Starting phenix.real_space_refine on Mon May 4 03:36:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nw1_49871/05_2026/9nw1_49871.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nw1_49871/05_2026/9nw1_49871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nw1_49871/05_2026/9nw1_49871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nw1_49871/05_2026/9nw1_49871.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nw1_49871/05_2026/9nw1_49871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nw1_49871/05_2026/9nw1_49871.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 110 5.16 5 C 10782 2.51 5 N 2840 2.21 5 O 3560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17292 Number of models: 1 Model: "" Number of chains: 56 Chain: "H" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1044 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'TYS:plan-2': 3} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "b" Number of atoms: 3530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3530 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "c" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "d" Number of atoms: 3530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3530 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "e" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "f" Number of atoms: 3530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3530 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "g" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 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: 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: "C" 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "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: "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: 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: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 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: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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: "b" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} 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: "e" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "g" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.73, per 1000 atoms: 0.22 Number of scatterers: 17292 At special positions: 0 Unit cell: (134.46, 132.8, 153.55, 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 110 16.00 O 3560 8.00 N 2840 7.00 C 10782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS b 54 " - pdb=" SG CYS b 74 " distance=2.03 Simple disulfide: pdb=" SG CYS b 119 " - pdb=" SG CYS b 205 " distance=2.03 Simple disulfide: pdb=" SG CYS b 126 " - pdb=" SG CYS b 196 " distance=2.03 Simple disulfide: pdb=" SG CYS b 131 " - pdb=" SG CYS b 157 " distance=2.03 Simple disulfide: pdb=" SG CYS b 201 " - pdb=" SG CYS b 433 " distance=2.03 Simple disulfide: pdb=" SG CYS b 218 " - pdb=" SG CYS b 247 " distance=2.03 Simple disulfide: pdb=" SG CYS b 228 " - pdb=" SG CYS b 239 " distance=2.03 Simple disulfide: pdb=" SG CYS b 296 " - pdb=" SG CYS b 331 " distance=2.03 Simple disulfide: pdb=" SG CYS b 378 " - pdb=" SG CYS b 445 " distance=2.04 Simple disulfide: pdb=" SG CYS b 385 " - pdb=" SG CYS b 418 " distance=2.03 Simple disulfide: pdb=" SG CYS b 501 " - pdb=" SG CYS c 605 " distance=2.03 Simple disulfide: pdb=" SG CYS c 598 " - pdb=" SG CYS c 604 " distance=2.03 Simple disulfide: pdb=" SG CYS d 54 " - pdb=" SG CYS d 74 " distance=2.05 Simple disulfide: pdb=" SG CYS d 119 " - pdb=" SG CYS d 205 " distance=2.03 Simple disulfide: pdb=" SG CYS d 126 " - pdb=" SG CYS d 196 " distance=2.01 Simple disulfide: pdb=" SG CYS d 131 " - pdb=" SG CYS d 157 " distance=2.03 Simple disulfide: pdb=" SG CYS d 201 " - pdb=" SG CYS d 433 " distance=1.80 Simple disulfide: pdb=" SG CYS d 218 " - pdb=" SG CYS d 247 " distance=2.03 Simple disulfide: pdb=" SG CYS d 228 " - pdb=" SG CYS d 239 " distance=2.03 Simple disulfide: pdb=" SG CYS d 296 " - pdb=" SG CYS d 331 " distance=2.03 Simple disulfide: pdb=" SG CYS d 378 " - pdb=" SG CYS d 445 " distance=2.04 Simple disulfide: pdb=" SG CYS d 385 " - pdb=" SG CYS d 418 " distance=2.03 Simple disulfide: pdb=" SG CYS d 501 " - pdb=" SG CYS e 605 " distance=2.02 Simple disulfide: pdb=" SG CYS e 598 " - pdb=" SG CYS e 604 " distance=2.03 Simple disulfide: pdb=" SG CYS f 54 " - pdb=" SG CYS f 74 " distance=2.04 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 205 " distance=2.03 Simple disulfide: pdb=" SG CYS f 126 " - pdb=" SG CYS f 196 " distance=2.03 Simple disulfide: pdb=" SG CYS f 131 " - pdb=" SG CYS f 157 " distance=2.03 Simple disulfide: pdb=" SG CYS f 201 " - pdb=" SG CYS f 433 " distance=2.03 Simple disulfide: pdb=" SG CYS f 218 " - pdb=" SG CYS f 247 " distance=2.03 Simple disulfide: pdb=" SG CYS f 228 " - pdb=" SG CYS f 239 " distance=2.03 Simple disulfide: pdb=" SG CYS f 296 " - pdb=" SG CYS f 331 " distance=2.03 Simple disulfide: pdb=" SG CYS f 378 " - pdb=" SG CYS f 445 " distance=2.04 Simple disulfide: pdb=" SG CYS f 385 " - pdb=" SG CYS f 418 " distance=2.03 Simple disulfide: pdb=" SG CYS f 501 " - pdb=" SG CYS g 605 " distance=2.03 Simple disulfide: pdb=" SG CYS g 598 " - pdb=" SG CYS g 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA E 3 " - " MAN E 4 " " BMA S 3 " - " MAN S 4 " " BMA l 3 " - " MAN l 4 " " BMA v 3 " - " MAN v 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " " BMA v 3 " - " MAN v 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " 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 o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " NAG-ASN " NAG A 1 " - " ASN b 392 " " NAG B 1 " - " ASN b 332 " " NAG C 1 " - " ASN b 262 " " NAG D 1 " - " ASN b 156 " " NAG E 1 " - " ASN b 160 " " NAG F 1 " - " ASN b 197 " " NAG G 1 " - " ASN b 234 " " NAG I 1 " - " ASN b 241 " " NAG J 1 " - " ASN b 276 " " NAG K 1 " - " ASN b 301 " " NAG M 1 " - " ASN b 386 " " NAG N 1 " - " ASN b 448 " " NAG O 1 " - " ASN b 465 " " NAG P 1 " - " ASN b 363 " " NAG Q 1 " - " ASN d 392 " " NAG R 1 " - " ASN d 332 " " NAG S 1 " - " ASN d 262 " " NAG T 1 " - " ASN d 156 " " NAG U 1 " - " ASN d 160 " " NAG V 1 " - " ASN d 197 " " NAG W 1 " - " ASN d 234 " " NAG X 1 " - " ASN d 241 " " NAG Y 1 " - " ASN d 276 " " NAG Z 1 " - " ASN d 301 " " NAG a 1 " - " ASN d 386 " " NAG b 601 " - " ASN b 88 " " NAG b 602 " - " ASN b 133 " " NAG b 603 " - " ASN b 339 " " NAG b 604 " - " ASN b 355 " " NAG b 605 " - " ASN b 269 " " NAG b 606 " - " ASN b 398 " " NAG c 701 " - " ASN c 611 " " NAG c 702 " - " ASN c 637 " " NAG c 703 " - " ASN c 625 " " NAG d 601 " - " ASN d 88 " " NAG d 602 " - " ASN d 133 " " NAG d 603 " - " ASN d 339 " " NAG d 604 " - " ASN d 355 " " NAG d 605 " - " ASN d 269 " " NAG d 606 " - " ASN d 398 " " NAG d 607 " - " ASN d 363 " " NAG e 701 " - " ASN e 611 " " NAG e 702 " - " ASN e 637 " " NAG e 703 " - " ASN e 625 " " NAG f 601 " - " ASN f 133 " " NAG f 602 " - " ASN f 