Starting phenix.real_space_refine on Mon May 4 03:07:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nvw_49866/05_2026/9nvw_49866.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nvw_49866/05_2026/9nvw_49866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nvw_49866/05_2026/9nvw_49866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nvw_49866/05_2026/9nvw_49866.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nvw_49866/05_2026/9nvw_49866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nvw_49866/05_2026/9nvw_49866.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 10747 2.51 5 N 2836 2.21 5 O 3531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s 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: 17222 Number of models: 1 Model: "" Number of chains: 51 Chain: "H" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1043 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "b" Number of atoms: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3522 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} 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: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3522 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} 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: 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 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: 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: 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: "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: 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 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: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 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: "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: "b" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: 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: "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: 4.47, per 1000 atoms: 0.26 Number of scatterers: 17222 At special positions: 0 Unit cell: (127.82, 133.63, 156.87, 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 108 16.00 O 3531 8.00 N 2836 7.00 C 10747 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 97 " 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=2.04 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=2.03 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=2.03 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=1.88 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=2.03 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=2.03 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=2.01 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 E 3 " - " MAN E 4 " " BMA Q 3 " - " MAN Q 4 " " BMA i 3 " - " MAN i 4 " " BMA r 3 " - " MAN r 4 " ALPHA1-6 " MAN E 4 " - " MAN E 5 " " BMA Q 3 " - " MAN Q 5 " " BMA i 3 " - " MAN i 5 " " BMA r 3 " - " MAN r 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " 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 h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 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 448 " " NAG N 1 " - " ASN b 465 " " NAG O 1 " - " ASN d 392 " " NAG P 1 " - " ASN d 332 " " NAG Q 1 " - " ASN d 262 " " NAG R 1 " - " ASN d 156 " " NAG S 1 " - " ASN d 160 " " NAG T 1 " - " ASN d 197 " " NAG U 1 " - " ASN d 234 " " NAG V 1 " - " ASN d 241 " " NAG W 1 " - " ASN d 276 " " NAG X 1 " - " ASN d 301 " " NAG Y 1 " - " ASN d 448 " " NAG Z 1 " - " ASN d 465 " " NAG a 1 " - " ASN f 392 " " NAG b 601 " - " ASN b 133 " " NAG b 602 " - " ASN b 339 " " NAG b 603 " - " ASN b 355 " " NAG b 604 " - " ASN b 269 " " NAG b 605 " - " ASN b 88 " " NAG b 606 " - " ASN b 398 " " NAG b 607 " - " ASN b 363 " " NAG b 608 " - " ASN b 386 " " NAG c 701 " - " ASN c 611 " " NAG c 702 " - " ASN c 637 " " NAG c 703 " - " ASN c 625 " " NAG d 601 " - " ASN d 133 " " NAG d 602 " - " ASN d 339 " " NAG d 603 " - " ASN d 355 " " NAG d 604 " - " ASN d 269 " " NAG d 605 " - " ASN d 88 " " NAG d 606 " - " ASN d 398 " " NAG d 607 " - " ASN d 386 " " NAG d 608 " - " 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 88 " " NAG f 602 " - " ASN f 133 " " NAG f 603 " - " ASN f 339 " " NAG f 604 " - " ASN f 355 " " NAG f 605 " - " ASN f 269 " " NAG f 606 " - " ASN f 398 " " NAG f 607 " - " ASN f 363 " " NAG g 701 " - " ASN g 611 " " NAG g 702 " - " ASN g 637 " " NAG g 703 " - " ASN g 625 " " NAG h 1 " - " ASN f 332 " " NAG i 1 " - " ASN f 262 " " NAG j 1 " - " ASN f 156 " " NAG k 1 " - " ASN f 197 " " NAG l 1 " - " ASN f 234 " " NAG m 1 " - " ASN f 241 " " NAG n 1 " - " ASN f 276 " " NAG o 1 " - " ASN f 301 " " NAG p 1 " - " ASN f 448 " " NAG q 1 " - " ASN f 465 " " NAG r 1 " - " ASN f 160 " " NAG s 1 " - " ASN f 386 " Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 601.9 milliseconds 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3644 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 30 sheets defined 21.9% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'H' and resid 95 through 99 Processing helix chain 'L' and resid 88 through 92 removed outlier: 3.891A pdb=" N VAL L 92 " --> pdb=" O PRO L 89 " (cutoff:3.500A) Processing helix chain 'b' and resid 70 through 74 Processing helix chain 'b' and resid 96 through 98 No H-bonds generated for 'chain 'b' and resid 96 through 98' Processing helix chain 'b' and resid 99 through 117 removed outlier: 3.772A pdb=" N HIS b 105 " --> pdb=" O VAL b 101 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU b 116 " --> pdb=" O TRP b 112 " (cutoff:3.500A) Processing helix chain 'b' and resid 334 through 351 removed outlier: 3.879A pdb=" N LYS b 340 " --> pdb=" O SER b 336 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR b 341 " --> pdb=" O ARG b 337 " (cutoff:3.500A) removed outlier: 3.866A 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 481 removed outlier: 4.413A pdb=" N TRP b 479 " --> pdb=" O MET b 475 " (cutoff:3.500A) Processing helix chain 'c' and resid 529 through 534 Processing helix chain 'c' and resid 536 through 543 removed outlier: 4.108A pdb=" N GLN c 540 " --> pdb=" O THR c 536 " (cutoff:3.500A) Processing helix chain 'c' and resid 569 through 596 removed outlier: 3.845A pdb=" N LEU c 592 " --> pdb=" O ARG c 588 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU c 593 " --> pdb=" O ASP c 589 " (cutoff:3.500A) Processing helix chain 'c' and resid 618 through 625 Processing helix chain 'c' and resid 627 through 634 removed outlier: 3.883A pdb=" N LYS c 633 " --> pdb=" O LEU c 629 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU c 634 " --> pdb=" O GLN c 630 " (cutoff:3.500A) Processing helix chain 'c' and resid 635 through 643 removed outlier: 3.814A pdb=" N GLN c 640 " --> pdb=" O GLY c 636 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU c 641 " --> pdb=" O ASN c 637 " (cutoff:3.500A) Processing helix chain 'c' and resid 646 through 658 removed outlier: 3.875A pdb=" N GLN c 653 " --> pdb=" O SER c 649 " (cutoff:3.500A) Processing helix chain 'd' and resid 99 through 116 removed outlier: 3.568A pdb=" N LEU d 116 " --> pdb=" O TRP d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 122 through 126 removed outlier: 3.805A pdb=" N CYS d 126 " --> pdb=" O THR d 123 " (cutoff:3.500A) Processing helix chain 