t0) cc_final: 0.8173 (t0) REVERT: J 530 MET cc_start: 0.8084 (mtm) cc_final: 0.7130 (mtt) outliers start: 90 outliers final: 20 residues processed: 382 average time/residue: 0.1686 time to fit residues: 97.1064 Evaluate side-chains 208 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN A 195 ASN A 422 GLN A 425 ASN B 625 ASN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS D 16 GLN D 81 GLN E 82 GLN ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 422 GLN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN H 81 GLN I 82 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 GLN ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 422 GLN ** I 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN L 81 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.095951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.074481 restraints weight = 79154.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.075350 restraints weight = 54078.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.075592 restraints weight = 41667.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.075817 restraints weight = 38621.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.075997 restraints weight = 36318.649| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22164 Z= 0.198 Angle : 1.063 16.967 30417 Z= 0.491 Chirality : 0.057 0.440 3909 Planarity : 0.006 0.092 3531 Dihedral : 16.164 85.709 6459 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.07 % Favored : 89.80 % Rotamer: Outliers : 0.62 % Allowed : 6.14 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -3.61 (0.15), residues: 2412 helix: -1.38 (0.23), residues: 417 sheet: -1.65 (0.21), residues: 573 loop : -3.20 (0.13), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 178 TYR 0.016 0.002 TYR I 40 PHE 0.024 0.002 PHE A 382 TRP 0.026 0.002 TRP F 610 HIS 0.007 0.001 HIS C 102 Details of bonding type rmsd covalent geometry : bond 0.00420 (21921) covalent geometry : angle 0.97076 (29781) SS BOND : bond 0.00433 ( 39) SS BOND : angle 2.39888 ( 78) hydrogen bonds : bond 0.04737 ( 516) hydrogen bonds : angle 7.27127 ( 1341) Misc. bond : bond 0.00260 ( 18) link_ALPHA1-2 : bond 0.00887 ( 6) link_ALPHA1-2 : angle 2.47708 ( 18) link_ALPHA1-3 : bond 0.01015 ( 21) link_ALPHA1-3 : angle 1.95542 ( 63) link_ALPHA1-6 : bond 0.00481 ( 18) link_ALPHA1-6 : angle 2.02409 ( 54) link_BETA1-4 : bond 0.00662 ( 81) link_BETA1-4 : angle 3.19943 ( 243) link_NAG-ASN : bond 0.00456 ( 60) link_NAG-ASN : angle 3.93532 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 318 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.8172 (p0) cc_final: 0.7955 (p0) REVERT: A 317 PHE cc_start: 0.7524 (t80) cc_final: 0.7011 (t80) REVERT: A 391 PHE cc_start: 0.8350 (m-80) cc_final: 0.7657 (m-10) REVERT: B 530 MET cc_start: 0.8125 (mtt) cc_final: 0.7468 (mtt) REVERT: B 543 ASN cc_start: 0.8586 (m110) cc_final: 0.7685 (t0) REVERT: B 624 ASP cc_start: 0.8402 (t70) cc_final: 0.7792 (t70) REVERT: C 53 GLU cc_start: 0.7221 (pp20) cc_final: 0.6734 (pp20) REVERT: C 72 ARG cc_start: 0.4970 (ptp-170) cc_final: 0.4734 (ptm160) REVERT: D 88 TYR cc_start: 0.8845 (m-80) cc_final: 0.8340 (m-10) REVERT: E 52 LEU cc_start: 0.9213 (mt) cc_final: 0.8556 (mt) REVERT: E 80 ASN cc_start: 0.8695 (t0) cc_final: 0.8485 (t0) REVERT: E 383 PHE cc_start: 0.6583 (m-10) cc_final: 0.5969 (m-10) REVERT: E 391 PHE cc_start: 0.8424 (m-80) cc_final: 0.8139 (m-80) REVERT: F 530 MET cc_start: 0.8090 (mtt) cc_final: 0.7863 (mpp) REVERT: F 545 LEU cc_start: 0.7771 (tp) cc_final: 0.7343 (tp) REVERT: F 567 LYS cc_start: 0.5715 (mttm) cc_final: 0.5471 (mtpt) REVERT: G 53 GLU cc_start: 0.7174 (pp20) cc_final: 0.6868 (pp20) REVERT: G 59 LYS cc_start: 0.8066 (tttm) cc_final: 0.7776 (tttm) REVERT: H 89 TYR cc_start: 0.7793 (m-80) cc_final: 0.7097 (m-80) REVERT: I 208 VAL cc_start: 0.7542 (OUTLIER) cc_final: 0.7320 (p) REVERT: J 543 ASN cc_start: 0.8499 (m-40) cc_final: 0.7574 (t0) REVERT: J 591 GLN cc_start: 0.8710 (mt0) cc_final: 0.8209 (mt0) REVERT: K 30 ARG cc_start: 0.7305 (mtm180) cc_final: 0.6432 (mpp80) REVERT: K 53 GLU cc_start: 0.7167 (pp20) cc_final: 0.6454 (pp20) outliers start: 13 outliers final: 2 residues processed: 328 average time/residue: 0.1692 time to fit residues: 84.1008 Evaluate side-chains 208 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 205 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 2 optimal weight: 5.9990 chunk 188 optimal weight: 0.0470 chunk 181 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 170 optimal weight: 3.9990 chunk 222 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 169 optimal weight: 0.5980 chunk 40 optimal weight: 0.0170 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN A 137 ASN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 HIS ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 ASN I 195 ASN I 302 ASN I 377 ASN I 425 ASN K 52 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.096645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075167 restraints weight = 79142.