339 " " NAG f 603 " - " ASN f 355 " " NAG f 604 " - " ASN f 269 " " NAG f 605 " - " ASN f 88 " " NAG f 606 " - " ASN f 398 " " NAG g 701 " - " ASN g 611 " " NAG g 702 " - " ASN g 637 " " NAG g 703 " - " ASN g 625 " " NAG h 1 " - " ASN d 448 " " NAG i 1 " - " ASN d 465 " " NAG j 1 " - " ASN f 392 " " NAG k 1 " - " ASN f 332 " " NAG l 1 " - " ASN f 262 " " NAG m 1 " - " ASN f 156 " " NAG n 1 " - " ASN f 197 " " NAG o 1 " - " ASN f 234 " " NAG p 1 " - " ASN f 241 " " NAG q 1 " - " ASN f 276 " " NAG r 1 " - " ASN f 301 " " NAG s 1 " - " ASN f 386 " " NAG t 1 " - " ASN f 448 " " NAG u 1 " - " ASN f 465 " " NAG w 1 " - " ASN f 363 " Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 644.7 milliseconds 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3650 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 29 sheets defined 23.5% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.955A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'b' and resid 70 through 74 removed outlier: 3.512A pdb=" N ALA b 73 " --> pdb=" O ALA b 70 " (cutoff:3.500A) Processing helix chain 'b' and resid 98 through 117 removed outlier: 4.248A pdb=" N GLU b 102 " --> pdb=" O ASN b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 126 removed outlier: 3.542A pdb=" N LEU b 125 " --> pdb=" O LEU b 122 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS b 126 " --> pdb=" O THR b 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 122 through 126' Processing helix chain 'b' and resid 334 through 351 removed outlier: 3.681A pdb=" N THR b 341 " --> pdb=" O ARG b 337 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR b 351 " --> pdb=" O GLU b 347 " (cutoff:3.500A) Processing helix chain 'b' and resid 368 through 373 Processing helix chain 'b' and resid 387 through 390 Processing helix chain 'b' and resid 475 through 484 removed outlier: 4.054A pdb=" N TRP b 479 " --> pdb=" O MET b 475 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU b 482 " --> pdb=" O ASN b 478 " (cutoff:3.500A) Processing helix chain 'c' and resid 529 through 534 Processing helix chain 'c' and resid 536 through 543 removed outlier: 4.141A pdb=" N GLN c 540 " --> pdb=" O THR c 536 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN c 543 " --> pdb=" O VAL c 539 " (cutoff:3.500A) Processing helix chain 'c' and resid 544 through 546 No H-bonds generated for 'chain 'c' and resid 544 through 546' Processing helix chain 'c' and resid 569 through 596 removed outlier: 3.709A pdb=" N LEU c 592 " --> pdb=" O ARG c 588 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU c 593 " --> pdb=" O ASP c 589 " (cutoff:3.500A) Processing helix chain 'c' and resid 618 through 625 removed outlier: 3.537A pdb=" N ILE c 622 " --> pdb=" O SER c 618 " (cutoff:3.500A) Processing helix chain 'c' and resid 627 through 636 removed outlier: 3.659A pdb=" N LYS c 633 " --> pdb=" O LEU c 629 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU c 634 " --> pdb=" O GLN c 630 " (cutoff:3.500A) Processing helix chain 'c' and resid 638 through 658 Processing helix chain 'd' and resid 70 through 74 Processing helix chain 'd' and resid 98 through 117 removed outlier: 4.314A pdb=" N GLU d 102 " --> pdb=" O ASN d 98 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU d 116 " --> pdb=" O TRP d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 122 through 126 removed outlier: 3.512A pdb=" N LEU d 125 " --> pdb=" O LEU d 122 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS d 126 " --> pdb=" O THR d 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 122 through 126' Processing helix chain 'd' and resid 179 through 181 No H-bonds generated for 'chain 'd' and resid 179 through 181' Processing helix chain 'd' and resid 334 through 351 removed outlier: 3.853A pdb=" N THR d 341 " --> pdb=" O ARG d 337 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR d 351 " --> pdb=" O GLU d 347 " (cutoff:3.500A) Processing helix chain 'd' and resid 352 through 354 No H-bonds generated for 'chain 'd' and resid 352 through 354' Processing helix chain 'd' and resid 387 through 390 Processing helix chain 'd' and resid 475 through 484 removed outlier: 4.063A pdb=" N TRP d 479 " --> pdb=" O MET d 475 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU d 482 " --> pdb=" O ASN d 478 " (cutoff:3.500A) Processing helix chain 'e' and resid 529 through 534 removed outlier: 3.584A pdb=" N SER e 534 " --> pdb=" O MET e 530 " (cutoff:3.500A) Processing helix chain 'e' and resid 536 through 543 removed outlier: 3.888A pdb=" N GLN e 540 " --> pdb=" O THR e 536 " (cutoff:3.500A) Processing helix chain 'e' and resid 544 through 546 No H-bonds generated for 'chain 'e' and resid 544 through 546' Processing helix chain 'e' and resid 569 through 596 removed outlier: 3.607A pdb=" N LYS e 574 " --> pdb=" O VAL e 570 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU e 592 " --> pdb=" O ARG e 588 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU e 593 " --> pdb=" O ASP e 589 " (cutoff:3.500A) Processing helix chain 'e' and resid 619 through 624 Processing helix chain 'e' and resid 627 through 636 removed outlier: 3.575A pdb=" N LYS e 633 " --> pdb=" O LEU e 629 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU e 634 " --> pdb=" O GLN e 630 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE e 635 " --> pdb=" O TRP e 631 " (cutoff:3.500A) Processing helix chain 'e' and resid 638 through 658 removed outlier: 3.798A pdb=" N ARG e 644 " --> pdb=" O GLN e 640 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 74 removed outlier: 3.535A pdb=" N ALA f 73 " --> pdb=" O ALA f 70 " (cutoff:3.500A) Processing helix chain 'f' and resid 98 through 117 removed outlier: 4.410A pdb=" N GLU f 102 " --> pdb=" O ASN f 98 " (cutoff:3.500A) Processing helix chain 'f' and resid 122 through 126 Processing helix chain 'f' and resid 334 through 351 removed outlier: 3.601A pdb=" N THR f 351 " --> pdb=" O GLU f 347 " (cutoff:3.500A) Processing helix chain 'f' and resid 368 through 373 Processing helix chain 'f' and resid 387 through 390 Processing helix chain 'f' and resid 475 through 484 removed outlier: 4.251A pdb=" N TRP f 479 " --> pdb=" O MET f 475 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU f 482 " --> pdb=" O ASN f 478 " (cutoff:3.500A) Processing helix chain 'g' and resid 529 through 534 Processing helix chain 'g' and resid 536 through 543 removed outlier: 3.726A pdb=" N GLN g 540 " --> pdb=" O THR g 536 " (cutoff:3.500A) Processing helix chain 'g' and resid 569 through 596 removed outlier: 3.529A pdb=" N LYS g 574 " --> pdb=" O VAL g 570 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU g 592 " --> pdb=" O ARG g 588 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU g 593 " --> pdb=" O ASP g 589 " (cutoff:3.500A) Processing helix chain 'g' and resid 619 through 624 Processing helix chain 'g' and resid 627 through 636 removed outlier: 3.908A pdb=" N LYS g 633 " --> pdb=" O LEU g 629 