'd' and resid 334 through 351 removed outlier: 3.758A pdb=" N THR d 351 " --> pdb=" O GLU d 347 " (cutoff:3.500A) Processing helix chain 'd' and resid 368 through 373 Processing helix chain 'd' and resid 475 through 481 removed outlier: 4.167A pdb=" N TRP d 479 " --> pdb=" O MET d 475 " (cutoff:3.500A) Processing helix chain 'e' and resid 529 through 534 Processing helix chain 'e' and resid 537 through 543 removed outlier: 3.796A pdb=" N GLN e 543 " --> pdb=" O VAL e 539 " (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: 3.527A pdb=" N LYS e 574 " --> pdb=" O VAL e 570 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU e 592 " --> pdb=" O ARG e 588 " (cutoff:3.500A) Processing helix chain 'e' and resid 619 through 624 removed outlier: 3.615A pdb=" N TRP e 623 " --> pdb=" O LEU e 619 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN e 624 " --> pdb=" O ASP e 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 619 through 624' Processing helix chain 'e' and resid 627 through 636 removed outlier: 3.752A pdb=" N LYS e 633 " --> pdb=" O LEU e 629 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU e 634 " --> pdb=" O GLN e 630 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE e 635 " --> pdb=" O TRP e 631 " (cutoff:3.500A) Processing helix chain 'e' and resid 638 through 658 removed outlier: 3.502A pdb=" N ASN e 651 " --> pdb=" O GLU e 647 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 74 removed outlier: 3.568A pdb=" N ALA f 73 " --> pdb=" O ALA f 70 " (cutoff:3.500A) Processing helix chain 'f' and resid 99 through 116 removed outlier: 3.697A pdb=" N HIS f 105 " --> pdb=" O VAL f 101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR f 106 " --> pdb=" O GLU f 102 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU f 116 " --> pdb=" O TRP f 112 " (cutoff:3.500A) Processing helix chain 'f' and resid 122 through 126 removed outlier: 3.616A pdb=" N LEU f 125 " --> pdb=" O LEU f 122 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS f 126 " --> pdb=" O THR f 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 122 through 126' Processing helix chain 'f' and resid 334 through 351 removed outlier: 4.195A pdb=" N LYS f 340 " --> pdb=" O SER f 336 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR f 341 " --> pdb=" O ARG f 337 " (cutoff:3.500A) removed outlier: 3.652A 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 481 removed outlier: 4.434A pdb=" N TRP f 479 " --> pdb=" O MET f 475 " (cutoff:3.500A) Processing helix chain 'g' and resid 529 through 534 Processing helix chain 'g' and resid 536 through 542 removed outlier: 3.989A pdb=" N GLN g 540 " --> pdb=" O THR g 536 " (cutoff:3.500A) Processing helix chain 'g' and resid 569 through 596 removed outlier: 3.686A pdb=" N LYS g 574 " --> pdb=" O VAL g 570 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP g 589 " --> pdb=" O ARG g 585 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU g 592 " --> pdb=" O ARG g 588 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU g 593 " --> pdb=" O ASP g 589 " (cutoff:3.500A) Processing helix chain 'g' and resid 618 through 623 removed outlier: 3.607A pdb=" N TRP g 623 " --> pdb=" O LEU g 619 " (cutoff:3.500A) Processing helix chain 'g' and resid 627 through 636 removed outlier: 4.244A pdb=" N LYS g 633 " --> pdb=" O LEU g 629 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU g 634 " --> pdb=" O GLN g 630 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE g 635 " --> pdb=" O TRP g 631 " (cutoff:3.500A) Processing helix chain 'g' and resid 638 through 658 removed outlier: 3.609A pdb=" N ARG g 644 " --> pdb=" O GLN g 640 " (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 12 through 13 removed outlier: 6.865A pdb=" N TRP H 39 " --> pdb=" O HIS H 55 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N HIS H 55 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TRP H 41 " --> pdb=" O ILE H 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 12 through 13 removed outlier: 4.103A pdb=" N VAL H 130 " --> pdb=" O ARG H 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 110 through 113 removed outlier: 5.969A pdb=" N GLU H 121 " --> pdb=" O ARG f 169 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LYS f 171 " --> pdb=" O GLU H 121 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASP H 123 " --> pdb=" O LYS f 171 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N TYR f 173 " --> pdb=" O ASP H 123 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.535A pdb=" N PHE L 21 " --> pdb=" O LEU L 82 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP L 79 " --> pdb=" O SER L 76 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.005A pdb=" N GLN L 43 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU L 52 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 494 through 499 removed outlier: 3.513A pdb=" N TRP b 35 " --> pdb=" O THR b 499 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N VAL c 608 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N VAL b 38 " --> pdb=" O THR c 606 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N THR c 606 " --> pdb=" O VAL b 38 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N TYR b 40 " --> pdb=" O CYS c 604 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N CYS c 604 " --> pdb=" O TYR b 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 45 through 47 removed outlier: 4.497A pdb=" N VAL b 242 " --> pdb=" O LEU b 86 " (cutoff:3.500A) 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: 6.062A 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 removed outlier: 3.732A pdb=" N GLY b 451 " --> pdb=" O LEU b 260 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N LYS b 444 " --> pdb=" O ILE b 294 " (cutoff:3.500A) removed outlier: 11.053A pdb=" N ILE b 294 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 9.698A pdb=" N GLU b 446 " --> pdb=" O VAL b 292 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N VAL b 292 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N ASN b 448 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N GLN b 290 " --> pdb=" O ASN b 448 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR b 450 " --> pdb=" O LEU b 288 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS b 330 " --> pdb=" O ILE b 297 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'b' and resid 271 through 273 removed outlier: 3.648A pdb=" N THR b 271 " --> pdb=" O GLN b 287 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR b 450 " --> pdb=" O LEU b 288 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N GLN b 290 " --> pdb=" O ASN b 448 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N ASN b 448 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N VAL b 292 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 9.698A pdb=" N GLU b 446 " --> pdb=" O VAL b 292 " (cutoff:3.500A) removed outlier: 11.053A pdb=" N ILE b 294 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N LYS b 444 " --> pdb=" O ILE b 294 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR b 357 " --> pdb=" O GLU b 466 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N PHE b 468 " --> pdb=" O THR b 357 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE b 359 " --> pdb=" O PHE b 468 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER b 393 " --> pdb=" O PHE b 361 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 302 through 312 removed outlier: 6.551A pdb=" N THR b 303 " --> pdb=" O GLY b 321 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLN b 315 " --> pdb=" O ILE b 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'd' and resid 494 through 499 removed outlier: 5.472A pdb=" N VAL e 608 " --> pdb=" O VAL d 36 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL d 38 " --> pdb=" O THR e 606 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR e 606 " --> pdb=" O VAL d 38 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N TYR d 40 " --> pdb=" O CYS e 604 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N CYS e 604 " --> pdb=" O TYR d 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'd' and resid 45 through 47 Processing sheet with id=AB8, first strand: chain 'd' and resid 91 through 94 removed outlier: 3.587A pdb=" N GLU d 91 " --> pdb=" O CYS d 239 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 169 through 177 Processing sheet with id=AC1, first strand: chain 'd' and resid 202 through 203 removed outlier: 6.442A pdb=" N THR d 202 " --> pdb=" O TYR d 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'd' and resid 259 through 261 removed outlier: 3.648A pdb=" N GLY d 451 " --> pdb=" O LEU d 260 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N LYS d 444 " --> pdb=" O ILE d 294 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N ILE d 294 " --> pdb=" O LYS d 444 " (cutoff:3.500A) removed outlier: 9.637A pdb=" N GLU d 446 " --> pdb=" O VAL d 292 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N VAL d 292 " --> pdb=" O GLU d 446 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N ASN d 448 " --> pdb=" O GLN d 290 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLN d 290 " --> pdb=" O ASN d 448 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR d 450 " --> pdb=" O LEU d 288 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS d 330 " --> pdb=" O ILE d 297 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS d 421 " --> pdb=" O PHE d 382 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE d 382 " --> pdb=" O LYS d 421 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'd' and resid 271 through 273 removed outlier: 3.641A pdb=" N THR d 271 " --> pdb=" O GLN d 287 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR d 450 " --> pdb=" O LEU d 288 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLN d 290 " --> pdb=" O ASN d 448 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N ASN d 448 " --> pdb=" O GLN d 290 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N VAL d 292 " --> pdb=" O GLU d 446 " (cutoff:3.500A) removed outlier: 9.637A pdb=" N GLU d 446 " --> pdb=" O VAL d 292 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N ILE d 294 " --> pdb=" O LYS d 444 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N LYS d 444 " --> pdb=" O ILE d 294 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR d 357 " --> pdb=" O GLU d 466 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE d 468 " --> pdb=" O THR d 357 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE d 359 " --> pdb=" O PHE d 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'd' and resid 302 through 312 removed outlier: 6.437A pdb=" N THR d 303 " --> pdb=" O GLY d 321 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLN d 315 " --> pdb=" O ILE d 309 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'f' and resid 494 through 499 removed outlier: 5.396A pdb=" N VAL g 608 " --> pdb=" O VAL f 36 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL f 38 " --> pdb=" O THR g 606 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N THR g 606 " --> pdb=" O VAL f 38 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N TYR f 40 " --> pdb=" O CYS g 604 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N CYS g 604 " --> pdb=" O TYR f 40 " (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 91 through 94 removed outlier: 3.622A pdb=" N GLU f 91 " --> pdb=" O CYS f 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'f' and resid 129 through 130 Processing sheet with id=AC9, first strand: chain 'f' and resid 202 through 203 removed outlier: 6.361A pdb=" N THR f 202 " --> pdb=" O TYR f 435 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET f 434 " --> pdb=" O ILE f 424 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'f' and resid 259 through 261 removed outlier: 3.559A pdb=" N GLY f 451 " --> pdb=" O LEU f 260 " (cutoff:3.500A) removed outlier: 10.034A pdb=" N LYS f 444 " --> pdb=" O ILE f 294 " (cutoff:3.500A) removed outlier: 11.408A pdb=" N ILE f 294 " --> pdb=" O LYS f 444 " (cutoff:3.500A) removed outlier: 9.777A pdb=" N GLU f 446 " --> pdb=" O VAL f 292 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N VAL f 292 " --> pdb=" O GLU f 446 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N ASN f 448 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 9.737A pdb=" N GLN f 290 " --> pdb=" O ASN f 448 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR f 450 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS f 330 " --> pdb=" O ILE f 297 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS f 421 " --> pdb=" O PHE f 382 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE f 382 " --> pdb=" O LYS f 421 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE f 383 " --> pdb=" O PHE f 376 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'f' and resid 271 through 273 removed outlier: 6.699A pdb=" N THR f 450 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 9.737A pdb=" N GLN f 290 " --> pdb=" O ASN f 448 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N ASN f 448 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N VAL f 292 " --> pdb=" O GLU f 446 " (cutoff:3.500A) removed outlier: 9.777A pdb=" N GLU f 446 " --> pdb=" O VAL f 292 " (cutoff:3.500A) removed outlier: 11.408A pdb=" N ILE f 294 " --> pdb=" O LYS f 444 " (cutoff:3.500A) removed outlier: 10.034A pdb=" N LYS f 444 " --> pdb=" O ILE f 294 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR f 357 " --> pdb=" O GLU f 466 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N PHE f 468 " --> pdb=" O THR f 357 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE f 359 " --> pdb=" O PHE f 468 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'f' and resid 302 through 312 removed outlier: 6.578A pdb=" N THR f 303 " --> pdb=" O GLY f 321 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN f 315 " --> pdb=" O ILE f 309 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1464 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: 2.91 Time building geometry restraints manager: 2.30 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: 5217 1.34 - 1.46: 4311 1.46 - 1.58: 7883 1.58 - 1.70: 1 1.70 - 1.82: 138 Bond restraints: 17550 Sorted by residual: bond pdb=" CA SER f 375 " pdb=" CB SER f 375 " ideal model delta sigma weight residual 1.530 1.464 0.065 1.43e-02 4.89e+03 2.08e+01 bond pdb=" C ASN d 80 " pdb=" N PRO d 81 " ideal model delta sigma weight residual 1.330 1.377 -0.047 1.19e-02 7.06e+03 1.58e+01 bond pdb=" CA PHE d 376 " pdb=" C PHE d 376 " ideal model delta sigma weight residual 1.520 1.491 0.030 1.20e-02 6.94e+03 6.05e+00 