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.076495 restraints weight = 49066.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.077083 restraints weight = 40420.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.077340 restraints weight = 35786.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.077431 restraints weight = 33352.428| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22164 Z= 0.183 Angle : 0.996 16.841 30417 Z= 0.458 Chirality : 0.056 0.442 3909 Planarity : 0.005 0.079 3531 Dihedral : 13.440 74.096 6459 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 0.14 % Allowed : 6.00 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -3.21 (0.16), residues: 2412 helix: -0.81 (0.25), residues: 405 sheet: -1.53 (0.20), residues: 615 loop : -2.96 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 419 TYR 0.022 0.002 TYR L 88 PHE 0.020 0.002 PHE I 317 TRP 0.017 0.002 TRP B 610 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00383 (21921) covalent geometry : angle 0.91254 (29781) SS BOND : bond 0.00419 ( 39) SS BOND : angle 1.96129 ( 78) hydrogen bonds : bond 0.04536 ( 516) hydrogen bonds : angle 6.91833 ( 1341) Misc. bond : bond 0.00298 ( 18) link_ALPHA1-2 : bond 0.00841 ( 6) link_ALPHA1-2 : angle 2.32237 ( 18) link_ALPHA1-3 : bond 0.01103 ( 21) link_ALPHA1-3 : angle 1.79671 ( 63) link_ALPHA1-6 : bond 0.00468 ( 18) link_ALPHA1-6 : angle 2.05476 ( 54) link_BETA1-4 : bond 0.00611 ( 81) link_BETA1-4 : angle 3.00812 ( 243) link_NAG-ASN : bond 0.00418 ( 60) link_NAG-ASN : angle 3.59024 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 310 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.7335 (t0) cc_final: 0.6360 (m-40) REVERT: A 378 CYS cc_start: 0.3161 (t) cc_final: 0.2035 (t) REVERT: A 391 PHE cc_start: 0.8184 (m-80) cc_final: 0.7965 (m-10) REVERT: A 445 CYS cc_start: 0.4091 (t) cc_final: 0.3869 (t) REVERT: B 543 ASN cc_start: 0.8566 (m110) cc_final: 0.7664 (t0) REVERT: B 624 ASP cc_start: 0.8182 (t70) cc_final: 0.7849 (t70) REVERT: C 53 GLU cc_start: 0.7134 (pp20) cc_final: 0.6652 (pp20) REVERT: D 88 TYR cc_start: 0.8672 (m-80) cc_final: 0.8278 (m-80) REVERT: E 52 LEU cc_start: 0.9081 (mt) cc_final: 0.8477 (mt) REVERT: E 80 ASN cc_start: 0.8654 (t0) cc_final: 0.8438 (t0) REVERT: E 251 ILE cc_start: 0.8710 (mt) cc_final: 0.8337 (mp) REVERT: E 377 ASN cc_start: 0.8080 (t0) cc_final: 0.7651 (m-40) REVERT: E 381 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7934 (mm-30) REVERT: E 391 PHE cc_start: 0.8272 (m-80) cc_final: 0.7981 (m-80) REVERT: F 530 MET cc_start: 0.8164 (mtt) cc_final: 0.6367 (mtt) REVERT: G 53 GLU cc_start: 0.7456 (pp20) cc_final: 0.6996 (pp20) REVERT: G 59 LYS cc_start: 0.8068 (tttm) cc_final: 0.7716 (tttm) REVERT: G 74 ASN cc_start: 0.7193 (m-40) cc_final: 0.6983 (m-40) REVERT: H 88 TYR cc_start: 0.8875 (m-10) cc_final: 0.8558 (m-80) REVERT: I 161 MET cc_start: 0.7800 (tpt) cc_final: 0.7551 (tpt) REVERT: I 377 ASN cc_start: 0.7628 (OUTLIER) cc_final: 0.7062 (m-40) REVERT: I 378 CYS cc_start: 0.3554 (t) cc_final: 0.2918 (t) REVERT: I 475 MET cc_start: 0.8703 (mmm) cc_final: 0.8318 (mpp) REVERT: J 545 LEU cc_start: 0.6884 (tp) cc_final: 0.6628 (mt) REVERT: J 591 GLN cc_start: 0.8727 (mt0) cc_final: 0.8383 (pt0) REVERT: K 30 ARG cc_start: 0.7346 (mtm180) cc_final: 0.6808 (mpp80) REVERT: K 53 GLU cc_start: 0.7182 (pp20) cc_final: 0.6718 (pp20) REVERT: L 88 TYR cc_start: 0.8621 (m-10) cc_final: 0.8328 (m-10) outliers start: 3 outliers final: 0 residues processed: 312 average time/residue: 0.1698 time to fit residues: 79.9794 Evaluate side-chains 201 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 195 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 151 optimal weight: 0.0770 chunk 98 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 219 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 overall best weight: 1.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN A 195 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 425 ASN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 302 ASN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 543 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.094380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.073557 restraints weight = 77145.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.073433 restraints weight = 47449.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.074319 restraints weight = 41454.