Starting phenix.real_space_refine on Mon May 4 03:12:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nvy_49868/05_2026/9nvy_49868.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nvy_49868/05_2026/9nvy_49868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nvy_49868/05_2026/9nvy_49868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nvy_49868/05_2026/9nvy_49868.map" model { file = "/net/cci-nas-00/data/ceres_data/9nvy_49868/05_2026/9nvy_49868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nvy_49868/05_2026/9nvy_49868.cif" } resolution = 3.8 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 10721 2.51 5 N 2832 2.21 5 O 3506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17169 Number of models: 1 Model: "" Number of chains: 51 Chain: "H" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1037 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} 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: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} 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: 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: "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: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3502 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 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: 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: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "g" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.52, per 1000 atoms: 0.26 Number of scatterers: 17169 At special positions: 0 Unit cell: (132.8, 133.63, 159.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 3506 8.00 N 2832 7.00 C 10721 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 101 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS b 54 " - pdb=" SG CYS b 74 " distance=2.04 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=2.03 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=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 205 " distance=2.03 Simple disulfide: pdb=" SG CYS f 126 " - pdb=" SG CYS f 196 " distance=2.03 Simple disulfide: pdb=" SG CYS f 131 " - pdb=" SG CYS f 157 " distance=2.03 Simple disulfide: pdb=" SG CYS f 201 " - pdb=" SG CYS f 433 " distance=2.03 Simple disulfide: pdb=" SG CYS f 218 " - pdb=" SG CYS f 247 " distance=2.03 Simple disulfide: pdb=" SG CYS f 228 " - pdb=" SG CYS f 239 " distance=2.03 Simple disulfide: pdb=" SG CYS f 296 " - pdb=" SG CYS f 331 " distance=2.03 Simple disulfide: pdb=" SG CYS f 378 " - pdb=" SG CYS f 445 " distance=2.03 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 s 3 " - " MAN s 4 " ALPHA1-6 " BMA s 3 " - " MAN s 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 D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " 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 O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " 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 k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-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 197 " " NAG F 1 " - " ASN b 234 " " NAG G 1 " - " ASN b 241 " " NAG I 1 " - " ASN b 276 " " NAG J 1 " - " ASN b 301 " " NAG K 1 " - " ASN b 448 " " NAG M 1 " - " ASN b 465 " " NAG N 1 " - " ASN d 392 " " NAG O 1 " - " ASN d 332 " " NAG P 1 " - " ASN d 262 " " NAG Q 1 " - " ASN d 156 " " NAG R 1 " - " ASN d 197 " " NAG S 1 " - " ASN d 234 " " NAG T 1 " - " ASN d 241 " " NAG U 1 " - " ASN d 276 " " NAG V 1 " - " ASN d 301 " " NAG W 1 " - " ASN d 448 " " NAG X 1 " - " ASN d 465 " " NAG Z 1 " - " ASN f 392 " " NAG a 1 " - " ASN f 332 " " NAG b 601 " - " ASN b 88 " " NAG b 602 " - " ASN b 133 " " NAG b 603 " - " ASN b 339 " " NAG b 604 " - " ASN b 355 " " NAG b 605 " - " ASN b 269 " " NAG b 606 " - " ASN b 160 " " NAG b 607 " - " ASN b 398 " " NAG b 608 " - " ASN b 386 " " NAG b 609 " - " ASN b 363 " " 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 g 701 " - " ASN g 611 " " NAG g 702 " - " ASN g 637 " " NAG g 703 " - " ASN g 625 " " NAG h 1 " - " ASN f 262 " " NAG i 1 " - " ASN f 156 " " NAG j 1 " - " ASN f 197 " " NAG k 1 " - " ASN f 234 " " NAG l 1 " - " ASN f 241 " " NAG m 1 " - " ASN f 276 " " NAG n 1 " - " ASN f 301 " " NAG q 1 " - " ASN f 448 " " NAG r 1 " - " ASN f 465 " " NAG s 1 " - " ASN f 160 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 760.8 milliseconds 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3630 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 31 sheets defined 23.0% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'H' and resid 92 through 96 Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.812A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 70 through 74 Processing helix chain 'b' and resid 98 through 115 removed outlier: 4.343A pdb=" N GLU b 102 " --> pdb=" O ASN b 98 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR b 106 " --> pdb=" O GLU b 102 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 126 Processing helix chain 'b' and resid 185 through 188A removed outlier: 3.634A pdb=" N GLY b 188A" --> pdb=" O GLU b 186 " (cutoff:3.500A) Processing helix chain 'b' and resid 335 through 351 removed outlier: 3.691A pdb=" N THR b 341 " --> pdb=" O ARG b 337 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN b 343 " --> pdb=" O ASN b 339 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU b 344 " --> pdb=" O LYS b 340 " (cutoff:3.500A) removed outlier: 3.827A 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 391 Processing helix chain 'b' and resid 475 through 484 removed outlier: 4.159A pdb=" N TRP b 479 " --> pdb=" O MET b 475 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU b 482 " --> pdb=" O ASN b 478 " (cutoff:3.500A) Processing helix chain 'c' and resid 529 through 534 Processing helix chain 'c' and resid 536 through 543 removed outlier: 3.739A pdb=" N GLN c 540 " --> pdb=" O THR c 536 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN c 543 " --> pdb=" O VAL c 539 " (cutoff:3.500A) Processing helix chain 'c' and resid 544 through 546 No H-bonds generated for 'chain 'c' and resid 544 through 546' Processing helix chain 'c' and resid 569 through 596 removed outlier: 3.593A pdb=" N LYS c 574 " --> pdb=" O VAL c 570 " (cutoff:3.500A) Processing helix chain 'c' and resid 618 through 625 Processing helix chain 'c' and resid 628 through 633 removed outlier: 4.253A pdb=" N LYS c 633 " --> pdb=" O LEU c 629 " (cutoff:3.500A) Processing helix chain 'c' and resid 635 through 658 removed outlier: 4.758A pdb=" N GLN c 640 " --> pdb=" O GLY c 636 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU c 641 " --> pdb=" O ASN c 637 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN c 656 " --> pdb=" O GLN c 652 " (cutoff:3.500A) Processing helix chain 'd' and resid 99 through 117 removed outlier: 3.776A pdb=" N LEU d 116 " --> pdb=" O TRP d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 122 through 126 Processing helix chain 'd' and resid 335 through 351 removed outlier: 3.813A pdb=" N GLN d 343 " --> pdb=" O ASN d 339 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR d 351 " --> pdb=" O GLU d 347 " (cutoff:3.500A) Processing helix chain 'd' and resid 368 through 373 removed outlier: 3.502A pdb=" N THR d 373 " --> pdb=" O LEU d 369 " (cutoff:3.500A) Processing helix chain 'd' and resid 387 through 391 Processing helix chain 'd' and resid 476 through 484 removed outlier: 3.548A pdb=" N ARG d 480 " --> pdb=" O ARG d 476 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER d 481 " --> pdb=" O ASP d 477 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU d 482 " --> pdb=" O ASN d 478 " (cutoff:3.500A) Processing helix chain 'e' and resid 529 through 534 Processing helix chain 'e' and resid 536 through 543 removed outlier: 3.819A pdb=" N GLN e 540 " --> pdb=" O THR e 536 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN e 543 " --> pdb=" O VAL e 539 " (cutoff:3.500A) Processing helix chain 'e' and resid 569 through 596 removed outlier: 4.078A pdb=" N LEU e 592 " --> pdb=" O ARG e 588 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU e 593 " --> pdb=" O ASP e 589 " (cutoff:3.500A) Processing helix chain 'e' and resid 618 through 625 removed outlier: 3.702A pdb=" N ILE e 622 " --> pdb=" O SER e 