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU g 634 " --> pdb=" O GLN g 630 " (cutoff:3.500A) Processing helix chain 'g' and resid 638 through 658 removed outlier: 3.514A pdb=" N GLU g 648 " --> pdb=" O ARG g 644 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER g 649 " --> pdb=" O LEU g 645 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 46 through 53 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 59 through 61 current: chain 'H' and resid 121 through 122 Processing sheet with id=AA3, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.521A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.765A pdb=" N PHE L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 494 through 499 removed outlier: 5.456A pdb=" N VAL c 608 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N VAL b 38 " --> pdb=" O THR c 606 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N THR c 606 " --> pdb=" O VAL b 38 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N TYR b 40 " --> pdb=" O CYS c 604 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N CYS c 604 " --> pdb=" O TYR b 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 45 through 47 removed outlier: 4.681A pdb=" N VAL b 242 " --> pdb=" O LEU b 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'b' and resid 91 through 94 Processing sheet with id=AB1, first strand: chain 'b' and resid 169 through 177 Processing sheet with id=AB2, first strand: chain 'b' and resid 202 through 203 removed outlier: 6.340A pdb=" N THR b 202 " --> pdb=" O TYR b 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 259 through 261 current: chain 'b' and resid 284 through 298 removed outlier: 3.642A pdb=" N HIS b 330 " --> pdb=" O ILE b 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 330 through 333 current: chain 'b' and resid 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 382 through 385 current: chain 'b' and resid 465 through 470 Processing sheet with id=AB4, first strand: chain 'b' and resid 301 through 312 removed outlier: 7.142A pdb=" N ASN b 301 " --> pdb=" O ILE b 323 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE b 323 " --> pdb=" O ASN b 301 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR b 303 " --> pdb=" O GLY b 321 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLN b 315 " --> pdb=" O ILE b 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'd' and resid 495 through 499 removed outlier: 5.589A pdb=" N VAL e 608 " --> pdb=" O VAL d 36 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL d 38 " --> pdb=" O THR e 606 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N THR e 606 " --> pdb=" O VAL d 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'd' and resid 45 through 47 Processing sheet with id=AB7, first strand: chain 'd' and resid 75 through 76 removed outlier: 3.552A pdb=" N VAL d 75 " --> pdb=" O CYS d 54 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'd' and resid 66 through 67 removed outlier: 7.209A pdb=" N HIS d 66 " --> pdb=" O SER d 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'd' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'd' and resid 169 through 177 Processing sheet with id=AC2, first strand: chain 'd' and resid 202 through 203 removed outlier: 6.588A pdb=" N THR d 202 " --> pdb=" O TYR d 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'd' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 259 through 261 current: chain 'd' and resid 284 through 298 removed outlier: 3.539A pdb=" N HIS d 330 " --> pdb=" O ILE d 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 330 through 333 current: chain 'd' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 381 through 385 current: chain 'd' and resid 465 through 470 Processing sheet with id=AC4, first strand: chain 'd' and resid 302 through 312 removed outlier: 6.404A pdb=" N THR d 303 " --> pdb=" O GLY d 321 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLN d 315 " --> pdb=" O ILE d 309 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'f' and resid 495 through 499 removed outlier: 5.399A pdb=" N VAL g 608 " --> pdb=" O VAL f 36 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL f 38 " --> pdb=" O THR g 606 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR g 606 " --> pdb=" O VAL f 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'f' and resid 45 through 47 Processing sheet with id=AC7, first strand: chain 'f' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'f' and resid 91 through 94 Processing sheet with id=AC9, first strand: chain 'f' and resid 169 through 177 Processing sheet with id=AD1, first strand: chain 'f' and resid 202 through 203 removed outlier: 6.509A pdb=" N THR f 202 " --> pdb=" O TYR f 435 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'f' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 259 through 261 current: chain 'f' and resid 284 through 312 removed outlier: 6.868A pdb=" N ASN f 301 " --> pdb=" O ILE f 323 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE f 323 " --> pdb=" O ASN f 301 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR f 303 " --> pdb=" O GLY f 321 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLN f 315 " --> pdb=" O ILE f 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 315 through 323A current: chain 'f' and resid 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 382 through 385 current: chain 'f' and resid 465 through 470 458 hydrogen bonds defined for protein. 1257 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: 2.86 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5212 1.34 - 1.47: 4570 1.47 - 1.59: 7696 1.59 - 1.72: 3 1.72 - 1.84: 138 Bond restraints: 17619 Sorted by residual: bond pdb=" C ASP d 368 " pdb=" O ASP d 368 " ideal model delta sigma weight residual 1.234 1.302 -0.068 1.09e-02 8.42e+03 3.86e+01 bond pdb=" N ILE d 371 " pdb=" CA ILE d 371 " ideal model delta sigma weight residual 1.456 1.495 -0.038 9.50e-03 1.11e+04 1.61e+01 bond pdb=" CA SER d 364 " pdb=" CB SER d 364 " ideal model delta sigma weight residual 1.530 1.478 0.053 1.66e-02 3.63e+03 1.00e+01 bond pdb=" N LEU g 566 " pdb=" CA LEU g 566 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.25e-02 6.40e+03 9.27e+00 bond pdb=" CA SER d 199 " pdb=" CB SER d 199 " ideal model delta sigma weight residual 1.531 1.481 0.050 1.67e-02 3.59e+03 9.04e+00 ... (remaining 17614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 23319 2.67 - 5.34: 548 5.34 - 8.02: 41 8.02 - 10.69: 2 10.69 - 13.36: 2 Bond angle restraints: 23912 Sorted by residual: angle pdb=" CA ASP d 368 " pdb=" C ASP d 368 " pdb=" O ASP d 368 " ideal model delta sigma weight residual 121.28 113.02 8.26 1.07e+00 8.73e-01 5.96e+01 angle pdb=" C ASN d 197 " pdb=" CA ASN d 197 " pdb=" CB ASN d 197 " ideal model delta sigma weight residual 110.42 123.78 -13.36 1.99e+00 2.53e-01 4.51e+01 angle pdb=" N ILE d 371 " pdb=" CA ILE d 371 " pdb=" C ILE d 371 " ideal model delta sigma weight residual 113.53 106.98 6.55 9.80e-01 