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.074668 restraints weight = 35920.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.074686 restraints weight = 33768.654| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22164 Z= 0.239 Angle : 1.021 16.004 30417 Z= 0.471 Chirality : 0.057 0.410 3909 Planarity : 0.006 0.078 3531 Dihedral : 11.786 64.096 6459 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer: Outliers : 0.24 % Allowed : 5.00 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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 are not related in a simple way. whole: -3.02 (0.16), residues: 2412 helix: -0.37 (0.27), residues: 366 sheet: -1.74 (0.21), residues: 543 loop : -2.68 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 298 TYR 0.040 0.002 TYR B 643 PHE 0.020 0.002 PHE I 159 TRP 0.020 0.002 TRP F 610 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00521 (21921) covalent geometry : angle 0.94051 (29781) SS BOND : bond 0.01384 ( 39) SS BOND : angle 2.16091 ( 78) hydrogen bonds : bond 0.04495 ( 516) hydrogen bonds : angle 6.92775 ( 1341) Misc. bond : bond 0.00221 ( 18) link_ALPHA1-2 : bond 0.00657 ( 6) link_ALPHA1-2 : angle 2.40819 ( 18) link_ALPHA1-3 : bond 0.01085 ( 21) link_ALPHA1-3 : angle 1.86422 ( 63) link_ALPHA1-6 : bond 0.00686 ( 18) link_ALPHA1-6 : angle 2.08836 ( 54) link_BETA1-4 : bond 0.00656 ( 81) link_BETA1-4 : angle 3.02897 ( 243) link_NAG-ASN : bond 0.00470 ( 60) link_NAG-ASN : angle 3.51255 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 286 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.7894 (t0) cc_final: 0.7685 (t0) REVERT: A 391 PHE cc_start: 0.8292 (m-80) cc_final: 0.8030 (m-10) REVERT: B 530 MET cc_start: 0.8125 (mtt) cc_final: 0.7733 (mtt) REVERT: B 543 ASN cc_start: 0.8655 (m110) cc_final: 0.7813 (t0) REVERT: B 624 ASP cc_start: 0.8090 (t70) cc_final: 0.7822 (t70) REVERT: B 650 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7777 (pm20) REVERT: C 53 GLU cc_start: 0.7247 (pp20) cc_final: 0.6791 (pp20) REVERT: D 88 TYR cc_start: 0.8826 (m-80) cc_final: 0.8450 (m-80) REVERT: E 52 LEU cc_start: 0.9203 (mt) cc_final: 0.8647 (mt) REVERT: E 251 ILE cc_start: 0.8651 (mt) cc_final: 0.8350 (mp) REVERT: E 391 PHE cc_start: 0.8331 (m-80) cc_final: 0.8012 (m-80) REVERT: F 535 MET cc_start: 0.8285 (mmm) cc_final: 0.8030 (mmp) REVERT: G 53 GLU cc_start: 0.7308 (pp20) cc_final: 0.7018 (pp20) REVERT: G 59 LYS cc_start: 0.7927 (tttm) cc_final: 0.7458 (tttm) REVERT: G 74 ASN cc_start: 0.7186 (m-40) cc_final: 0.6950 (m-40) REVERT: H 88 TYR cc_start: 0.8893 (m-10) cc_final: 0.8508 (m-80) REVERT: K 30 ARG cc_start: 0.7458 (mtm180) cc_final: 0.6932 (mpp80) REVERT: K 53 GLU cc_start: 0.7226 (pp20) cc_final: 0.6738 (pp20) REVERT: L 88 TYR cc_start: 0.8761 (m-10) cc_final: 0.8555 (m-10) outliers start: 5 outliers final: 1 residues processed: 291 average time/residue: 0.1715 time to fit residues: 74.7381 Evaluate side-chains 192 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 377 ASN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 ASN ** I 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 302 ASN I 352 HIS ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.092291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.071594 restraints weight = 81517.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.071293 restraints weight = 50892.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.072062 restraints weight = 51073.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.072467 restraints weight = 41496.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.072519 restraints weight = 39106.330| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 22164 Z= 0.263 Angle : 1.023 15.888 30417 Z= 0.473 Chirality : 0.057 0.392 3909 Planarity : 0.006 0.076 3531 Dihedral : 11.089 57.054 6459 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.48 % Favored : 87.52 % Rotamer: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -3.10 (0.16), residues: 2412 helix: -0.50 (0.26), residues: 381 sheet: -1.64 (0.20), residues: 603 loop : -2.82 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 298 TYR 0.035 0.002 TYR B 643 PHE 0.021 0.002 PHE I 159 TRP 0.018 0.002 TRP A 427 HIS 0.003 0.001 HIS K 102 Details of bonding type rmsd covalent geometry : bond 0.00579 (21921) covalent geometry : angle 0.94440 (29781) SS BOND : bond 0.00489 ( 39) SS BOND : angle 2.38938 ( 78) hydrogen bonds : bond 0.04557 ( 516) hydrogen bonds : angle 6.95198 ( 1341) Misc. bond : bond 0.00232 ( 18) link_ALPHA1-2 : bond 0.00543 ( 6) link_ALPHA1-2 : angle 2.47127 ( 18) link_ALPHA1-3 : bond 0.01141 ( 21) link_ALPHA1-3 : angle 1.93958 ( 63) link_ALPHA1-6 : bond 