618 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP e 623 " --> pdb=" O LEU e 619 " (cutoff:3.500A) Processing helix chain 'e' and resid 627 through 658 removed outlier: 3.831A pdb=" N LYS e 633 " --> pdb=" O LEU e 629 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU e 634 " --> pdb=" O GLN e 630 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ASN e 637 " --> pdb=" O LYS e 633 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TYR e 638 " --> pdb=" O GLU e 634 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLN e 640 " --> pdb=" O GLY e 636 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU e 641 " --> pdb=" O ASN e 637 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 74 removed outlier: 3.624A pdb=" N ALA f 73 " --> pdb=" O ALA f 70 " (cutoff:3.500A) Processing helix chain 'f' and resid 98 through 117 removed outlier: 4.321A pdb=" N GLU f 102 " --> pdb=" O ASN f 98 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS f 117 " --> pdb=" O ASP f 113 " (cutoff:3.500A) Processing helix chain 'f' and resid 122 through 126 removed outlier: 3.554A pdb=" N CYS f 126 " --> pdb=" O THR f 123 " (cutoff:3.500A) Processing helix chain 'f' and resid 335 through 351 removed outlier: 3.770A pdb=" N THR f 341 " --> pdb=" O ARG f 337 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN f 343 " --> pdb=" O ASN f 339 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU f 344 " --> pdb=" O LYS f 340 " (cutoff:3.500A) removed outlier: 3.629A 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 475 through 484 removed outlier: 4.106A pdb=" N TRP f 479 " --> pdb=" O MET f 475 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU f 482 " --> pdb=" O ASN f 478 " (cutoff:3.500A) Processing helix chain 'g' and resid 536 through 543 removed outlier: 3.645A pdb=" N GLN g 540 " --> pdb=" O THR g 536 " (cutoff:3.500A) Processing helix chain 'g' and resid 544 through 546 No H-bonds generated for 'chain 'g' and resid 544 through 546' Processing helix chain 'g' and resid 569 through 596 removed outlier: 3.539A pdb=" N ASP g 589 " --> pdb=" O ARG g 585 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU g 592 " --> pdb=" O ARG g 588 " (cutoff:3.500A) Processing helix chain 'g' and resid 618 through 626 removed outlier: 3.528A pdb=" N TRP g 623 " --> pdb=" O LEU g 619 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN g 624 " --> pdb=" O ASP g 620 " (cutoff:3.500A) Processing helix chain 'g' and resid 627 through 636 removed outlier: 3.876A pdb=" N LYS g 633 " --> pdb=" O LEU g 629 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU g 634 " --> pdb=" O GLN g 630 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE g 635 " --> pdb=" O TRP g 631 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY g 636 " --> pdb=" O ASP g 632 " (cutoff:3.500A) Processing helix chain 'g' and resid 638 through 658 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 35 through 41 removed outlier: 6.448A pdb=" N TRP H 36 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR H 52 " --> pdb=" O LYS H 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 62 through 64 current: chain 'H' and resid 123 through 127 Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.716A pdb=" N ASP L 75 " --> pdb=" O SER L 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.543A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE L 53 " --> pdb=" O TRP L 40 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU L 42 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU L 51 " --> pdb=" O LEU L 42 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 494 through 499 removed outlier: 5.464A pdb=" N VAL c 608 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL b 38 " --> pdb=" O THR c 606 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR c 606 " --> pdb=" O VAL b 38 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N TYR b 40 " --> pdb=" O CYS c 604 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N CYS c 604 " --> pdb=" O TYR b 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 45 through 47 removed outlier: 3.718A pdb=" N ILE b 225 " --> pdb=" O