1.04e+00 4.47e+01 angle pdb=" O ASP d 368 " pdb=" C ASP d 368 " pdb=" N LEU d 369 " ideal model delta sigma weight residual 123.29 128.94 -5.65 1.00e+00 1.00e+00 3.19e+01 angle pdb=" CA ASN d 197 " pdb=" CB ASN d 197 " pdb=" CG ASN d 197 " ideal model delta sigma weight residual 112.60 118.17 -5.57 1.00e+00 1.00e+00 3.10e+01 ... (remaining 23907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.15: 11434 21.15 - 42.30: 587 42.30 - 63.45: 160 63.45 - 84.60: 63 84.60 - 105.75: 19 Dihedral angle restraints: 12263 sinusoidal: 6615 harmonic: 5648 Sorted by residual: dihedral pdb=" CB CYS b 126 " pdb=" SG CYS b 126 " pdb=" SG CYS b 196 " pdb=" CB CYS b 196 " ideal model delta sinusoidal sigma weight residual 93.00 159.57 -66.57 1 1.00e+01 1.00e-02 5.78e+01 dihedral pdb=" CB CYS f 126 " pdb=" SG CYS f 126 " pdb=" SG CYS f 196 " pdb=" CB CYS f 196 " ideal model delta sinusoidal sigma weight residual 93.00 155.89 -62.89 1 1.00e+01 1.00e-02 5.23e+01 dihedral pdb=" CB CYS d 54 " pdb=" SG CYS d 54 " pdb=" SG CYS d 74 " pdb=" CB CYS d 74 " ideal model delta sinusoidal sigma weight residual -86.00 -25.90 -60.10 1 1.00e+01 1.00e-02 4.81e+01 ... (remaining 12260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 3012 0.184 - 0.367: 28 0.367 - 0.550: 3 0.550 - 0.734: 1 0.734 - 0.917: 2 Chirality restraints: 3046 Sorted by residual: chirality pdb=" C1 NAG w 2 " pdb=" O4 NAG w 1 " pdb=" C2 NAG w 2 " pdb=" O5 NAG w 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-02 2.50e+03 1.29e+03 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-02 2.50e+03 5.31e+02 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-02 2.50e+03 5.04e+02 ... (remaining 3043 not shown) Planarity restraints: 2925 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 606 " 0.283 2.00e-02 2.50e+03 2.43e-01 7.37e+02 pdb=" C7 NAG f 606 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG f 606 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG f 606 " -0.426 2.00e-02 2.50e+03 pdb=" O7 NAG f 606 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " 0.160 2.00e-02 2.50e+03 1.32e-01 2.16e+02 pdb=" C7 NAG M 1 " -0.042 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " 0.118 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " -0.211 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 2 " -0.138 2.00e-02 2.50e+03 1.13e-01 1.61e+02 pdb=" C7 NAG P 2 " 0.042 2.00e-02 2.50e+03 pdb=" C8 NAG P 2 " -0.105 2.00e-02 2.50e+03 pdb=" N2 NAG P 2 " 0.179 2.00e-02 2.50e+03 pdb=" O7 NAG P 2 " 0.022 2.00e-02 2.50e+03 ... (remaining 2922 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 91 2.56 - 3.15: 14166 3.15 - 3.73: 25235 3.73 - 4.32: 36056 4.32 - 4.90: 59990 Nonbonded interactions: 135538 Sorted by model distance: nonbonded pdb=" O ASP d 368 " pdb=" OG1 THR d 372 " model vdw 1.978 3.040 nonbonded pdb=" OG1 THR d 303 " pdb=" OD1 ASP d 322 " model vdw 2.120 3.040 nonbonded pdb=" OD1 ASP b 322 " pdb=" N ILE b 323 " model vdw 2.174 3.120 nonbonded pdb=" OD1 ASP f 322 " pdb=" N ILE f 323 " model vdw 2.207 3.120 nonbonded pdb=" ND2 ASN d 195 " pdb=" CG2 ILE d 423 " model vdw 2.250 3.540 ... (remaining 135533 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'w' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'R' selection = chain 'X' selection = chain 'k' selection = chain 'm' selection = chain 'p' } ncs_group { reference = chain 'C' selection = chain 'v' } ncs_group { reference = chain 'E' selection = chain 'S' selection = chain 'l' } ncs_group { reference = chain 'b' selection = (chain 'd' and resid 33 through 606) selection = chain 'f' } ncs_group { reference = chain 'c' selection = chain 'e' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.790 Find NCS groups from input model: 0.470 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: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.229 17785 Z= 0.277 Angle : 1.059 17.236 24372 Z= 0.539 Chirality : 0.061 0.917 3046 Planarity : 0.008 0.243 2857 Dihedral : 14.280 105.752 8499 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.75 % Allowed : 8.57 % Favored : 90.68 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.18), residues: 1908 helix: -0.37 (0.26), residues: 396 sheet: -0.61 (0.26), residues: 388 loop : -1.05 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 18 TYR 0.010 0.001 TYR d 302 PHE 0.018 0.001 PHE L 98 TRP 0.036 0.002 TRP g 631 HIS 0.005 0.001 HIS b 216 Details of bonding type rmsd covalent geometry : bond 0.00472 (17619) covalent geometry : angle 0.91525 (23912) SS BOND : bond 0.03765 ( 38) SS BOND : angle 1.94786 ( 76) hydrogen bonds : bond 0.22767 ( 458) hydrogen bonds : angle 8.02110 ( 1257) link_ALPHA1-3 : bond 0.04234 ( 5) link_ALPHA1-3 : angle 5.06915 ( 15) link_ALPHA1-6 : bond 0.02760 ( 2) link_ALPHA1-6 : angle 3.16031 ( 6) link_BETA1-4 : bond 0.02328 ( 53) link_BETA1-4 : angle 4.90173 ( 159) link_NAG-ASN : bond 0.00690 ( 68) link_NAG-ASN : angle 3.67483 ( 204) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.544 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: H 95 TYR cc_start: 0.7649 (m-80) cc_final: 0.7355 (m-10) REVERT: L 103 LYS cc_start: 0.7352 (tttt) cc_final: 0.7075 (ttpp) REVERT: c 655 LYS cc_start: 0.8004 (tttp) cc_final: 0.7692 (tptt) REVERT: d 320 MET cc_start: 0.8873 (mpp) cc_final: 0.8452 (mtm) REVERT: d 477 ASP cc_start: 0.8855 (m-30) cc_final: 0.8538 (m-30) REVERT: d 491 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8515 (pp) REVERT: f 475 MET cc_start: 0.8640 (tpp) cc_final: 0.8362 (tpp) REVERT: g 584 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8931 (mt-10) REVERT: g 624 ASN cc_start: 0.9222 (m-40) cc_final: 0.8936 (m-40) REVERT: g 655 LYS cc_start: 0.7799 (tmtm) cc_final: 0.7588 (ttpt) outliers start: 13 outliers final: 11 residues processed: 158 average time/residue: 0.1403 time to fit residues: 33.2003 Evaluate side-chains 116 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain b residue 339 ASN Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 339 ASN Chi-restraints excluded: chain d residue 364 SER Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 339 ASN Chi-restraints excluded: chain f residue 463 ASN Chi-restraints excluded: chain g residue 539 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.5980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100 GLN L 79 GLN b 195 ASN ** b 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 66 HIS d 425 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.074548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.056384 restraints weight = 54904.151| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 4.39 r_work: 0.2961 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 17785 Z= 0.199 Angle : 0.794 17.011 24372 Z= 0.353 Chirality : 0.048 0.286 3046 Planarity : 0.004 0.035 2857 Dihedral : 9.880 73.892 4812 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.03 % Allowed : 8.80 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.18), residues: 1908 