bond pdb=" N ASN f 156 " pdb=" CA ASN f 156 " ideal model delta sigma weight residual 1.463 1.493 -0.031 1.28e-02 6.10e+03 5.70e+00 bond pdb=" CA PHE f 376 " pdb=" C PHE f 376 " ideal model delta sigma weight residual 1.526 1.502 0.024 1.03e-02 9.43e+03 5.56e+00 ... (remaining 17545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 23360 2.67 - 5.34: 399 5.34 - 8.00: 41 8.00 - 10.67: 8 10.67 - 13.34: 3 Bond angle restraints: 23811 Sorted by residual: angle pdb=" C ASN f 377 " pdb=" CA ASN f 377 " pdb=" CB ASN f 377 " ideal model delta sigma weight residual 110.06 100.51 9.55 1.39e+00 5.18e-01 4.72e+01 angle pdb=" C CYS f 378 " pdb=" CA CYS f 378 " pdb=" CB CYS f 378 " ideal model delta sigma weight residual 109.80 99.18 10.62 1.70e+00 3.46e-01 3.90e+01 angle pdb=" N VAL b 464 " pdb=" CA VAL b 464 " pdb=" C VAL b 464 " ideal model delta sigma weight residual 112.83 107.64 5.19 9.90e-01 1.02e+00 2.75e+01 angle pdb=" C ASN d 377 " pdb=" CA ASN d 377 " pdb=" CB ASN d 377 " ideal model delta sigma weight residual 109.84 101.36 8.48 1.63e+00 3.76e-01 2.71e+01 angle pdb=" CA PHE f 376 " pdb=" CB PHE f 376 " pdb=" CG PHE f 376 " ideal model delta sigma weight residual 113.80 118.52 -4.72 1.00e+00 1.00e+00 2.22e+01 ... (remaining 23806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.02: 11557 24.02 - 48.05: 423 48.05 - 72.07: 129 72.07 - 96.10: 43 96.10 - 120.12: 24 Dihedral angle restraints: 12176 sinusoidal: 6532 harmonic: 5644 Sorted by residual: dihedral pdb=" CB CYS d 378 " pdb=" SG CYS d 378 " pdb=" SG CYS d 445 " pdb=" CB CYS d 445 " ideal model delta sinusoidal sigma weight residual -86.00 -168.30 82.30 1 1.00e+01 1.00e-02 8.31e+01 dihedral pdb=" CB CYS f 378 " pdb=" SG CYS f 378 " pdb=" SG CYS f 445 " pdb=" CB CYS f 445 " ideal model delta sinusoidal sigma weight residual -86.00 -164.55 78.55 1 1.00e+01 1.00e-02 7.69e+01 dihedral pdb=" CB CYS d 126 " pdb=" SG CYS d 126 " pdb=" SG CYS d 196 " pdb=" CB CYS d 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.97 -60.97 1 1.00e+01 1.00e-02 4.94e+01 ... (remaining 12173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.211: 3004 0.211 - 0.422: 17 0.422 - 0.633: 0 0.633 - 0.845: 1 0.845 - 1.056: 1 Chirality restraints: 3023 Sorted by residual: chirality pdb=" C1 NAG n 2 " pdb=" O4 NAG n 1 " pdb=" C2 NAG n 2 " pdb=" O5 NAG n 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.76e+02 chirality pdb=" C1 NAG r 2 " pdb=" O4 NAG r 1 " pdb=" C2 NAG r 2 " pdb=" O5 NAG r 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-02 2.50e+03 1.03e+02 chirality pdb=" C1 NAG p 2 " pdb=" O4 NAG p 1 " pdb=" C2 NAG p 2 " pdb=" O5 NAG p 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-02 2.50e+03 9.82e+01 ... (remaining 3020 not shown) Planarity restraints: 2922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 2 " -0.311 2.00e-02 2.50e+03 2.70e-01 9.10e+02 pdb=" C7 NAG j 2 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG j 2 " -0.141 2.00e-02 2.50e+03 pdb=" N2 NAG j 2 " 0.482 2.00e-02 2.50e+03 pdb=" O7 NAG j 2 " -0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG l 1 " -0.162 2.00e-02 2.50e+03 1.33e-01 2.22e+02 pdb=" C7 NAG l 1 " 0.044 2.00e-02 2.50e+03 pdb=" C8 NAG l 1 " -0.120 2.00e-02 2.50e+03 pdb=" N2 NAG l 1 " 0.214 2.00e-02 2.50e+03 pdb=" O7 NAG l 1 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG q 1 " 0.114 2.00e-02 2.50e+03 9.39e-02 1.10e+02 pdb=" C7 NAG q 1 " -0.030 2.00e-02 2.50e+03 pdb=" C8 NAG q 1 " 0.085 2.00e-02 2.50e+03 pdb=" N2 NAG q 1 " -0.150 2.00e-02 2.50e+03 pdb=" O7 NAG q 1 " -0.018 2.00e-02 2.50e+03 ... (remaining 2919 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 5280 2.84 - 3.35: 15175 3.35 - 3.87: 27619 3.87 - 4.38: 30324 4.38 - 4.90: 54079 Nonbonded interactions: 132477 Sorted by model distance: nonbonded pdb=" O VAL d 496 " pdb=" NE1 TRP e 631 " model vdw 2.319 3.120 nonbonded pdb=" O ILE e 535 " pdb=" ND2 ASN g 651 " model vdw 2.331 3.120 nonbonded pdb=" OG1 THR f 37 " pdb=" O ALA f 497 " model vdw 2.345 3.040 nonbonded pdb=" NH1 ARG d 46 " pdb=" OD2 ASP e 632 " model vdw 2.351 3.120 nonbonded pdb=" OE1 GLU L 27 " pdb=" NH1 ARG f 132 " model vdw 2.354 3.120 ... (remaining 132472 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 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 's' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'I' selection = chain 'P' selection = chain 'V' selection = chain 'h' selection = chain 'j' selection = chain 'm' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'i' selection = chain 'r' } ncs_group { reference = (chain 'b' and resid 33 through 607) selection = (chain 'd' and (resid 33 through 401 or resid 410 through 607)) 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: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 16.540 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 : 0.004 0.149 17714 Z= 0.216 Angle : 0.977 22.779 24265 Z= 0.462 Chirality : 0.057 1.056 3023 Planarity : 0.008 0.270 2853 Dihedral : 14.415 120.119 8418 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 2.50 % 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: -1.51 (0.18), residues: 1912 helix: -2.03 (0.21), residues: 388 sheet: -0.46 (0.23), residues: 504 loop : -0.75 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 46 TYR 0.018 0.001 TYR c 643 PHE 0.020 0.002 PHE f 376 TRP 0.016 0.002 TRP b 338 HIS 0.004 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00380 (17550) covalent geometry : angle 0.83247 (23811) SS BOND : bond 0.02450 ( 38) SS BOND : angle 2.33966 ( 76) hydrogen bonds : bond 0.25217 ( 517) hydrogen bonds : angle 9.09621 ( 1464) link_ALPHA1-3 : bond 0.03179 ( 4) link_ALPHA1-3 : angle 5.94837 ( 12) link_ALPHA1-6 : bond 0.02591 ( 4) link_ALPHA1-6 : angle 2.86870 ( 12) link_BETA1-4 : bond 0.02403 ( 49) link_BETA1-4 : angle 5.04751 ( 147) link_NAG-ASN : bond 0.00449 ( 69) link_NAG-ASN : angle 3.09617 ( 207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: L 88 GLN cc_start: 0.8489 (mp10) cc_final: 0.7527 (mp10) REVERT: d 320 MET cc_start: 0.8703 (ptp) cc_final: 0.8259 (ptp) REVERT: e 520 ARG cc_start: 0.8539 (mmm-85) cc_final: 0.8213 (mmm160) REVERT: e 584 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7822 (mt-10) REVERT: e 626 MET cc_start: 0.7869 (ttm) cc_final: 0.7537 (ttm) REVERT: e 647 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7484 (mt-10) REVERT: f 377 ASN cc_start: 0.8648 (t0) cc_final: 0.7992 (p0) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1516 time to fit residues: 39.2242 Evaluate side-chains 121 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 HIS b 130 HIS b 249 HIS d 195 ASN d 425 ASN f 82 GLN ** f 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.068346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.051717 restraints weight = 59847.174| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 4.51 r_work: 0.2810 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17714 Z= 0.206 Angle : 0.761 15.445 24265 Z= 0.340 Chirality : 0.047 0.312 3023 Planarity : 0.004 0.042 2853 Dihedral : 10.045 98.828 4707 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.64 % Allowed : 8.28 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.78 (0.19), residues: 1912 helix: -0.59 (0.26), residues: 404 sheet: -0.40 (0.22), residues: 540 loop : -0.41 