VAL b 245 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'b' and resid 66 through 67 removed outlier: 7.040A pdb=" N HIS b 66 " --> pdb=" O SER b 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 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 170 through 177 Processing sheet with id=AB2, first strand: chain 'b' and resid 202 through 203 removed outlier: 6.615A pdb=" N THR b 202 " --> pdb=" O TYR b 435 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET b 434 " --> pdb=" O ILE b 424 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 259 through 261 current: chain 'b' and resid 284 through 297 removed outlier: 7.953A pdb=" N THR b 293 " --> pdb=" O SER b 334 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N SER b 334 " --> pdb=" O THR b 293 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS b 330 " --> pdb=" O ILE b 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 330 through 334 current: chain 'b' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 381 through 385 current: chain 'b' and resid 465 through 469 Processing sheet with id=AB4, first strand: chain 'b' and resid 301 through 304 removed outlier: 7.026A pdb=" N ASN b 301 " --> pdb=" O ILE b 323 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ILE b 323 " --> pdb=" O ASN b 301 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N THR b 303 " --> pdb=" O GLY b 321 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 307 through 312 removed outlier: 7.260A 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: 5.632A pdb=" N VAL e 608 " --> pdb=" O VAL d 36 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N VAL d 38 " --> pdb=" O THR e 606 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N THR e 606 " --> pdb=" O VAL d 38 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N TYR d 40 " --> pdb=" O CYS e 604 " (cutoff:3.500A) removed outlier: 9.453A 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 53 through 55 Processing sheet with id=AB9, first strand: chain 'd' and resid 91 through 94 removed outlier: 3.529A pdb=" N GLU d 91 " --> pdb=" O CYS d 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'd' and resid 130 through 132 Processing sheet with id=AC2, first strand: chain 'd' and resid 181 through 183 Processing sheet with id=AC3, first strand: chain 'd' and resid 202 through 203 removed outlier: 6.491A pdb=" N THR d 202 " --> pdb=" O TYR d 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'd' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 259 through 261 current: chain 'd' and resid 284 through 298 removed outlier: 7.834A pdb=" N THR d 293 " --> pdb=" O SER d 334 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER d 334 " --> pdb=" O THR d 293 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS d 330 " --> pdb=" O ILE d 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 330 through 334 current: chain 'd' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 381 through 385 current: chain 'd' and resid 465 through 470 Processing sheet with id=AC5, first strand: chain 'd' and resid 301 through 312 removed outlier: 6.590A pdb=" N ASN d 301 " --> pdb=" O ILE d 323 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE d 323 " --> pdb=" O ASN d 301 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR d 303 " --> pdb=" O GLY d 321 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLN d 315 " --> pdb=" O ILE d 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'f' and resid 495 through 499 removed outlier: 5.430A pdb=" N VAL g 608 " --> pdb=" O VAL f 36 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL f 38 " --> pdb=" O THR g 606 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR g 606 " --> pdb=" O VAL f 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'f' and resid 45 through 47 Processing sheet with id=AC8, first strand: chain 'f' and resid 53 through 55 Processing sheet with id=AC9, first strand: chain 'f' and resid 91 through 94 Processing sheet with id=AD1, first strand: chain 'f' and resid 169 through 177 removed outlier: 3.586A pdb=" N VAL f 172 " --> pdb=" O PHE f 159 