helix: 0.32 (0.27), residues: 387 sheet: -0.51 (0.23), residues: 463 loop : -0.75 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 520 TYR 0.013 0.001 TYR H 116 PHE 0.013 0.002 PHE H 119 TRP 0.013 0.002 TRP b 96 HIS 0.004 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00471 (17619) covalent geometry : angle 0.69572 (23912) SS BOND : bond 0.00372 ( 38) SS BOND : angle 0.99152 ( 76) hydrogen bonds : bond 0.04990 ( 458) hydrogen bonds : angle 5.65330 ( 1257) link_ALPHA1-3 : bond 0.01413 ( 5) link_ALPHA1-3 : angle 1.99781 ( 15) link_ALPHA1-6 : bond 0.00430 ( 2) link_ALPHA1-6 : angle 1.54254 ( 6) link_BETA1-4 : bond 0.00711 ( 53) link_BETA1-4 : angle 3.21502 ( 159) link_NAG-ASN : bond 0.00407 ( 68) link_NAG-ASN : angle 3.13901 ( 204) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 61 ARG cc_start: 0.7481 (ptt180) cc_final: 0.7069 (ptt180) REVERT: L 79 GLN cc_start: 0.8313 (mp10) cc_final: 0.7655 (mp10) REVERT: L 103 LYS cc_start: 0.7384 (tttt) cc_final: 0.7020 (ttpp) REVERT: b 100 MET cc_start: 0.9242 (mtp) cc_final: 0.9022 (mtm) REVERT: c 617 LYS cc_start: 0.9214 (mttp) cc_final: 0.8973 (mtpt) REVERT: c 621 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8925 (pp20) REVERT: d 320 MET cc_start: 0.8847 (mpp) cc_final: 0.8449 (mtm) REVERT: d 355 ASN cc_start: 0.6402 (p0) cc_final: 0.6078 (m110) REVERT: d 467 THR cc_start: 0.7784 (OUTLIER) cc_final: 0.7470 (p) REVERT: d 477 ASP cc_start: 0.8847 (m-30) cc_final: 0.8554 (m-30) REVERT: e 617 LYS cc_start: 0.9310 (mttm) cc_final: 0.8940 (mttt) REVERT: e 657 GLU cc_start: 0.8516 (tt0) cc_final: 0.8085 (tm-30) REVERT: g 584 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8889 (mt-10) REVERT: g 624 ASN cc_start: 0.9280 (m-40) cc_final: 0.8949 (m-40) REVERT: g 653 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8304 (tm-30) outliers start: 35 outliers final: 21 residues processed: 145 average time/residue: 0.1312 time to fit residues: 29.9538 Evaluate side-chains 129 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain b residue 194 ILE Chi-restraints excluded: chain b residue 248 THR Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain c residue 621 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 364 SER Chi-restraints excluded: chain d residue 467 THR Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain e residue 606 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 21 optimal weight: 0.0000 chunk 162 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 139 optimal weight: 0.4980 chunk 47 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN b 195 ASN ** b 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.075548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.057404 restraints weight = 55166.438| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 4.40 r_work: 0.2988 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17785 Z= 0.108 Angle : 0.691 16.016 24372 Z= 0.303 Chirality : 0.046 0.287 3046 Planarity : 0.003 0.040 2857 Dihedral : 8.957 66.541 4798 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.62 % Allowed : 9.73 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.47 (0.19), residues: 1908 helix: 0.57 (0.27), residues: 387 sheet: -0.34 (0.23), residues: 463 loop : -0.57 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 520 TYR 0.008 0.001 TYR f 191 PHE 0.008 0.001 PHE f 53 TRP 0.019 0.001 TRP g 631 HIS 0.003 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00234 (17619) covalent geometry : angle 0.59700 (23912) SS BOND : bond 0.00214 ( 38) SS BOND : angle 0.68909 ( 76) hydrogen bonds : bond 0.03976 ( 458) hydrogen bonds : angle 5.13957 ( 1257) link_ALPHA1-3 : bond 0.01386 ( 5) link_ALPHA1-3 : angle 2.02560 ( 15) link_ALPHA1-6 : bond 0.00572 ( 2) link_ALPHA1-6 : angle 1.74742 ( 6) link_BETA1-4 : bond 0.00665 ( 53) link_BETA1-4 : angle 2.90365 ( 159) link_NAG-ASN : bond 0.00378 ( 68) link_NAG-ASN : angle 2.84290 ( 204) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 51 GLU cc_start: 0.8476 (pt0) cc_final: 0.8275 (pt0) REVERT: H 66 LYS cc_start: 0.5169 (pttt) cc_final: 0.4964 (ttpp) REVERT: L 39 LYS cc_start: 0.6311 (tptt) cc_final: 0.6014 (tptt) REVERT: L 61 ARG cc_start: 0.7389 (ptt180) cc_final: 0.7053 (ptt180) REVERT: L 79 GLN cc_start: 0.8211 (mp10) cc_final: 0.7729 (mp10) REVERT: L 103 LYS cc_start: 0.7406 (tttt) cc_final: 0.7028 (ttpp) REVERT: c 617 LYS cc_start: 0.9228 (mttp) cc_final: 0.8927 (mtpt) REVERT: c 621 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8927 (pp20) REVERT: d 320 MET cc_start: 0.8803 (mpp) cc_final: 0.8440 (mtm) REVERT: d 477 ASP cc_start: 0.8804 (m-30) cc_final: 0.8517 (m-30) REVERT: e 617 LYS cc_start: 0.9294 (mttm) cc_final: 0.9038 (mttt) REVERT: e 657 GLU cc_start: 0.8427 (tt0) cc_final: 0.8025 (tm-30) REVERT: g 584 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8925 (mt-10) REVERT: g 653 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8234 (tm-30) REVERT: g 654 GLU cc_start: 0.7372 (tt0) cc_final: 0.7163 (tt0) outliers start: 28 outliers final: 18 residues processed: 140 average time/residue: 0.1269 time to fit residues: 27.7921 Evaluate side-chains 125 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 194 ILE Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain c residue 621 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 606 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 445 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 150 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 330 HIS f 130 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.072863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.054368 restraints weight = 55789.771| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 4.43 r_work: 0.2907 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 17785 Z= 0.231 Angle : 0.761 16.189 24372 Z= 0.340 Chirality : 0.048 0.282 3046 Planarity : 0.004 0.039 2857 Dihedral : 8.759 59.935 4795 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.55 % Allowed : 10.77 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.19), residues: 1908 helix: 0.47 (0.27), residues: 387 sheet: -0.51 (0.23), residues: 509 loop : -0.56 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 476 TYR 0.013 0.002 TYR f 191 PHE 0.018 0.002 PHE H 119 TRP 0.016 0.002 TRP H 34 HIS 0.004 0.001 HIS f 374 Details of bonding type rmsd covalent geometry : bond 0.00552 (17619) covalent geometry : angle 0.67516 (23912) SS BOND : bond 0.00344 ( 38) SS BOND : angle 0.91631 ( 76) hydrogen bonds : bond 0.04101 ( 458) hydrogen bonds : angle 5.03374 ( 1257) link_ALPHA1-3 : bond 0.01199 ( 5) link_ALPHA1-3 : angle 2.21697 ( 15) link_ALPHA1-6 : bond 0.00558 ( 2) link_ALPHA1-6 : angle 1.73235 ( 6) link_BETA1-4 : bond 0.00643 ( 53) link_BETA1-4 : angle 2.81280 ( 159) link_NAG-ASN : bond 0.00412 ( 68) link_NAG-ASN : angle 2.96547 ( 204) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 107 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 51 GLU