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 644 TYR 0.014 0.001 TYR c 643 PHE 0.016 0.002 PHE H 87 TRP 0.020 0.001 TRP c 571 HIS 0.008 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00474 (17550) covalent geometry : angle 0.68140 (23811) SS BOND : bond 0.00441 ( 38) SS BOND : angle 0.88404 ( 76) hydrogen bonds : bond 0.04767 ( 517) hydrogen bonds : angle 6.01807 ( 1464) link_ALPHA1-3 : bond 0.00632 ( 4) link_ALPHA1-3 : angle 3.71056 ( 12) link_ALPHA1-6 : bond 0.00860 ( 4) link_ALPHA1-6 : angle 2.01318 ( 12) link_BETA1-4 : bond 0.00571 ( 49) link_BETA1-4 : angle 3.05760 ( 147) link_NAG-ASN : bond 0.00359 ( 69) link_NAG-ASN : angle 2.54001 ( 207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: H 81 ASP cc_start: 0.8607 (t0) cc_final: 0.8073 (t0) REVERT: L 118 GLU cc_start: 0.6576 (tp30) cc_final: 0.5777 (tp30) REVERT: c 530 MET cc_start: 0.8018 (mtp) cc_final: 0.7348 (mtp) REVERT: c 626 MET cc_start: 0.7469 (tpp) cc_final: 0.7000 (tpp) REVERT: d 320 MET cc_start: 0.8936 (ptp) cc_final: 0.8595 (ptp) REVERT: e 520 ARG cc_start: 0.8929 (mmm-85) cc_final: 0.8531 (mmm160) REVERT: e 584 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8446 (mt-10) REVERT: f 102 GLU cc_start: 0.9089 (tp30) cc_final: 0.8801 (mp0) REVERT: g 584 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8586 (mt-10) REVERT: g 657 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7072 (tm-30) outliers start: 11 outliers final: 7 residues processed: 132 average time/residue: 0.1324 time to fit residues: 27.0773 Evaluate side-chains 120 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 589 ASP Chi-restraints excluded: chain c residue 632 ASP Chi-restraints excluded: chain d residue 187 ASN Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 535 ILE Chi-restraints excluded: chain e residue 634 GLU Chi-restraints excluded: chain f residue 286 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 116 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 67 optimal weight: 0.0050 chunk 21 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.068344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.051919 restraints weight = 59832.124| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 4.48 r_work: 0.2812 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17714 Z= 0.134 Angle : 0.669 15.245 24265 Z= 0.294 Chirality : 0.046 0.329 3023 Planarity : 0.003 0.039 2853 Dihedral : 8.710 81.476 4707 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.39 % Allowed : 9.55 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.49 (0.19), residues: 1912 helix: -0.07 (0.27), residues: 400 sheet: -0.42 (0.21), residues: 538 loop : -0.22 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 644 TYR 0.013 0.001 TYR c 638 PHE 0.014 0.001 PHE H 87 TRP 0.014 0.001 TRP H 39 HIS 0.005 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00304 (17550) covalent geometry : angle 0.58889 (23811) SS BOND : bond 0.00262 ( 38) SS BOND : angle 0.48468 ( 76) hydrogen bonds : bond 0.04096 ( 517) hydrogen bonds : angle 5.40563 ( 1464) link_ALPHA1-3 : bond 0.00641 ( 4) link_ALPHA1-3 : angle 3.46977 ( 12) link_ALPHA1-6 : bond 0.00940 ( 4) link_ALPHA1-6 : angle 1.87401 ( 12) link_BETA1-4 : bond 0.00558 ( 49) link_BETA1-4 : angle 2.89235 ( 147) link_NAG-ASN : bond 0.00308 ( 69) link_NAG-ASN : angle 2.36458 ( 207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 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: 24 poor density : 123 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 17 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8591 (mt-10) REVERT: H 81 ASP cc_start: 0.8475 (t0) cc_final: 0.8098 (t0) REVERT: H 109 PHE cc_start: 0.8236 (t80) cc_final: 0.7937 (t80) REVERT: L 88 GLN cc_start: 0.8124 (mp10) cc_final: 0.7828 (mm-40) REVERT: L 118 GLU cc_start: 0.6606 (tp30) cc_final: 0.5832 (tp30) REVERT: c 530 MET cc_start: 0.8083 (mtp) cc_final: 0.7494 (mtp) REVERT: c 626 MET cc_start: 0.7534 (tpp) cc_final: 0.7159 (tpp) REVERT: c 644 ARG cc_start: 0.9125 (mtm110) cc_final: 0.8790 (ptt90) REVERT: e 520 ARG cc_start: 0.8936 (mmm-85) cc_final: 0.8544 (mmm160) REVERT: f 102 GLU cc_start: 0.9091 (tp30) cc_final: 0.8841 (mp0) REVERT: f 475 MET cc_start: 0.8674 (tpp) cc_final: 0.8259 (tpp) REVERT: g 584 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8446 (mt-10) REVERT: g 657 GLU cc_start: 0.7552 (tm-30) cc_final: 0.6878 (tm-30) outliers start: 24 outliers final: 12 residues processed: 140 average time/residue: 0.1315 time to fit residues: 28.7656 Evaluate side-chains 128 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain c residue 632 ASP Chi-restraints excluded: chain d residue 187 ASN Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 443 ILE Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 535 ILE Chi-restraints excluded: chain e residue 618 SER Chi-restraints excluded: chain e residue 634 GLU Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain g residue 568 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 4 optimal weight: 0.0980 chunk 38 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 185 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 169 optimal weight: 0.4980 chunk 110 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 130 HIS ** 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 = 0.3406 r_free = 0.3406 target = 0.068937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.052591 restraints weight = 59127.890| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 4.45 r_work: 0.2833 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17714 Z= 0.099 Angle : 0.633 15.003 24265 Z= 0.276 Chirality : 0.045 0.308 3023 Planarity : 0.003 0.040 2853 Dihedral : 8.295 71.696 4707 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.04 % Allowed : 10.19 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.38 (0.19), residues: 1912 helix: 0.11 (0.27), residues: 400 sheet: -0.35 (0.22), residues: 540 loop : -0.20 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG g 520 TYR 0.013 0.001 TYR L 55 PHE 0.012 0.001 PHE H 87 TRP 0.013 0.001 TRP H 39 HIS 0.004 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00216 (17550) covalent geometry : angle 0.55508 (23811) SS BOND : bond 0.00209 ( 38) SS BOND : angle 0.38356 ( 76) hydrogen bonds : bond 0.03431 ( 517) hydrogen bonds : angle 5.09607 ( 1464) link_ALPHA1-3 : bond 0.00579 ( 4) link_ALPHA1-3 : angle 3.31427 ( 12) link_ALPHA1-6 : bond 0.01165 ( 4) link_ALPHA1-6 : angle 1.77506 ( 12) link_BETA1-4 : bond 0.00583 ( 49) link_BETA1-4 : angle 2.78161 ( 147) link_NAG-ASN : bond 0.00296 ( 69) link_NAG-ASN : angle 2.25957 ( 207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8442 (tp-100) cc_final: 0.7700 (mp10) REVERT: H 17 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8606 (mt-10) REVERT: H 81 ASP cc_start: 0.8436 (t0) cc_final: 0.8185 (t0) REVERT: H 109 PHE cc_start: 0.8099 (t80) cc_final: 0.7824 (t80) REVERT: L 118 GLU cc_start: 0.6487 (tp30) cc_final: 0.5731 (tp30) REVERT: c 530 MET cc_start: 0.8096 (mtp) cc_final: 0.7577 (mtp) REVERT: c 626 MET cc_start: 0.7628 (tpp) cc_final: 0.7085 (tpp) REVERT: e 520 ARG cc_start: 0.8927 (mmm-85) cc_final: 0.8525 (mmm160) REVERT: e 564 HIS cc_start: 0.7653 (p90) cc_final: 0.7267 (p90) REVERT: e 567 LYS cc_start: 0.7483 (tptp) cc_final: 0.7219 (tptp) REVERT: e 584 