0.00855 ( 18) link_ALPHA1-6 : angle 2.02208 ( 54) link_BETA1-4 : bond 0.00644 ( 81) link_BETA1-4 : angle 2.92554 ( 243) link_NAG-ASN : bond 0.00557 ( 60) link_NAG-ASN : angle 3.48378 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 273 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ILE cc_start: 0.8782 (mp) cc_final: 0.8467 (mp) REVERT: A 377 ASN cc_start: 0.8156 (t0) cc_final: 0.7809 (t0) REVERT: A 378 CYS cc_start: 0.3863 (t) cc_final: 0.2671 (t) REVERT: A 391 PHE cc_start: 0.8350 (m-80) cc_final: 0.8042 (m-10) REVERT: B 624 ASP cc_start: 0.8246 (t70) cc_final: 0.8044 (t70) REVERT: B 648 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8370 (tm-30) REVERT: C 2 ILE cc_start: 0.9202 (pt) cc_final: 0.8768 (tt) REVERT: C 53 GLU cc_start: 0.7278 (pp20) cc_final: 0.6889 (pp20) REVERT: D 88 TYR cc_start: 0.8875 (m-80) cc_final: 0.8567 (m-80) REVERT: E 52 LEU cc_start: 0.9176 (mt) cc_final: 0.8678 (mt) REVERT: E 391 PHE cc_start: 0.8310 (m-80) cc_final: 0.7961 (m-80) REVERT: F 530 MET cc_start: 0.8002 (mpp) cc_final: 0.7599 (mpp) REVERT: G 2 ILE cc_start: 0.8927 (pt) cc_final: 0.8413 (tt) REVERT: G 53 GLU cc_start: 0.7320 (pp20) cc_final: 0.7036 (pp20) REVERT: G 59 LYS cc_start: 0.8110 (tttm) cc_final: 0.7648 (tttm) REVERT: G 74 ASN cc_start: 0.6848 (m-40) cc_final: 0.6552 (m-40) REVERT: H 88 TYR cc_start: 0.8881 (m-10) cc_final: 0.8570 (m-10) REVERT: I 100 MET cc_start: 0.8929 (mmm) cc_final: 0.8619 (mmm) REVERT: I 161 MET cc_start: 0.7694 (tpt) cc_final: 0.7466 (tpt) REVERT: I 251 ILE cc_start: 0.8648 (mt) cc_final: 0.8359 (mt) REVERT: I 378 CYS cc_start: 0.3640 (t) cc_final: 0.3194 (t) REVERT: I 475 MET cc_start: 0.8596 (mmm) cc_final: 0.8281 (mpp) REVERT: K 2 ILE cc_start: 0.8860 (pt) cc_final: 0.8377 (tt) REVERT: K 30 ARG cc_start: 0.7450 (mtm180) cc_final: 0.6846 (mpp80) REVERT: K 53 GLU cc_start: 0.7173 (pp20) cc_final: 0.6693 (pp20) REVERT: L 88 TYR cc_start: 0.8808 (m-10) cc_final: 0.8465 (m-10) outliers start: 2 outliers final: 0 residues processed: 275 average time/residue: 0.1609 time to fit residues: 67.9755 Evaluate side-chains 178 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 212 optimal weight: 2.9990 chunk 127 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 193 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 ASN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 302 ASN I 428 GLN J 650 GLN ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.095149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.074072 restraints weight = 78452.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.074545 restraints weight = 48872.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.075073 restraints weight = 44749.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.075345 restraints weight = 38743.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075584 restraints weight = 36291.621| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22164 Z= 0.171 Angle : 0.943 15.499 30417 Z= 0.434 Chirality : 0.054 0.421 3909 Planarity : 0.005 0.072 3531 Dihedral : 10.227 59.318 6459 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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 are not related in a simple way. whole: -2.88 (0.16), residues: 2412 helix: -0.13 (0.27), residues: 366 sheet: -1.78 (0.20), residues: 579 loop : -2.56 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 298 TYR 0.037 0.002 TYR B 643 PHE 0.018 0.001 PHE E 382 TRP 0.014 0.002 TRP B 610 HIS 0.004 0.001 HIS K 102 Details of bonding type rmsd covalent geometry : bond 0.00363 (21921) covalent geometry : angle 0.86903 (29781) SS BOND : bond 0.00383 ( 39) SS BOND : angle 1.78621 ( 78) hydrogen bonds : bond 0.04160 ( 516) hydrogen bonds : angle 6.57333 ( 1341) Misc. bond : bond 0.00241 ( 18) link_ALPHA1-2 : bond 0.00714 ( 6) link_ALPHA1-2 : angle 2.54835 ( 18) link_ALPHA1-3 : bond 0.01146 ( 21) link_ALPHA1-3 : angle 1.70075 ( 63) link_ALPHA1-6 : bond 0.00689 ( 18) link_ALPHA1-6 : angle 1.81075 ( 54) link_BETA1-4 : bond 0.00560 ( 81) link_BETA1-4 : angle 2.74855 ( 243) link_NAG-ASN : bond 0.00379 ( 60) link_NAG-ASN : angle 3.31908 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.8090 (t0) cc_final: 0.7723 (t0) REVERT: A 391 PHE cc_start: 0.8381 (m-80) cc_final: 0.8144 (m-10) REVERT: B 543 ASN cc_start: 0.8758 (m110) cc_final: 0.7506 (t0) REVERT: B 624 ASP cc_start: 0.8270 (t70) cc_final: 0.8044 (t70) REVERT: C 2 ILE cc_start: 0.9162 (pt) cc_final: 0.8739 (tt) REVERT: D 88 TYR cc_start: 0.8809 (m-80) cc_final: 0.8424 (m-10) REVERT: E 52 LEU cc_start: 0.9359 (mt) cc_final: 0.8824 (mt) REVERT: E 391 PHE cc_start: 0.8364 (m-80) cc_final: 0.8082 (m-80) REVERT: E 476 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.8169 (mtm-85) REVERT: F 530 MET cc_start: 0.8084 (mpp) cc_final: 0.7673 (mpp) REVERT: F 535 MET cc_start: 0.7834 (mmm) cc_final: 0.7618 (mmp) REVERT: F 543 ASN cc_start: 0.8741 (m110) cc_final: 0.7729 (t0) REVERT: G 2 ILE cc_start: 0.8851 (pt) cc_final: 0.8284 (tt) REVERT: G 30 ARG cc_start: 0.7604 (mpp80) cc_final: 0.7282 (mpp80) REVERT: G 53 GLU cc_start: 0.7231 (pp20) cc_final: 0.6891 (pp20) REVERT: G 59 LYS cc_start: 0.8016 (tttm) cc_final: 0.7650 (tttm) REVERT: H 88 TYR cc_start: 0.8637 (m-10) cc_final: 0.8304 (m-80) REVERT: I 251 ILE cc_start: 0.8549 (mt) cc_final: 0.8236 (mt) REVERT: I 377 ASN cc_start: 0.7947 (t0) cc_final: 0.7325 (m-40) REVERT: I 378 CYS cc_start: 0.2601 (t) cc_final: 0.2222 (t) REVERT: I 475 MET cc_start: 0.8626 (mmm) cc_final: 0.8254 (mpp) REVERT: I 476 ARG cc_start: 0.8309 (mtm-85) cc_final: 0.8096 (mtm180) REVERT: J 530 MET cc_start: 0.7405 (mmm) cc_final: 0.6623 (mmm) REVERT: J 543 ASN cc_start: 0.8568 (m110) cc_final: 0.7078 (t0) REVERT: J 545 LEU cc_start: 0.7466 (tp) cc_final: 0.7143 (mt) REVERT: K 2 ILE cc_start: 0.8860 (pt) cc_final: 0.8359 (tt) REVERT: K 30 ARG cc_start: 0.7770 (mtm180) cc_final: 0.7226 (mpp80) REVERT: K 53 GLU cc_start: 0.7346 (pp20) cc_final: 0.6826 (pp20) REVERT: L 88 TYR cc_start: 0.8904 (m-80) cc_final: 0.8385 (m-10) outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 0.1618 time to fit residues: 70.7099 Evaluate side-chains 190 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 161 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 216 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 GLN ** I 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 302 ASN ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.094814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.073733 restraints weight = 79224.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.074568 restraints weight = 49833.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.074934 restraints weight = 45010.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.075120 restraints weight = 40514.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075577 restraints weight = 36483.836| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22164 Z= 0.176 Angle : 0.933 15.359 30417 Z= 0.431 Chirality : 0.054 0.428 3909 Planarity : 0.005 0.071 3531 Dihedral : 9.764 59.920 6459 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.36 % Favored : 88.56 % Rotamer: Outliers : 0.05 % Allowed : 1.67 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -2.79 (0.16), residues: 2412 helix: -0.09 (0.27), residues: 366 sheet: -1.65 (0.20), residues: 579 loop : -2.52 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 588 TYR 0.027 0.002 TYR D 89 PHE 0.025 0.001 PHE E 382 TRP 0.018 0.002 TRP E 427 HIS 0.003 0.000 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00379 (21921) covalent geometry : angle 0.86127 (29781) SS BOND : bond 0.00483 ( 39) SS BOND : angle 2.00565 ( 78) hydrogen bonds : bond 0.04141 ( 516) hydrogen bonds : angle 6.50937 ( 1341) Misc. bond : bond 0.00225 ( 18) link_ALPHA1-2 : bond 0.00698 ( 6) link_ALPHA1-2 : angle 2.43138 ( 18) link_ALPHA1-3 : bond 0.01152 ( 21) link_ALPHA1-3 : angle 1.66404 ( 63) link_ALPHA1-6 : bond 0.00682 ( 18) link_ALPHA1-6 : angle 1.81270 ( 54) link_BETA1-4 : bond 0.00582 ( 81) link_BETA1-4 : angle 2.65690 ( 243) link_NAG-ASN : bond 0.00403 ( 60) link_NAG-ASN : angle 3.23117 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.8075 (t0) cc_final: 0.7672 (t0) REVERT: A 378 CYS cc_start: 0.3951 (t) cc_final: 0.3019 (t) REVERT: A 391 PHE cc_start: 0.8368 (m-80) cc_final: 0.8100 (m-10) REVERT: A 476 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.8054 (mtm-85) REVERT: B 624 ASP cc_start: 0.8241 (t70) cc_final: 0.7920 (t70) REVERT: C 2 ILE cc_start: 0.9151 (pt) cc_final: 0.8660 (tt) REVERT: D 88 TYR cc_start: 0.8738 (m-80) cc_final: 0.8247 (m-10) REVERT: E 52 LEU cc_start: 0.9293 (mt) cc_final: 0.8702 (mt) REVERT: E 391 PHE cc_start: 0.8211 (m-80) cc_final: 0.7924 (m-10) REVERT: E 476 ARG cc_start: 0.8357 (mtm-85) cc_final: 0.8079 (mtm-85) REVERT: F 530 MET cc_start: 0.8181 (mpp) cc_final: 0.7743 (mpp) REVERT: F 543 ASN cc_start: 0.8737 (m110) cc_final: 0.7877 (t0) REVERT: F 652 GLN cc_start: 0.8408 (pp30) cc_final: 0.8090 (pp30) REVERT: G 30 ARG cc_start: 0.7572 (mpp80) cc_final: 0.7272 (mpp80) REVERT: G 53 GLU cc_start: 0.7172 (pp20) cc_final: 0.6882 (pp20) REVERT: G 59 LYS cc_start: 0.8181 (tttm) cc_final: 0.7817 (tttm) REVERT: H 88 TYR cc_start: 0.8578 (m-80) cc_final: 0.8201 (m-80) REVERT: I 251 ILE cc_start: 0.8559 (mt) cc_final: 0.8271 (mm) REVERT: I 377 ASN cc_start: 0.7905 (t0) cc_final: 0.7347 (m-40) REVERT: I 378 CYS cc_start: 0.3046 (t) cc_final: 0.2282 (t) REVERT: I 445 CYS cc_start: 0.4199 (t) cc_final: 0.3783 (t) REVERT: I 475 MET cc_start: 0.8631 (mmm) cc_final: 0.8234 (mpp) REVERT: J 530 MET cc_start: 0.7203 (mmt) cc_final: 0.6494 (mmt) REVERT: J 543 ASN cc_start: 0.8577 (m110) cc_final: 0.7108 (t0) REVERT: J 545 LEU cc_start: 0.7416 (tp) cc_final: 0.7195 (mt) REVERT: K 2 ILE cc_start: 0.8920 (pt) cc_final: 0.8359 (tt) REVERT: K 53 GLU cc_start: 0.7321 (pp20) cc_final: 0.6913 (pp20) REVERT: L 88 TYR cc_start: 0.8801 (m-80) cc_final: 0.8413 (m-10) outliers start: 1 outliers final: 0 residues processed: 275 average time/residue: 0.1503 time to fit residues: 64.6942 Evaluate side-chains 189 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 200 optimal weight: 10.0000 chunk 208 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 225 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 229 optimal weight: 8.9990 chunk 21 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 302 ASN ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.095781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.074794 restraints weight = 79431.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.075534 restraints weight = 49575.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.075973 restraints weight = 48114.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.076206 restraints weight = 40012.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.076705 restraints weight = 37156.219| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22164 Z= 0.168 Angle : 0.927 14.773 30417 Z= 0.430 Chirality : 0.054 0.435 3909 Planarity : 0.005 0.077 3531 Dihedral : 9.416 59.381 6459 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.41 % Favored : 89.51 % Rotamer: Outliers : 0.05 % Allowed : 1.24 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -2.73 (0.16), residues: 2412 helix: -0.05 (0.27), residues: 363 sheet: -1.57 (0.20), residues: 582 loop : -2.50 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 588 TYR 0.021 0.002 TYR B 643 PHE 0.024 0.001 PHE E 382 TRP 0.051 0.002 TRP I 35 HIS 0.002 0.000 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00359 (21921) covalent geometry : angle 0.85546 (29781) SS BOND : bond 0.00475 ( 39) SS BOND : angle 1.88858 ( 78) hydrogen bonds : bond 0.03998 ( 516) hydrogen bonds : angle 6.37268 ( 1341) Misc. bond : bond 0.00238 ( 18) link_ALPHA1-2 : bond 0.00710 ( 6) link_ALPHA1-2 : angle 2.42786 ( 18) link_ALPHA1-3 : bond 0.01165 ( 21) link_ALPHA1-3 : angle 1.60343 ( 63) link_ALPHA1-6 : bond 0.00682 ( 18) link_ALPHA1-6 : angle 1.75795 ( 54) link_BETA1-4 : bond 0.00579 ( 81) link_BETA1-4 : angle 2.62555 ( 243) link_NAG-ASN : bond 0.00489 ( 60) link_NAG-ASN : angle 3.31196 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8643 (ttt) cc_final: 0.8399 (ttp) REVERT: A 377 ASN cc_start: 0.8157 (t0) cc_final: 0.7800 (t0) REVERT: A 391 PHE cc_start: 0.8360 (m-80) cc_final: 0.8035 (m-10) REVERT: A 476 ARG cc_start: 0.8331 (mtm-85) cc_final: 0.8119 (mtm-85) REVERT: B 543 ASN cc_start: 0.8746 (m110) cc_final: 0.7640 (t0) REVERT: C 2 ILE cc_start: 0.9213 (pt) cc_final: 0.8771 (tt) REVERT: D 88 TYR cc_start: 0.8596 (m-80) cc_final: 0.8064 (m-80) REVERT: E 52 LEU cc_start: 0.9288 (mt) cc_final: 0.8719 (mt) REVERT: E 391 PHE cc_start: 0.8215 (m-80) cc_final: 0.7900 (m-10) REVERT: E 434 MET cc_start: 0.7189 (tmm) cc_final: 0.6901 (tmm) REVERT: E 476 ARG cc_start: 0.8412 (mtm-85) cc_final: 0.8051 (mtm-85) REVERT: F 530 MET cc_start: 0.8205 (mpp) cc_final: 0.7765 (mpp) REVERT: F 543 ASN cc_start: 0.8741 (m110) cc_final: 0.7767 (t0) REVERT: G 53 GLU cc_start: 0.7211 (pp20) cc_final: 0.6928 (pp20) REVERT: H 88 TYR cc_start: 0.8563 (m-80) cc_final: 0.8209 (m-10) REVERT: I 150 MET cc_start: 0.1512 (ttm) cc_final: 0.1258 (ttt) REVERT: I 251 ILE cc_start: 0.8461 (mt) cc_final: 0.8216 (mm) REVERT: I 377 ASN cc_start: 0.8023 (t0) cc_final: 0.7447 (m-40) REVERT: I 378 CYS cc_start: 0.3096 (t) cc_final: 0.2402 (t) REVERT: I 445 CYS cc_start: 0.4136 (t) cc_final: 0.3590 (t) REVERT: I 475 MET cc_start: 0.8682 (mmm) cc_final: 0.8308 (mpp) REVERT: J 530 MET cc_start: 0.7217 (mmt) cc_final: 0.6980 (mmt) REVERT: J 543 ASN cc_start: 0.8545 (m110) cc_final: 0.7147 (t0) REVERT: J 655 LYS cc_start: 0.8363 (tppt) cc_final: 0.7209 (mtmt) REVERT: K 2 ILE cc_start: 0.8924 (pt) cc_final: 0.8365 (tt) REVERT: K 53 GLU cc_start: 0.7410 (pp20) cc_final: 0.7006 (pp20) REVERT: L 88 TYR cc_start: 0.8823 (m-80) cc_final: 0.8490 (m-10) outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.1384 time to fit residues: 59.6648 Evaluate side-chains 197 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 228 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 152 optimal weight: 6.9990 chunk 164 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 287 GLN I 302 ASN I 478 ASN ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.094380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.073511 restraints weight = 80141.