cc_start: 0.8388 (pt0) cc_final: 0.8185 (pt0) REVERT: H 66 LYS cc_start: 0.5296 (pttt) cc_final: 0.5089 (ttpp) REVERT: L 79 GLN cc_start: 0.8176 (mp10) cc_final: 0.7708 (mp10) REVERT: L 103 LYS cc_start: 0.7387 (tttt) cc_final: 0.7033 (ttpp) REVERT: b 426 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7530 (tpp) REVERT: c 617 LYS cc_start: 0.9293 (mttp) cc_final: 0.8793 (mtpt) REVERT: c 621 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8968 (pp20) REVERT: d 320 MET cc_start: 0.8892 (mpp) cc_final: 0.8573 (mtm) REVERT: e 617 LYS cc_start: 0.9313 (mttm) cc_final: 0.8909 (mttt) REVERT: e 657 GLU cc_start: 0.8347 (tt0) cc_final: 0.7945 (tm-30) REVERT: g 653 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8175 (tm-30) outliers start: 44 outliers final: 29 residues processed: 140 average time/residue: 0.1163 time to fit residues: 26.1296 Evaluate side-chains 128 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 194 ILE Chi-restraints excluded: chain b residue 248 THR Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 426 MET Chi-restraints excluded: chain c residue 621 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 184 ILE Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain e residue 606 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 491 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 158 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 40 GLN ** b 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 540 GLN ** 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 = 0.3534 r_free = 0.3534 target = 0.073882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.055428 restraints weight = 54741.117| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 4.43 r_work: 0.2941 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17785 Z= 0.138 Angle : 0.684 15.844 24372 Z= 0.303 Chirality : 0.046 0.297 3046 Planarity : 0.003 0.040 2857 Dihedral : 8.425 59.349 4795 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.37 % Allowed : 11.18 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.19), residues: 1908 helix: 0.70 (0.28), residues: 384 sheet: -0.30 (0.23), residues: 472 loop : -0.55 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e 520 TYR 0.009 0.001 TYR f 191 PHE 0.010 0.001 PHE H 119 TRP 0.021 0.001 TRP c 631 HIS 0.002 0.001 HIS d 374 Details of bonding type rmsd covalent geometry : bond 0.00319 (17619) covalent geometry : angle 0.59716 (23912) SS BOND : bond 0.00235 ( 38) SS BOND : angle 0.75957 ( 76) hydrogen bonds : bond 0.03657 ( 458) hydrogen bonds : angle 4.83408 ( 1257) link_ALPHA1-3 : bond 0.01284 ( 5) link_ALPHA1-3 : angle 2.25811 ( 15) link_ALPHA1-6 : bond 0.00682 ( 2) link_ALPHA1-6 : angle 1.82361 ( 6) link_BETA1-4 : bond 0.00636 ( 53) link_BETA1-4 : angle 2.70614 ( 159) link_NAG-ASN : bond 0.00327 ( 68) link_NAG-ASN : angle 2.77857 ( 204) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 79 GLN cc_start: 0.8117 (mp10) cc_final: 0.7906 (mp10) REVERT: L 103 LYS cc_start: 0.7313 (tttt) cc_final: 0.6963 (ttpp) REVERT: b 161 MET cc_start: 0.8719 (tpp) cc_final: 0.7711 (tpp) REVERT: c 617 LYS cc_start: 0.9365 (mttp) cc_final: 0.8742 (mtpt) REVERT: d 320 MET cc_start: 0.8832 (mpp) cc_final: 0.8498 (mtm) REVERT: d 426 MET cc_start: 0.8603 (mmm) cc_final: 0.7932 (tmm) REVERT: e 617 LYS cc_start: 0.9289 (mttm) cc_final: 0.8943 (mttt) REVERT: e 657 GLU cc_start: 0.8216 (tt0) cc_final: 0.7847 (tm-30) REVERT: g 584 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8636 (mp0) REVERT: g 653 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8202 (tm-30) outliers start: 41 outliers final: 26 residues processed: 137 average time/residue: 0.1273 time to fit residues: 27.3185 Evaluate side-chains 124 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 194 ILE Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 184 ILE Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 606 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 445 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 31 optimal weight: 0.3980 chunk 163 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.074120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.055774 restraints weight = 54627.734| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 4.41 r_work: 0.2951 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17785 Z= 0.127 Angle : 0.667 15.637 24372 Z= 0.294 Chirality : 0.046 0.308 3046 Planarity : 0.003 0.039 2857 Dihedral : 8.141 59.124 4795 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.26 % Allowed : 11.58 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.19), residues: 1908 helix: 0.83 (0.28), residues: 384 sheet: -0.29 (0.23), residues: 503 loop : -0.43 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.008 0.001 TYR L 49 PHE 0.010 0.001 PHE b 317 TRP 0.018 0.001 TRP c 631 HIS 0.003 0.001 HIS d 374 Details of bonding type rmsd covalent geometry : bond 0.00293 (17619) covalent geometry : angle 0.58250 (23912) SS BOND : bond 0.00219 ( 38) SS BOND : angle 0.69461 ( 76) hydrogen bonds : bond 0.03424 ( 458) hydrogen bonds : angle 4.71217 ( 1257) link_ALPHA1-3 : bond 0.01238 ( 5) link_ALPHA1-3 : angle 2.18188 ( 15) link_ALPHA1-6 : bond 0.00749 ( 2) link_ALPHA1-6 : angle 1.74348 ( 6) link_BETA1-4 : bond 0.00632 ( 53) link_BETA1-4 : angle 2.63486 ( 159) link_NAG-ASN : bond 0.00324 ( 68) link_NAG-ASN : angle 2.69917 ( 204) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 44 LYS cc_start: 0.4967 (mtpp) cc_final: 0.4716 (mtpt) REVERT: H 74 ASP cc_start: 0.8613 (t0) cc_final: 0.8404 (t0) REVERT: H 77 GLU cc_start: 0.7819 (pm20) cc_final: 0.7583 (pm20) REVERT: L 61 ARG cc_start: 0.7061 (ptt180) cc_final: 0.6640 (ptt180) REVERT: L 79 GLN cc_start: 0.8219 (mp10) cc_final: 0.7635 (mp10) REVERT: L 103 LYS cc_start: 0.7305 (tttt) cc_final: 0.6968 (ttpp) REVERT: b 104 MET cc_start: 0.9123 (ttt) cc_final: 0.8797 (ttt) REVERT: b 475 MET cc_start: 0.8457 (mmt) cc_final: 0.8182 (mmt) REVERT: d 320 MET cc_start: 0.8819 (mpp) cc_final: 0.8504 (mtm) REVERT: d 426 MET cc_start: 0.8600 (mmm) cc_final: 0.7945 (tmm) REVERT: e 617 LYS cc_start: 0.9270 (mttm) cc_final: 0.8976 (mttt) REVERT: e 657 GLU cc_start: 0.8179 (tt0) cc_final: 0.7829 (tm-30) REVERT: g 584 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8652 (mp0) REVERT: g 653 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8205 (tm-30) outliers start: 39 outliers final: 30 residues processed: 135 average time/residue: 0.1183 time to fit residues: 25.1461 Evaluate side-chains 123 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 193 LEU Chi-restraints excluded: chain b residue 194 ILE Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 544 LEU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 184 ILE Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 606 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 0.0020 chunk 130 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 92 optimal weight: 0.0670 chunk 93 