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8594 (mt-10) REVERT: f 102 GLU cc_start: 0.9054 (tp30) cc_final: 0.8846 (mp0) outliers start: 18 outliers final: 12 residues processed: 138 average time/residue: 0.1384 time to fit residues: 29.3974 Evaluate side-chains 126 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain c residue 632 ASP Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 187 ASN Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 443 ILE Chi-restraints excluded: chain e residue 535 ILE Chi-restraints excluded: chain e residue 604 CYS Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 286 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 107 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 157 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 377 ASN ** f 72 HIS ** 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 = 0.3373 r_free = 0.3373 target = 0.067431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.050595 restraints weight = 59457.228| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 4.51 r_work: 0.2778 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17714 Z= 0.174 Angle : 0.671 15.046 24265 Z= 0.297 Chirality : 0.045 0.313 3023 Planarity : 0.003 0.037 2853 Dihedral : 8.242 68.330 4707 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.62 % Allowed : 10.13 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.26 (0.19), residues: 1912 helix: 0.23 (0.27), residues: 400 sheet: -0.33 (0.21), residues: 558 loop : -0.09 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG c 644 TYR 0.015 0.001 TYR L 55 PHE 0.013 0.002 PHE H 87 TRP 0.011 0.001 TRP H 52 HIS 0.004 0.001 HIS d 374 Details of bonding type rmsd covalent geometry : bond 0.00406 (17550) covalent geometry : angle 0.59636 (23811) SS BOND : bond 0.00268 ( 38) SS BOND : angle 0.48480 ( 76) hydrogen bonds : bond 0.03554 ( 517) hydrogen bonds : angle 5.01544 ( 1464) link_ALPHA1-3 : bond 0.00605 ( 4) link_ALPHA1-3 : angle 3.23768 ( 12) link_ALPHA1-6 : bond 0.01171 ( 4) link_ALPHA1-6 : angle 1.62244 ( 12) link_BETA1-4 : bond 0.00541 ( 49) link_BETA1-4 : angle 2.77282 ( 147) link_NAG-ASN : bond 0.00326 ( 69) link_NAG-ASN : angle 2.36195 ( 207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 17 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8553 (mt-10) REVERT: H 90 ARG cc_start: 0.9112 (mmm-85) cc_final: 0.8882 (mmm-85) REVERT: H 109 PHE cc_start: 0.8278 (t80) cc_final: 0.8001 (t80) REVERT: L 118 GLU cc_start: 0.6469 (tp30) cc_final: 0.5704 (tp30) REVERT: c 626 MET cc_start: 0.7702 (tpp) cc_final: 0.7340 (tpp) REVERT: c 644 ARG cc_start: 0.9186 (mtm110) cc_final: 0.8777 (ptt90) REVERT: c 661 LEU cc_start: 0.4243 (OUTLIER) cc_final: 0.3987 (tt) REVERT: e 520 ARG cc_start: 0.8924 (mmm-85) cc_final: 0.8527 (mmm160) REVERT: e 564 HIS cc_start: 0.7641 (p90) cc_final: 0.7277 (p90) REVERT: e 567 LYS cc_start: 0.7488 (tptp) cc_final: 0.7203 (tptp) REVERT: f 102 GLU cc_start: 0.9124 (tp30) cc_final: 0.8838 (tm-30) REVERT: g 567 LYS cc_start: 0.8164 (tppt) cc_final: 0.7325 (mmtm) REVERT: g 584 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8580 (mt-10) outliers start: 28 outliers final: 17 residues processed: 144 average time/residue: 0.1454 time to fit residues: 31.5580 Evaluate side-chains 134 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain c residue 632 ASP Chi-restraints excluded: chain c residue 661 LEU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 187 ASN Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 443 ILE Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 535 ILE Chi-restraints excluded: chain e residue 618 SER Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 320 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 51 optimal weight: 0.5980 chunk 185 optimal weight: 5.9990 chunk 121 optimal weight: 0.1980 chunk 78 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 80 ASN ** f 72 HIS ** 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 = 0.3371 r_free = 0.3371 target = 0.067383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.050830 restraints weight = 59325.882| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 4.46 r_work: 0.2781 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17714 Z= 0.143 Angle : 0.651 14.956 24265 Z= 0.287 Chirality : 0.045 0.307 3023 Planarity : 0.003 0.038 2853 Dihedral : 8.078 62.866 4707 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.97 % Allowed : 10.13 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.20 (0.19), residues: 1912 helix: 0.32 (0.27), residues: 400 sheet: -0.28 (0.22), residues: 553 loop : -0.10 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG e 644 TYR 0.014 0.001 TYR L 55 PHE 0.011 0.001 PHE H 87 TRP 0.012 0.001 TRP H 39 HIS 0.004 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00331 (17550) covalent geometry : angle 0.57577 (23811) SS BOND : bond 0.00223 ( 38) SS BOND : angle 0.47542 ( 76) hydrogen bonds : bond 0.03397 ( 517) hydrogen bonds : angle 4.92344 ( 1464) link_ALPHA1-3 : bond 0.00586 ( 4) link_ALPHA1-3 : angle 3.21742 ( 12) link_ALPHA1-6 : bond 0.01252 ( 4) link_ALPHA1-6 : angle 1.47986 ( 12) link_BETA1-4 : bond 0.00551 ( 49) link_BETA1-4 : angle 2.73608 ( 147) link_NAG-ASN : bond 0.00293 ( 69) link_NAG-ASN : angle 2.31620 ( 207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 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: 34 poor density : 122 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8405 (tp-100) cc_final: 0.7699 (mp-120) REVERT: H 17 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8578 (mt-10) REVERT: H 90 ARG cc_start: 0.9104 (mmm-85) cc_final: 0.8877 (mmm-85) REVERT: H 109 PHE cc_start: 0.8260 (t80) cc_final: 0.7957 (t80) REVERT: L 118 GLU cc_start: 0.6512 (tp30) cc_final: 0.5753 (tp30) REVERT: c 626 MET cc_start: 0.7719 (tpp) cc_final: 0.7222 (tpp) REVERT: c 661 LEU cc_start: 0.4300 (OUTLIER) cc_final: 0.4022 (tt) REVERT: e 520 ARG cc_start: 0.8931 (mmm-85) cc_final: 0.8532 (mmm160) REVERT: e 564 HIS cc_start: 0.7678 (p90) cc_final: 0.7351 (p90) REVERT: e 567 LYS cc_start: 0.7509 (tptp) cc_final: 0.7214 (tptp) REVERT: f 102 GLU cc_start: 0.9125 (tp30) cc_final: 0.8844 (tm-30) REVERT: g 567 LYS cc_start: 0.8174 (tppt) cc_final: 0.7350 (mmtm) REVERT: g 584 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8458 (mt-10) outliers start: 34 outliers final: 23 residues processed: 148 average time/residue: 0.1406 time to fit residues: 31.8082 Evaluate side-chains 138 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain c residue 632 ASP Chi-restraints excluded: chain c residue 661 LEU Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 187 ASN Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 443 ILE Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 535 ILE Chi-restraints excluded: chain e residue 618 SER Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 294 ILE Chi-restraints excluded: chain f residue 320 MET Chi-restraints excluded: chain g residue 568 LEU Chi-restraints excluded: chain g residue 606 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 7 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 80 ASN d 330 HIS ** f 72 HIS ** 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 = 0.3362 r_free = 0.3362 target = 0.066957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.050092 