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.073614 restraints weight = 50624.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.074102 restraints weight = 50668.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.074506 restraints weight = 41648.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.074785 restraints weight = 39079.505| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22164 Z= 0.185 Angle : 0.929 14.742 30417 Z= 0.431 Chirality : 0.054 0.428 3909 Planarity : 0.005 0.069 3531 Dihedral : 9.180 59.569 6459 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.65 % Favored : 88.35 % Rotamer: Outliers : 0.05 % Allowed : 0.52 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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 are not related in a simple way. whole: -2.71 (0.16), residues: 2412 helix: -0.13 (0.27), residues: 363 sheet: -1.53 (0.20), residues: 588 loop : -2.47 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 588 TYR 0.022 0.002 TYR J 586 PHE 0.026 0.002 PHE E 382 TRP 0.039 0.002 TRP I 35 HIS 0.002 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00404 (21921) covalent geometry : angle 0.85934 (29781) SS BOND : bond 0.00511 ( 39) SS BOND : angle 2.03907 ( 78) hydrogen bonds : bond 0.04070 ( 516) hydrogen bonds : angle 6.37876 ( 1341) Misc. bond : bond 0.00220 ( 18) link_ALPHA1-2 : bond 0.00602 ( 6) link_ALPHA1-2 : angle 2.37907 ( 18) link_ALPHA1-3 : bond 0.01109 ( 21) link_ALPHA1-3 : angle 1.62145 ( 63) link_ALPHA1-6 : bond 0.00702 ( 18) link_ALPHA1-6 : angle 1.76012 ( 54) link_BETA1-4 : bond 0.00596 ( 81) link_BETA1-4 : angle 2.60258 ( 243) link_NAG-ASN : bond 0.00455 ( 60) link_NAG-ASN : angle 3.21732 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8729 (ttt) cc_final: 0.8437 (ttp) REVERT: A 377 ASN cc_start: 0.8391 (t0) cc_final: 0.7919 (t0) REVERT: A 391 PHE cc_start: 0.8527 (m-80) cc_final: 0.8227 (m-10) REVERT: C 2 ILE cc_start: 0.9220 (pt) cc_final: 0.8871 (tt) REVERT: D 88 TYR cc_start: 0.8534 (m-80) cc_final: 0.8000 (m-80) REVERT: E 52 LEU cc_start: 0.9292 (mt) cc_final: 0.8807 (mt) REVERT: E 116 LEU cc_start: 0.8385 (tp) cc_final: 0.8086 (tp) REVERT: E 391 PHE cc_start: 0.8342 (m-80) cc_final: 0.8057 (m-10) REVERT: E 434 MET cc_start: 0.7153 (tmm) cc_final: 0.6894 (tmm) REVERT: E 476 ARG cc_start: 0.8564 (mtm-85) cc_final: 0.8227 (mtm-85) REVERT: F 530 MET cc_start: 0.8194 (mpp) cc_final: 0.7688 (mpp) REVERT: F 543 ASN cc_start: 0.8808 (m110) cc_final: 0.7801 (t0) REVERT: G 30 ARG cc_start: 0.7556 (mpp80) cc_final: 0.7206 (mpp80) REVERT: G 53 GLU cc_start: 0.7336 (pp20) cc_final: 0.6982 (pp20) REVERT: H 88 TYR cc_start: 0.8686 (m-80) cc_final: 0.8315 (m-10) REVERT: I 150 MET cc_start: 0.1571 (ttm) cc_final: 0.1266 (ttt) REVERT: I 251 ILE cc_start: 0.8449 (mt) cc_final: 0.8199 (mm) REVERT: I 377 ASN cc_start: 0.8117 (t0) cc_final: 0.7537 (m-40) REVERT: I 378 CYS cc_start: 0.3221 (t) cc_final: 0.2386 (t) REVERT: I 445 CYS cc_start: 0.4228 (t) cc_final: 0.3507 (t) REVERT: I 475 MET cc_start: 0.8681 (mmm) cc_final: 0.8296 (mpp) REVERT: J 530 MET cc_start: 0.7226 (mmt) cc_final: 0.6993 (mmt) REVERT: J 543 ASN cc_start: 0.8634 (m110) cc_final: 0.7290 (t0) REVERT: J 655 LYS cc_start: 0.8508 (tppt) cc_final: 0.7492 (mtmt) REVERT: K 2 ILE cc_start: 0.8952 (pt) cc_final: 0.8494 (tt) REVERT: K 53 GLU cc_start: 0.7540 (pp20) cc_final: 0.7181 (pp20) REVERT: K 57 GLU cc_start: 0.8088 (tp30) cc_final: 0.7881 (tp30) REVERT: L 83 GLU cc_start: 0.7343 (pm20) cc_final: 0.6956 (pm20) REVERT: L 88 TYR cc_start: 0.8891 (m-80) cc_final: 0.8549 (m-10) outliers start: 1 outliers final: 1 residues processed: 269 average time/residue: 0.1494 time to fit residues: 63.5434 Evaluate side-chains 189 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 146 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 233 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 166 optimal weight: 0.9990 chunk 232 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 374 HIS B 651 ASN D 36 HIS ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN F 591 GLN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 HIS ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.091560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.070791 restraints weight = 81499.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.071647 restraints weight = 49647.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.072107 restraints weight = 48599.