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 overall best weight: 0.5528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.075192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.057077 restraints weight = 54127.996| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 4.37 r_work: 0.2985 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17785 Z= 0.097 Angle : 0.636 15.423 24372 Z= 0.280 Chirality : 0.045 0.322 3046 Planarity : 0.003 0.041 2857 Dihedral : 7.792 59.060 4795 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.03 % Allowed : 12.28 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.19), residues: 1908 helix: 1.04 (0.29), residues: 384 sheet: -0.15 (0.24), residues: 493 loop : -0.39 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.006 0.001 TYR g 643 PHE 0.009 0.001 PHE d 223 TRP 0.016 0.001 TRP c 631 HIS 0.003 0.000 HIS d 374 Details of bonding type rmsd covalent geometry : bond 0.00208 (17619) covalent geometry : angle 0.55478 (23912) SS BOND : bond 0.00174 ( 38) SS BOND : angle 0.62400 ( 76) hydrogen bonds : bond 0.03037 ( 458) hydrogen bonds : angle 4.58887 ( 1257) link_ALPHA1-3 : bond 0.01218 ( 5) link_ALPHA1-3 : angle 2.01676 ( 15) link_ALPHA1-6 : bond 0.00963 ( 2) link_ALPHA1-6 : angle 1.44033 ( 6) link_BETA1-4 : bond 0.00649 ( 53) link_BETA1-4 : angle 2.54954 ( 159) link_NAG-ASN : bond 0.00328 ( 68) link_NAG-ASN : angle 2.58530 ( 204) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.612 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: H 44 LYS cc_start: 0.5056 (mtpp) cc_final: 0.4849 (mtpt) REVERT: H 66 LYS cc_start: 0.5355 (pttt) cc_final: 0.5145 (ttpp) REVERT: L 79 GLN cc_start: 0.8269 (mp10) cc_final: 0.7937 (mp10) REVERT: L 103 LYS cc_start: 0.7384 (tttt) cc_final: 0.7011 (ttpp) REVERT: b 104 MET cc_start: 0.9164 (ttt) cc_final: 0.8806 (ttt) REVERT: c 644 ARG cc_start: 0.8639 (mmp80) cc_final: 0.8213 (mmt180) REVERT: d 320 MET cc_start: 0.8748 (mpp) cc_final: 0.8452 (mtm) REVERT: d 426 MET cc_start: 0.8549 (mmm) cc_final: 0.7962 (tmm) REVERT: d 477 ASP cc_start: 0.8831 (m-30) cc_final: 0.8573 (m-30) REVERT: e 617 LYS cc_start: 0.9282 (mttm) cc_final: 0.8989 (mttt) REVERT: e 626 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8604 (ttm) REVERT: e 657 GLU cc_start: 0.8112 (tt0) cc_final: 0.7814 (tm-30) REVERT: g 653 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8269 (tm-30) outliers start: 35 outliers final: 30 residues processed: 132 average time/residue: 0.1227 time to fit residues: 25.7034 Evaluate side-chains 130 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 193 LEU Chi-restraints excluded: chain b residue 194 ILE Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 544 LEU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 184 ILE Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 339 ASN Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 606 THR Chi-restraints excluded: chain e residue 626 MET Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 194 ILE Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 434 MET Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 84 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 123 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 174 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.074912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.056635 restraints weight = 54515.948| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.41 r_work: 0.2972 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17785 Z= 0.110 Angle : 0.639 15.334 24372 Z= 0.284 Chirality : 0.045 0.320 3046 Planarity : 0.003 0.042 2857 Dihedral : 7.728 58.447 4795 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.03 % Allowed : 12.39 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.19), residues: 1908 helix: 1.05 (0.29), residues: 384 sheet: -0.09 (0.24), residues: 493 loop : -0.34 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.006 0.001 TYR L 49 PHE 0.008 0.001 PHE b 317 TRP 0.014 0.001 TRP c 631 HIS 0.003 0.001 HIS d 374 Details of bonding type rmsd covalent geometry : bond 0.00247 (17619) covalent geometry : angle 0.56002 (23912) SS BOND : bond 0.00189 ( 38) SS BOND : angle 0.63883 ( 76) hydrogen bonds : bond 0.03100 ( 458) hydrogen bonds : angle 4.53846 ( 1257) link_ALPHA1-3 : bond 0.01108 ( 5) link_ALPHA1-3 : angle 1.97451 ( 15) link_ALPHA1-6 : bond 0.00858 ( 2) link_ALPHA1-6 : angle 1.46084 ( 6) link_BETA1-4 : bond 0.00633 ( 53) link_BETA1-4 : angle 2.51206 ( 159) link_NAG-ASN : bond 0.00320 ( 68) link_NAG-ASN : angle 2.57855 ( 204) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 103 time to evaluate : 0.682 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: L 79 GLN cc_start: 0.8260 (mp10) cc_final: 0.8040 (mp10) REVERT: L 103 LYS cc_start: 0.7333 (tttt) cc_final: 0.6956 (ttpp) REVERT: b 104 MET cc_start: 0.9118 (ttt) cc_final: 0.8747 (ttt) REVERT: b 161 MET cc_start: 0.8455 (tpp) cc_final: 0.7790 (tpp) REVERT: c 617 LYS cc_start: 0.9360 (mtpt) cc_final: 0.9105 (mtpt) REVERT: c 644 ARG cc_start: 0.8660 (mmp80) cc_final: 0.8239 (mmt180) REVERT: d 320 MET cc_start: 0.8740 (mpp) cc_final: 0.8463 (mtm) REVERT: d 426 MET cc_start: 0.8601 (mmm) cc_final: 0.7966 (tmm) REVERT: d 477 ASP cc_start: 0.8891 (m-30) cc_final: 0.8592 (m-30) REVERT: e 617 LYS cc_start: 0.9280 (mttm) cc_final: 0.8912 (mttt) REVERT: e 657 GLU cc_start: 0.8094 (tt0) cc_final: 0.7802 (tm-30) REVERT: g 653 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8248 (tm-30) outliers start: 35 outliers final: 31 residues processed: 129 average time/residue: 0.1131 time to fit residues: 23.3394 Evaluate side-chains 126 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 193 LEU Chi-restraints excluded: chain b residue 194 ILE Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 544 LEU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 184 ILE Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 339 ASN Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 606 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 491 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 171 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 82 GLN ** g 540 GLN ** 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 = 0.3531 r_free = 0.3531 target = 0.073704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.055392 restraints weight = 54811.836| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 4.41 r_work: 0.2940 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17785 Z= 0.155 Angle : 0.666 15.292 24372 Z= 0.298 Chirality : 0.045 0.311 3046 Planarity : 0.003 0.041 2857 Dihedral : 7.771 59.255 4795 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.20 % Allowed : 12.39 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.04 (0.19), residues: 1908 helix: 1.02 (0.28), residues: 384 sheet: 0.04 (0.24), residues: 461 loop : -0.38 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG d 166 TYR 0.008 0.001 TYR H 116 PHE 0.011 0.001 