restraints weight = 59456.767| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 4.50 r_work: 0.2763 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17714 Z= 0.172 Angle : 0.666 15.010 24265 Z= 0.296 Chirality : 0.045 0.304 3023 Planarity : 0.003 0.037 2853 Dihedral : 8.057 59.592 4707 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.08 % Allowed : 10.25 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1912 helix: 0.46 (0.28), residues: 388 sheet: -0.26 (0.22), residues: 555 loop : -0.03 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG c 644 TYR 0.015 0.001 TYR L 55 PHE 0.013 0.002 PHE H 87 TRP 0.011 0.001 TRP H 39 HIS 0.004 0.001 HIS d 374 Details of bonding type rmsd covalent geometry : bond 0.00402 (17550) covalent geometry : angle 0.59219 (23811) SS BOND : bond 0.00277 ( 38) SS BOND : angle 0.47993 ( 76) hydrogen bonds : bond 0.03460 ( 517) hydrogen bonds : angle 4.90546 ( 1464) link_ALPHA1-3 : bond 0.00575 ( 4) link_ALPHA1-3 : angle 3.18854 ( 12) link_ALPHA1-6 : bond 0.01203 ( 4) link_ALPHA1-6 : angle 1.51177 ( 12) link_BETA1-4 : bond 0.00537 ( 49) link_BETA1-4 : angle 2.72041 ( 147) link_NAG-ASN : bond 0.00325 ( 69) link_NAG-ASN : angle 2.37805 ( 207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8391 (tp-100) cc_final: 0.7697 (mp-120) REVERT: H 90 ARG cc_start: 0.9112 (mmm-85) cc_final: 0.8890 (mmm-85) REVERT: H 109 PHE cc_start: 0.8328 (t80) cc_final: 0.8029 (t80) REVERT: L 118 GLU cc_start: 0.6500 (tp30) cc_final: 0.5732 (tp30) REVERT: c 626 MET cc_start: 0.7820 (tpp) cc_final: 0.7417 (tpp) REVERT: c 644 ARG cc_start: 0.9166 (mtm110) cc_final: 0.8797 (ptt90) REVERT: c 661 LEU cc_start: 0.4506 (OUTLIER) cc_final: 0.4189 (tt) REVERT: d 469 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7979 (mtp85) REVERT: e 520 ARG cc_start: 0.8933 (mmm-85) cc_final: 0.8545 (mmm160) REVERT: e 564 HIS cc_start: 0.7692 (p90) cc_final: 0.7392 (p90) REVERT: e 567 LYS cc_start: 0.7538 (tptp) cc_final: 0.7229 (tptp) REVERT: f 102 GLU cc_start: 0.9126 (tp30) cc_final: 0.8849 (tm-30) REVERT: f 475 MET cc_start: 0.8704 (tpp) cc_final: 0.8288 (tpp) REVERT: g 567 LYS cc_start: 0.8149 (tppt) cc_final: 0.7317 (mmtm) REVERT: g 584 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8408 (mt-10) outliers start: 36 outliers final: 25 residues processed: 146 average time/residue: 0.1419 time to fit residues: 31.2852 Evaluate side-chains 139 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain c residue 632 ASP Chi-restraints excluded: chain c residue 661 LEU Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 187 ASN Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 443 ILE Chi-restraints excluded: chain d residue 469 ARG Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 618 SER Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 294 ILE Chi-restraints excluded: chain f residue 320 MET Chi-restraints excluded: chain g residue 568 LEU Chi-restraints excluded: chain g residue 606 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 55 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 147 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 80 ASN ** f 72 HIS ** 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 = 0.3370 r_free = 0.3370 target = 0.067291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.050400 restraints weight = 59729.735| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 4.54 r_work: 0.2769 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17714 Z= 0.149 Angle : 0.658 14.972 24265 Z= 0.293 Chirality : 0.045 0.298 3023 Planarity : 0.003 0.037 2853 Dihedral : 7.942 58.982 4707 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.74 % Allowed : 10.89 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1912 helix: 0.70 (0.28), residues: 370 sheet: -0.24 (0.22), residues: 553 loop : -0.12 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG c 644 TYR 0.015 0.001 TYR L 55 PHE 0.012 0.001 PHE H 87 TRP 0.013 0.001 TRP H 39 HIS 0.003 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00345 (17550) covalent geometry : angle 0.58530 (23811) SS BOND : bond 0.00267 ( 38) SS BOND : angle 0.47185 ( 76) hydrogen bonds : bond 0.03380 ( 517) hydrogen bonds : angle 4.87188 ( 1464) link_ALPHA1-3 : bond 0.00560 ( 4) link_ALPHA1-3 : angle 3.15774 ( 12) link_ALPHA1-6 : bond 0.01210 ( 4) link_ALPHA1-6 : angle 1.54727 ( 12) link_BETA1-4 : bond 0.00537 ( 49) link_BETA1-4 : angle 2.69163 ( 147) link_NAG-ASN : bond 0.00300 ( 69) link_NAG-ASN : angle 2.34009 ( 207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8387 (tp-100) cc_final: 0.7690 (mp-120) REVERT: H 90 ARG cc_start: 0.9117 (mmm-85) cc_final: 0.8902 (mmm-85) REVERT: H 109 PHE cc_start: 0.8306 (t80) cc_final: 0.7989 (t80) REVERT: L 118 GLU cc_start: 0.6551 (tp30) cc_final: 0.5777 (tp30) REVERT: c 626 MET cc_start: 0.7805 (tpp) cc_final: 0.7311 (tpp) REVERT: c 644 ARG cc_start: 0.9169 (mtm110) cc_final: 0.8753 (ptt90) REVERT: c 661 LEU cc_start: 0.4506 (OUTLIER) cc_final: 0.4197 (tt) REVERT: d 192 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8518 (ptt-90) REVERT: e 520 ARG cc_start: 0.8923 (mmm-85) cc_final: 0.8506 (mmm160) REVERT: e 564 HIS cc_start: 0.7702 (p90) cc_final: 0.7419 (p90) REVERT: e 567 LYS cc_start: 0.7537 (tptp) cc_final: 0.7226 (tptp) REVERT: e 584 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8601 (mt-10) REVERT: f 102 GLU cc_start: 0.9131 (tp30) cc_final: 0.8856 (tm-30) REVERT: f 475 MET cc_start: 0.8710 (tpp) cc_final: 0.8285 (tpp) REVERT: g 567 LYS cc_start: 0.8119 (tppt) cc_final: 0.7304 (mmtm) outliers start: 30 outliers final: 25 residues processed: 142 average time/residue: 0.1507 time to fit residues: 31.8379 Evaluate side-chains 140 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain c residue 632 ASP Chi-restraints excluded: chain c residue 661 LEU Chi-restraints excluded: chain d residue 80 ASN Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 187 ASN Chi-restraints excluded: chain d residue 192 ARG Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 443 ILE Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 618 SER Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 182 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 294 ILE Chi-restraints excluded: chain f residue 320 MET Chi-restraints excluded: chain g residue 606 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 50 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 115 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.067955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.051406 restraints weight = 59567.547| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 4.49 r_work: 0.2799 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17714 Z= 0.103 Angle : 0.636 14.942 24265 Z= 0.283 Chirality : 0.045 0.286 3023 Planarity : 0.003 0.063 2853 Dihedral : 7.716 59.242 4707 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.39 % Allowed : 11.35 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1912 helix: 0.80 (0.28), residues: 370 sheet: -0.18 (0.22), residues: 556 loop : -0.09 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG e 644 TYR 0.012 0.001 TYR L 55 PHE 0.012 0.001 PHE H 87 TRP 0.016 0.001 TRP H 39 HIS 0.004 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00230 (17550) covalent geometry : angle 