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'f' and resid 202 through 203 removed outlier: 6.400A pdb=" N THR f 202 " --> pdb=" O TYR f 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'f' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 259 through 261 current: chain 'f' and resid 284 through 298 removed outlier: 7.706A pdb=" N THR f 293 " --> pdb=" O SER f 334 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER f 334 " --> pdb=" O THR f 293 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS f 330 " --> pdb=" O ILE f 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 330 through 334 current: chain 'f' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 381 through 385 current: chain 'f' and resid 465 through 470 Processing sheet with id=AD4, first strand: chain 'f' and resid 301 through 312 removed outlier: 6.795A pdb=" N ASN f 301 " --> pdb=" O ILE f 323 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE f 323 " --> pdb=" O ASN f 301 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR f 303 " --> pdb=" O GLY f 321 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLN f 315 " --> pdb=" O ILE f 309 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1206 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: 2.79 Time building geometry restraints manager: 2.54 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: 5168 1.34 - 1.46: 4058 1.46 - 1.58: 8131 1.58 - 1.70: 1 1.70 - 1.82: 142 Bond restraints: 17500 Sorted by residual: bond pdb=" N CYS d 385 " pdb=" CA CYS d 385 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.19e-02 7.06e+03 1.10e+01 bond pdb=" N ILE b 323 " pdb=" CA ILE b 323 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.14e-02 7.69e+03 9.93e+00 bond pdb=" N ASP b 322 " pdb=" CA ASP b 322 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.17e-02 7.31e+03 9.54e+00 bond pdb=" N ASN d 386 " pdb=" CA ASN d 386 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.17e-02 7.31e+03 9.08e+00 bond pdb=" N TYR c 638 " pdb=" CA TYR c 638 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.27e-02 6.20e+03 8.28e+00 ... (remaining 17495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 23139 2.34 - 4.68: 535 4.68 - 7.02: 49 7.02 - 9.37: 12 9.37 - 11.71: 2 Bond angle restraints: 23737 Sorted by residual: angle pdb=" CA ASN d 339 " pdb=" CB ASN d 339 " pdb=" CG ASN d 339 " ideal model delta sigma weight residual 112.60 118.85 -6.25 1.00e+00 1.00e+00 3.91e+01 angle pdb=" C ASN d 339 " pdb=" CA ASN d 339 " pdb=" CB ASN d 339 " ideal model delta sigma weight residual 110.17 121.67 -11.50 2.04e+00 2.40e-01 3.18e+01 angle pdb=" C ASN b 386 " pdb=" CA ASN b 386 " pdb=" CB ASN b 386 " ideal model delta sigma weight residual 109.90 117.91 -8.01 1.56e+00 4.11e-01 2.64e+01 angle pdb=" CA ASN d 386 " pdb=" C ASN d 386 " pdb=" O ASN d 386 " ideal model delta sigma weight residual 121.00 116.37 4.63 1.05e+00 9.07e-01 1.94e+01 angle pdb=" CA ILE f 424 " pdb=" C ILE f 424 " pdb=" O ILE f 424 " ideal model delta sigma weight residual 121.64 117.45 4.19 9.80e-01 1.04e+00 1.83e+01 ... (remaining 23732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.22: 11275 21.22 - 42.44: 561 42.44 - 63.67: 155 63.67 - 84.89: 67 84.89 - 106.11: 23 Dihedral angle restraints: 12081 sinusoidal: 6449 harmonic: 5632 Sorted by residual: dihedral pdb=" CB CYS b 126 " pdb=" SG CYS b 126 " pdb=" SG CYS b 196 " pdb=" CB CYS b 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.05 -60.05 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" CB CYS f 119 " pdb=" SG CYS f 119 " pdb=" SG CYS f 205 " pdb=" CB CYS f 205 " ideal model delta sinusoidal sigma weight residual -86.00 -137.76 51.76 1 1.00e+01 1.00e-02 3.66e+01 dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 101 " pdb=" CB CYS H 101 " ideal model delta sinusoidal sigma weight residual 93.00 42.61 50.39 1 1.00e+01 1.00e-02 3.48e+01 ... (remaining 12078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2768 0.105 - 0.210: 199 0.210 - 0.315: 10 0.315 - 0.420: 3 0.420 - 0.525: 3 Chirality restraints: 2983 Sorted by residual: chirality pdb=" C1 NAG s 2 " pdb=" O4 NAG s 1 " pdb=" C2 