PHE b 317 TRP 0.013 0.001 TRP e 631 HIS 0.003 0.001 HIS d 374 Details of bonding type rmsd covalent geometry : bond 0.00363 (17619) covalent geometry : angle 0.58796 (23912) SS BOND : bond 0.00244 ( 38) SS BOND : angle 0.73465 ( 76) hydrogen bonds : bond 0.03253 ( 458) hydrogen bonds : angle 4.59816 ( 1257) link_ALPHA1-3 : bond 0.01008 ( 5) link_ALPHA1-3 : angle 1.97688 ( 15) link_ALPHA1-6 : bond 0.00828 ( 2) link_ALPHA1-6 : angle 1.42672 ( 6) link_BETA1-4 : bond 0.00617 ( 53) link_BETA1-4 : angle 2.50848 ( 159) link_NAG-ASN : bond 0.00337 ( 68) link_NAG-ASN : angle 2.63463 ( 204) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 0.621 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: L 61 ARG cc_start: 0.7000 (ptt180) cc_final: 0.6734 (ptt180) REVERT: L 79 GLN cc_start: 0.8269 (mp10) cc_final: 0.7855 (mp10) REVERT: L 103 LYS cc_start: 0.7326 (tttt) cc_final: 0.6948 (ttpp) REVERT: b 104 MET cc_start: 0.9117 (ttt) cc_final: 0.8734 (ttt) REVERT: b 161 MET cc_start: 0.8495 (tpp) cc_final: 0.7863 (tpp) REVERT: c 617 LYS cc_start: 0.9361 (mtpt) cc_final: 0.9036 (mttt) REVERT: c 644 ARG cc_start: 0.8675 (mmp80) cc_final: 0.8261 (mmt180) REVERT: d 320 MET cc_start: 0.8775 (mpp) cc_final: 0.8503 (mtm) REVERT: d 426 MET cc_start: 0.8691 (mmm) cc_final: 0.7991 (tmm) REVERT: e 617 LYS cc_start: 0.9275 (mttm) cc_final: 0.8859 (mttt) REVERT: e 657 GLU cc_start: 0.8099 (tt0) cc_final: 0.7797 (tm-30) REVERT: g 653 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8196 (tm-30) outliers start: 38 outliers final: 34 residues processed: 132 average time/residue: 0.1313 time to fit residues: 27.4050 Evaluate side-chains 133 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 193 LEU Chi-restraints excluded: chain b residue 194 ILE Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 544 LEU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 184 ILE Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 339 ASN Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 606 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 194 ILE Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 434 MET Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 491 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 6 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 40 GLN ** b 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 540 GLN ** 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 = 0.3528 r_free = 0.3528 target = 0.073512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.055043 restraints weight = 54649.759| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 4.45 r_work: 0.2931 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17785 Z= 0.164 Angle : 0.679 15.400 24372 Z= 0.306 Chirality : 0.046 0.312 3046 Planarity : 0.003 0.041 2857 Dihedral : 7.800 59.669 4795 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.91 % Allowed : 12.91 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.09 (0.19), residues: 1908 helix: 0.95 (0.28), residues: 384 sheet: 0.03 (0.24), residues: 461 loop : -0.42 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG e 520 TYR 0.009 0.001 TYR f 191 PHE 0.011 0.001 PHE b 317 TRP 0.014 0.001 TRP b 96 HIS 0.004 0.001 HIS d 374 Details of bonding type rmsd covalent geometry : bond 0.00384 (17619) covalent geometry : angle 0.60232 (23912) SS BOND : bond 0.00257 ( 38) SS BOND : angle 0.76073 ( 76) hydrogen bonds : bond 0.03375 ( 458) hydrogen bonds : angle 4.62370 ( 1257) link_ALPHA1-3 : bond 0.00943 ( 5) link_ALPHA1-3 : angle 1.97367 ( 15) link_ALPHA1-6 : bond 0.00807 ( 2) link_ALPHA1-6 : angle 1.40478 ( 6) link_BETA1-4 : bond 0.00608 ( 53) link_BETA1-4 : angle 2.49325 ( 159) link_NAG-ASN : bond 0.00333 ( 68) link_NAG-ASN : angle 2.66108 ( 204) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.600 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: L 79 GLN cc_start: 0.8205 (mp10) cc_final: 0.7775 (mp10) REVERT: L 103 LYS cc_start: 0.7375 (tttt) cc_final: 0.6987 (ttpp) REVERT: b 104 MET cc_start: 0.9128 (ttt) cc_final: 0.8727 (ttt) REVERT: b 161 MET cc_start: 0.8485 (tpp) cc_final: 0.7900 (tpp) REVERT: c 617 LYS cc_start: 0.9374 (mtpt) cc_final: 0.9052 (mttt) REVERT: c 644 ARG cc_start: 0.8701 (mmp80) cc_final: 0.8288 (mmt180) REVERT: c 655 LYS cc_start: 0.8014 (tptm) cc_final: 0.7705 (tptm) REVERT: d 320 MET cc_start: 0.8810 (mpp) cc_final: 0.8561 (mtm) REVERT: d 426 MET cc_start: 0.8668 (mmm) cc_final: 0.7987 (tmm) REVERT: e 657 GLU cc_start: 0.8135 (tt0) cc_final: 0.7813 (tm-30) REVERT: g 653 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8227 (tm-30) outliers start: 33 outliers final: 33 residues processed: 127 average time/residue: 0.1252 time to fit residues: 25.1431 Evaluate side-chains 130 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 193 LEU Chi-restraints excluded: chain b residue 194 ILE Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 544 LEU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 184 ILE Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 339 ASN Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 606 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 194 ILE Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 434 MET Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 491 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 109 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 40 GLN ** b 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 540 GLN ** 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 = 0.3544 r_free = 0.3544 target = 0.074342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.055993 restraints weight = 54851.865| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 4.43 r_work: 0.2953 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17785 Z= 0.119 Angle : 0.653 15.335 24372 Z= 0.292 Chirality : 0.045 0.320 3046 Planarity : 0.003 0.041 2857 Dihedral : 7.669 59.854 4795 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.03 % Allowed : 12.80 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.01 (0.19), residues: 1908 helix: 1.07 (0.28), residues: 384 sheet: 0.07 (0.24), residues: 461 loop : -0.38 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG e 520 TYR 0.007 0.001 TYR L 49 PHE 0.009 0.001 PHE b 317 TRP 0.012 0.001 TRP c 631 HIS 0.003 0.001 HIS d 374 Details of bonding type rmsd covalent geometry : bond 0.00273 (17619) covalent geometry : angle 0.57664 (23912) SS BOND : bond 0.00202 ( 38) SS BOND : angle 0.68741 ( 76) hydrogen bonds : bond 0.03143 ( 458) hydrogen bonds : angle 4.57031 ( 1257) link_ALPHA1-3 : bond 0.00953 ( 5) link_ALPHA1-3 : angle 1.94556 ( 15) link_ALPHA1-6 : bond 0.00828 ( 2) link_ALPHA1-6 : angle 1.38384 ( 6) link_BETA1-4 : bond 0.00620 ( 53) link_BETA1-4 : angle 2.45795 ( 159) link_NAG-ASN : bond 0.00315 ( 68) link_NAG-ASN : angle 2.59232 ( 204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3419.35 seconds wall clock time: 59 minutes 56.23 seconds (3596.23 seconds total)