0.56455 (23811) SS BOND : bond 0.00185 ( 38) SS BOND : angle 0.42836 ( 76) hydrogen bonds : bond 0.03158 ( 517) hydrogen bonds : angle 4.80441 ( 1464) link_ALPHA1-3 : bond 0.00571 ( 4) link_ALPHA1-3 : angle 3.05905 ( 12) link_ALPHA1-6 : bond 0.01203 ( 4) link_ALPHA1-6 : angle 1.59868 ( 12) link_BETA1-4 : bond 0.00576 ( 49) link_BETA1-4 : angle 2.64702 ( 147) link_NAG-ASN : bond 0.00296 ( 69) link_NAG-ASN : angle 2.25245 ( 207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 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: 24 poor density : 118 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8370 (tp-100) cc_final: 0.7727 (mp-120) REVERT: H 90 ARG cc_start: 0.9183 (mmm-85) cc_final: 0.8980 (mmm-85) REVERT: H 109 PHE cc_start: 0.8130 (t80) cc_final: 0.7687 (t80) REVERT: L 88 GLN cc_start: 0.8114 (mp10) cc_final: 0.7863 (mm-40) REVERT: L 118 GLU cc_start: 0.6540 (tp30) cc_final: 0.5773 (tp30) REVERT: c 626 MET cc_start: 0.7774 (tpp) cc_final: 0.7293 (tpp) REVERT: c 644 ARG cc_start: 0.9170 (mtm110) cc_final: 0.8787 (ptt90) REVERT: c 661 LEU cc_start: 0.4323 (OUTLIER) cc_final: 0.4002 (tt) REVERT: d 192 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8515 (ptt-90) REVERT: d 469 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.8006 (mtp85) REVERT: e 520 ARG cc_start: 0.8937 (mmm-85) cc_final: 0.8506 (mmm160) REVERT: e 564 HIS cc_start: 0.7690 (p90) cc_final: 0.7441 (p90) REVERT: e 567 LYS cc_start: 0.7547 (tptp) cc_final: 0.7242 (tptp) REVERT: e 584 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8597 (mt-10) REVERT: f 102 GLU cc_start: 0.9098 (tp30) cc_final: 0.8835 (tm-30) REVERT: g 567 LYS cc_start: 0.8122 (tppt) cc_final: 0.7319 (mmtm) outliers start: 24 outliers final: 17 residues processed: 136 average time/residue: 0.1382 time to fit residues: 28.5058 Evaluate side-chains 132 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain c residue 661 LEU Chi-restraints excluded: chain d residue 80 ASN Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 187 ASN Chi-restraints excluded: chain d residue 192 ARG Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 443 ILE Chi-restraints excluded: chain d residue 469 ARG Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 182 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 320 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 88 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 134 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 80 ASN ** f 72 HIS ** 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 = 0.3367 r_free = 0.3367 target = 0.067134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.050629 restraints weight = 58901.099| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 4.42 r_work: 0.2779 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17714 Z= 0.155 Angle : 0.659 14.942 24265 Z= 0.293 Chirality : 0.045 0.285 3023 Planarity : 0.003 0.051 2853 Dihedral : 7.750 58.668 4707 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.33 % Allowed : 11.70 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1912 helix: 0.80 (0.28), residues: 372 sheet: -0.19 (0.22), residues: 555 loop : -0.08 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG d 166 TYR 0.015 0.001 TYR L 55 PHE 0.012 0.001 PHE H 87 TRP 0.011 0.001 TRP H 39 HIS 0.003 0.001 HIS d 374 Details of bonding type rmsd covalent geometry : bond 0.00361 (17550) covalent geometry : angle 0.58892 (23811) SS BOND : bond 0.00258 ( 38) SS BOND : angle 0.46069 ( 76) hydrogen bonds : bond 0.03279 ( 517) hydrogen bonds : angle 4.79749 ( 1464) link_ALPHA1-3 : bond 0.00553 ( 4) link_ALPHA1-3 : angle 3.04655 ( 12) link_ALPHA1-6 : bond 0.01153 ( 4) link_ALPHA1-6 : angle 1.63907 ( 12) link_BETA1-4 : bond 0.00543 ( 49) link_BETA1-4 : angle 2.64353 ( 147) link_NAG-ASN : bond 0.00325 ( 69) link_NAG-ASN : angle 2.29692 ( 207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8353 (tp-100) cc_final: 0.7648 (mp-120) REVERT: H 90 ARG cc_start: 0.9171 (mmm-85) cc_final: 0.8962 (mmm-85) REVERT: H 109 PHE cc_start: 0.8220 (t80) cc_final: 0.7817 (t80) REVERT: L 118 GLU cc_start: 0.6582 (tp30) cc_final: 0.5828 (tp30) REVERT: c 626 MET cc_start: 0.7837 (tpp) cc_final: 0.7421 (tpp) REVERT: c 644 ARG cc_start: 0.9171 (mtm110) cc_final: 0.8764 (ptt90) REVERT: c 661 LEU cc_start: 0.4442 (OUTLIER) cc_final: 0.4123 (tt) REVERT: d 192 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8500 (ptt-90) REVERT: d 469 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7990 (mtp85) REVERT: e 520 ARG cc_start: 0.8922 (mmm-85) cc_final: 0.8494 (mmm160) REVERT: e 536 THR cc_start: 0.9296 (p) cc_final: 0.9082 (t) REVERT: e 564 HIS cc_start: 0.7699 (p90) cc_final: 0.7469 (p90) REVERT: e 567 LYS cc_start: 0.7515 (tptp) cc_final: 0.7253 (tptp) REVERT: e 584 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8610 (mt-10) REVERT: f 102 GLU cc_start: 0.9116 (tp30) cc_final: 0.8855 (tm-30) REVERT: g 567 LYS cc_start: 0.8129 (tppt) cc_final: 0.7337 (mmtm) outliers start: 23 outliers final: 17 residues processed: 132 average time/residue: 0.1451 time to fit residues: 29.0044 Evaluate side-chains 132 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain c residue 661 LEU Chi-restraints excluded: chain d residue 187 ASN Chi-restraints excluded: chain d residue 192 ARG Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 443 ILE Chi-restraints excluded: chain d residue 469 ARG Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 182 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 320 MET Chi-restraints excluded: chain g residue 606 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 53 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 125 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.0170 chunk 106 optimal weight: 10.0000 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 72 HIS ** 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 = 0.3423 r_free = 0.3423 target = 0.069382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.052450 restraints weight = 59358.968| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 4.55 r_work: 0.2828 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17714 Z= 0.104 Angle : 0.637 14.940 24265 Z= 0.283 Chirality : 0.044 0.274 3023 Planarity : 0.003 0.041 2853 Dihedral : 7.560 58.853 4707 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.98 % Allowed : 12.16 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1912 helix: 0.68 (0.28), residues: 382 sheet: -0.12 (0.22), residues: 556 loop : 0.01 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 476 TYR 0.011 0.001 TYR L 55 PHE 0.011 0.001 PHE H 87 TRP 0.016 0.001 TRP H 39 HIS 0.003 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00235 (17550) covalent geometry : angle 0.56859 (23811) SS BOND : bond 0.00189 ( 38) SS BOND : angle 0.41191 ( 76) hydrogen bonds : bond 0.03049 ( 517) hydrogen bonds : angle 4.73590 ( 1464) link_ALPHA1-3 : bond 0.00554 ( 4) link_ALPHA1-3 : angle 2.94244 ( 12) link_ALPHA1-6 : bond 0.01149 ( 4) link_ALPHA1-6 : angle 1.62578 ( 12) link_BETA1-4 : bond 0.00578 ( 49) link_BETA1-4 : angle 2.60316 ( 147) link_NAG-ASN : bond 0.00295 ( 69) link_NAG-ASN : angle 2.21377 ( 207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3454.45 seconds wall clock time: 60 minutes 32.32 seconds (3632.32 seconds total)