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.072272 restraints weight = 38637.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.072799 restraints weight = 36099.702| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 22164 Z= 0.288 Angle : 1.039 14.833 30417 Z= 0.484 Chirality : 0.057 0.378 3909 Planarity : 0.006 0.071 3531 Dihedral : 9.629 57.731 6459 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.39 % Favored : 86.48 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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 are not related in a simple way. whole: -2.84 (0.16), residues: 2412 helix: -0.38 (0.26), residues: 363 sheet: -1.52 (0.20), residues: 600 loop : -2.57 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 588 TYR 0.033 0.003 TYR H 89 PHE 0.032 0.002 PHE I 159 TRP 0.039 0.003 TRP I 35 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00638 (21921) covalent geometry : angle 0.96651 (29781) SS BOND : bond 0.00627 ( 39) SS BOND : angle 2.68641 ( 78) hydrogen bonds : bond 0.04520 ( 516) hydrogen bonds : angle 6.78741 ( 1341) Misc. bond : bond 0.00219 ( 18) link_ALPHA1-2 : bond 0.00389 ( 6) link_ALPHA1-2 : angle 2.51829 ( 18) link_ALPHA1-3 : bond 0.01010 ( 21) link_ALPHA1-3 : angle 1.87902 ( 63) link_ALPHA1-6 : bond 0.00761 ( 18) link_ALPHA1-6 : angle 1.97269 ( 54) link_BETA1-4 : bond 0.00712 ( 81) link_BETA1-4 : angle 2.81403 ( 243) link_NAG-ASN : bond 0.00626 ( 60) link_NAG-ASN : angle 3.34298 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.8492 (t0) cc_final: 0.8019 (t0) REVERT: A 391 PHE cc_start: 0.8463 (m-80) cc_final: 0.8146 (m-10) REVERT: C 2 ILE cc_start: 0.9254 (pt) cc_final: 0.8965 (tt) REVERT: D 88 TYR cc_start: 0.8598 (m-80) cc_final: 0.8110 (m-80) REVERT: E 391 PHE cc_start: 0.8200 (m-80) cc_final: 0.7838 (m-10) REVERT: F 530 MET cc_start: 0.8056 (mpp) cc_final: 0.7407 (mpp) REVERT: G 53 GLU cc_start: 0.7348 (pp20) cc_final: 0.7071 (pp20) REVERT: H 88 TYR cc_start: 0.8560 (m-80) cc_final: 0.8281 (m-10) REVERT: I 377 ASN cc_start: 0.8250 (t0) cc_final: 0.7786 (m-40) REVERT: I 378 CYS cc_start: 0.3116 (t) cc_final: 0.2253 (t) REVERT: I 445 CYS cc_start: 0.4480 (t) cc_final: 0.3740 (t) REVERT: J 530 MET cc_start: 0.7141 (mmt) cc_final: 0.6582 (mmt) REVERT: J 543 ASN cc_start: 0.8601 (m110) cc_final: 0.7338 (t0) REVERT: J 655 LYS cc_start: 0.8571 (tppt) cc_final: 0.7612 (mtmt) REVERT: K 2 ILE cc_start: 0.9009 (pt) cc_final: 0.8598 (tt) REVERT: K 53 GLU cc_start: 0.7473 (pp20) cc_final: 0.7191 (pp20) REVERT: L 88 TYR cc_start: 0.8795 (m-80) cc_final: 0.8455 (m-10) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1471 time to fit residues: 57.8910 Evaluate side-chains 174 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 97 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 213 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 287 GLN D 36 HIS ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 HIS ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 287 GLN ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.094582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.073932 restraints weight = 80587.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.075443 restraints weight = 48828.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075787 restraints weight = 45250.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.075795 restraints weight = 36353.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.076208 restraints weight = 34360.900| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22164 Z= 0.171 Angle : 0.930 14.849 30417 Z= 0.433 Chirality : 0.053 0.420 3909 Planarity : 0.005 0.068 3531 Dihedral : 9.088 57.561 6459 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -2.74 (0.16), residues: 2412 helix: -0.20 (0.27), residues: 360 sheet: -1.51 (0.20), residues: 624 loop : -2.51 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 298 TYR 0.027 0.002 TYR D 89 PHE 0.023 0.001 PHE E 382 TRP 0.023 0.002 TRP I 35 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00370 (21921) covalent geometry : angle 0.86391 (29781) SS BOND : bond 0.00469 ( 39) SS BOND : angle 1.85439 ( 78) hydrogen bonds : bond 0.04023 ( 516) hydrogen bonds : angle 6.46128 ( 1341) Misc. bond : bond 0.00229 ( 18) link_ALPHA1-2 : bond 0.00583 ( 6) link_ALPHA1-2 : angle 2.51193 ( 18) link_ALPHA1-3 : bond 0.01103 ( 21) link_ALPHA1-3 : angle 1.56028 ( 63) link_ALPHA1-6 : bond 0.00664 ( 18) link_ALPHA1-6 : angle 1.63206 ( 54) link_BETA1-4 : bond 0.00558 ( 81) link_BETA1-4 : angle 2.58527 ( 243) link_NAG-ASN : bond 0.00397 ( 60) link_NAG-ASN : angle 3.12842 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3222.13 seconds wall clock time: 57 minutes 16.29 seconds (3436.29 seconds total)