NAG s 2 " pdb=" O5 NAG s 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-02 2.50e+03 6.88e+02 chirality pdb=" C1 MAN s 4 " pdb=" O3 BMA s 3 " pdb=" C2 MAN s 4 " pdb=" O5 MAN s 4 " both_signs ideal model delta sigma weight residual False 2.40 2.00 0.40 2.00e-02 2.50e+03 4.00e+02 chirality pdb=" C1 BMA Z 3 " pdb=" O4 NAG Z 2 " pdb=" C2 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.75e+01 ... (remaining 2980 not shown) Planarity restraints: 2923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 608 " 0.334 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG d 608 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG d 608 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG d 608 " -0.501 2.00e-02 2.50e+03 pdb=" O7 NAG d 608 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 607 " 0.318 2.00e-02 2.50e+03 2.76e-01 9.51e+02 pdb=" C7 NAG d 607 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG d 607 " 0.041 2.00e-02 2.50e+03 pdb=" N2 NAG d 607 " -0.482 2.00e-02 2.50e+03 pdb=" O7 NAG d 607 " 0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 608 " 0.291 2.00e-02 2.50e+03 2.53e-01 7.99e+02 pdb=" C7 NAG b 608 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG b 608 " 0.017 2.00e-02 2.50e+03 pdb=" N2 NAG b 608 " -0.439 2.00e-02 2.50e+03 pdb=" O7 NAG b 608 " 0.195 2.00e-02 2.50e+03 ... (remaining 2920 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 116 2.56 - 3.14: 14084 3.14 - 3.73: 25460 3.73 - 4.31: 34998 4.31 - 4.90: 57983 Nonbonded interactions: 132641 Sorted by model distance: nonbonded pdb=" O SER L 57 " pdb=" OD1 ASP L 58 " model vdw 1.971 3.040 nonbonded pdb=" OG1 THR d 37 " pdb=" O ALA d 497 " model vdw 2.120 3.040 nonbonded pdb=" O TRP f 401 " pdb=" O3 NAG f 603 " model vdw 2.134 3.040 nonbonded pdb=" O VAL b 36 " pdb=" OG1 THR c 606 " model vdw 2.147 3.040 nonbonded pdb=" OG1 THR f 303 " pdb=" OD1 ASP f 322 " model vdw 2.148 3.040 ... (remaining 132636 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 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'j' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'O' selection = chain 'P' selection = chain 'T' selection = chain 'Z' selection = chain 'a' selection = chain 'h' selection = chain 'i' selection = chain 'l' } ncs_group { reference = (chain 'b' and (resid 33 through 501 or resid 604 through 608)) selection = (chain 'd' and (resid 33 through 501 or resid 604 through 608)) selection = (chain 'f' and resid 33 through 605) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.280 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 17656 Z= 0.270 Angle : 0.987 23.162 24167 Z= 0.481 Chirality : 0.053 0.525 2983 Planarity : 0.011 0.285 2857 Dihedral : 14.410 106.110 8337 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.29 % Allowed : 9.33 % Favored : 90.38 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.41 % 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: -1.17 (0.19), residues: 1913 helix: 0.04 (0.28), residues: 366 sheet: -1.09 (0.24), residues: 453 loop : -0.86 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 82 TYR 0.029 0.001 TYR c 638 PHE 0.024 0.001 PHE L 103 TRP 0.030 0.001 TRP e 631 HIS 0.006 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00443 (17500) covalent geometry : angle 0.81616 (23737) SS BOND : bond 0.00248 ( 38) SS BOND : angle 0.61471 ( 76) hydrogen bonds : bond 0.25017 ( 446) hydrogen bonds : angle 8.94909 ( 1206) link_ALPHA1-3 : bond 0.04602 ( 1) link_ALPHA1-3 : angle 6.01811 ( 3) link_ALPHA1-6 : bond 0.03780 ( 1) link_ALPHA1-6 : angle 4.35671 ( 3) link_BETA1-4 : bond 0.01812 ( 50) link_BETA1-4 : angle 4.80714 ( 150) link_NAG-ASN : bond 0.03163 ( 66) link_NAG-ASN : angle 4.54139 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 155 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 LYS cc_start: 0.9385 (mtpt) cc_final: 0.8988 (ttpp) REVERT: L 39 ASP cc_start: 0.8475 (m-30) cc_final: 0.8185 (m-30) REVERT: L 82 ARG cc_start: 0.9387 (mtp-110) cc_final: 0.9129 (mmm-85) REVERT: b 95 MET cc_start: 0.8672 (ptm) cc_final: 0.8445 (ptt) REVERT: b 125 LEU cc_start: 0.9282 (mm) cc_final: 0.9037 (mt) REVERT: c 530 MET cc_start: 0.8998 (mtm) cc_final: 0.8670 (mmm) REVERT: d 161 MET cc_start: 0.7943 (tpp) cc_final: 0.7632 (tpp) REVERT: d 182 VAL cc_start: 0.9213 (OUTLIER) cc_final: 0.9008 (m) REVERT: e 601 LYS cc_start: 0.8694 (mttt) cc_final: 0.8491 (mppt) REVERT: e 658 LYS cc_start: 0.8163 (mttt) cc_final: 0.7730 (tppt) REVERT: f 477 ASP cc_start: 0.9075 (m-30) cc_final: 0.8676 (m-30) outliers start: 5 outliers final: 4 residues processed: 160 average time/residue: 0.1514 time to fit residues: 35.8527 Evaluate side-chains 112 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 622 ILE Chi-restraints excluded: chain d residue 182 VAL Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain f residue 445 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 195 ASN c 563 GLN c 656 ASN d 85 HIS d 185 ASN d 195 ASN e 651 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.047363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.037339 restraints weight = 103583.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.038644 restraints weight = 54124.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.039519 restraints weight = 36017.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.040102 restraints weight = 27630.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.040525 restraints weight = 23210.766| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17656 Z= 0.149 Angle : 0.786 14.592 24167 Z= 0.345 Chirality : 0.048 0.332 2983 Planarity : 0.004 0.042 2857 Dihedral : 9.335 72.802 4619 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.27 % Allowed : 10.60 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -0.68 (0.19), residues: 1913 helix: 0.64 (0.27), residues: 375 sheet: -0.88 (0.23), residues: 467 loop : -0.57 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 24 TYR 0.012 0.001 TYR d 217 PHE 0.017 0.001 PHE b 317 TRP 0.021 0.001 TRP H 38 HIS 0.003 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00324 (17500) covalent geometry : angle 0.70448 (23737) SS BOND : bond 0.00428 ( 38) SS BOND : angle 0.70141 ( 76) hydrogen bonds : bond 0.05546 ( 446) hydrogen bonds : angle 6.34060 ( 1206) link_ALPHA1-3 : bond 0.01917 ( 1) link_ALPHA1-3 : angle 2.96747 ( 3) link_ALPHA1-6 : bond 0.00707 ( 1) link_ALPHA1-6 : angle 1.44690 ( 3) link_BETA1-4 : bond 0.00690 ( 50) link_BETA1-4 : angle 3.24186 ( 150) link_NAG-ASN : bond 0.00412 ( 66) link_NAG-ASN : angle 2.75882 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 LYS cc_start: 0.9303 (mtpt) cc_final: 0.8980 (ttpt) REVERT: H 86 LEU cc_start: 0.9037 (tt) cc_final: 0.8832 (tp) REVERT: L 43 GLN cc_start: 0.7957 (tp40) cc_final: 0.7497 (tp40) REVERT: L 52 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8532 (mm) REVERT: b 95 MET cc_start: 0.8833 (ptm) cc_final: 0.8617 (ptt) REVERT: c 563 GLN cc_start: 0.6223 (OUTLIER) cc_final: 0.5717 (tp40) REVERT: d 161 MET cc_start: 0.8330 (tpp) cc_final: 0.8053 (tpp) REVERT: d 182 VAL cc_start: 0.9294 (OUTLIER) cc_final: 0.9074 (m) REVERT: d 320 MET cc_start: 0.8575 (mpp) cc_final: 0.8369 (mpp) REVERT: e 651 ASN cc_start: 0.9403 (OUTLIER) cc_final: 0.8877 (p0) REVERT: f 161 MET cc_start: 0.9012 (tpp) cc_final: 0.8775 (tpp) REVERT: f 434 MET cc_start: 0.8410 (tmm) cc_final: 0.8142 (tmm) REVERT: f 477 ASP cc_start: 0.9104 (m-30) cc_final: 0.8765 (m-30) REVERT: g 633 LYS cc_start: 0.8985 (pttm) cc_final: 0.8728 (pttm) outliers start: 22 outliers final: 12 residues processed: 144 average time/residue: 0.1478 time to fit residues: 31.7751 Evaluate side-chains 123 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 563 GLN Chi-restraints excluded: chain c residue 606 THR Chi-restraints excluded: chain c residue 622 ILE Chi-restraints excluded: chain d residue 182 VAL Chi-restraints excluded: chain d residue 195 ASN Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain e residue 589 ASP Chi-restraints excluded: chain e residue 651 ASN Chi-restraints excluded: chain f residue 326 ILE Chi-restraints excluded: chain f residue 445 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 563 GLN c 651 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.046710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.036562 restraints weight = 104813.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.037864 restraints weight = 54503.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.038742 restraints weight = 36087.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.039349 restraints weight = 27742.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.039762 restraints weight = 23217.854| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17656 Z= 0.144 Angle : 0.727 14.552 24167 Z= 0.319 Chirality : 0.047 0.301 2983 Planarity : 0.003 0.045 2857 Dihedral : 8.425 59.143 4619 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.39 % Allowed : 10.95 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1913 helix: 0.88 (0.27), residues: 379 sheet: -0.66 (0.24), residues: 472 loop : -0.54 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG g 520 TYR 0.014 0.001 TYR L 41 PHE 0.019 0.001 PHE H 84 TRP 0.014 0.001 TRP H 38 HIS 0.002 0.001 HIS H 83 Details of bonding type rmsd covalent geometry : bond 0.00314 (17500) covalent geometry : angle 0.64870 (23737) SS BOND : bond 0.00207 ( 38) SS BOND : angle 0.68340 ( 76) hydrogen bonds : bond 0.04679 ( 446) hydrogen bonds : angle 5.84916 ( 1206) link_ALPHA1-3 : bond 0.01924 ( 1) link_ALPHA1-3 : angle 3.20195 ( 3) link_ALPHA1-6 : bond 0.01030 ( 1) link_ALPHA1-6 : angle 1.27233 ( 3) link_BETA1-4 : bond 0.00636 ( 50) link_BETA1-4 : angle 3.06343 ( 150) link_NAG-ASN : bond 0.00328 ( 66) link_NAG-ASN : angle 2.57580 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 LYS cc_start: 0.9294 (mtpt) cc_final: 0.8951 (ttpp) REVERT: L 39 ASP cc_start: 0.8548 (m-30) cc_final: 0.7955 (p0) REVERT: L 43 GLN cc_start: 0.7975 (tp40) cc_final: 0.7613 (tp-100) REVERT: L 54 TYR cc_start: 0.8732 (t80) cc_final: 0.8299 (t80) REVERT: b 95 MET cc_start: 0.8967 (ptm) cc_final: 0.8676 (ptt) REVERT: b 161 MET cc_start: 0.9197 (tpp) cc_final: 0.8923 (tpp) REVERT: e 535 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.8937 (tp) REVERT: e 589 ASP cc_start: 0.9469 (OUTLIER) cc_final: 0.8919 (t0) REVERT: e 651 ASN cc_start: 0.9415 (t0) cc_final: 0.9037 (p0) REVERT: f 477 ASP cc_start: 0.9119 (m-30) cc_final: 0.8796 (m-30) REVERT: g 633 LYS cc_start: 0.9082 (pttm) cc_final: 0.8819 (pttm) outliers start: 24 outliers final: 18 residues processed: 133 average time/residue: 0.1391 time to fit residues: 28.2185 Evaluate side-chains 123 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain b residue 123 THR Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 606 THR Chi-restraints excluded: chain c residue 622 ILE Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 274 SER Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain e residue 535 ILE Chi-restraints excluded: chain e residue 589 ASP Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 326 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 110 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 175 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 189 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 0.0020 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 425 ASN d 195 ASN e 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.046981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.036763 restraints weight = 104589.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.038077 restraints weight = 54729.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.038962 restraints weight = 36315.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.039580 restraints weight = 27932.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.039984 restraints weight = 23368.758| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17656 Z= 0.123 Angle : 0.696 14.396 24167 Z= 0.303 Chirality : 0.046 0.288 2983 Planarity : 0.003 0.033 2857 Dihedral : 7.896 59.331 4617 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.09 % Allowed : 10.72 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -0.33 (0.19), residues: 1913 helix: 1.07 (0.28), residues: 379 sheet: -0.62 (0.24), residues: 476 loop : -0.43 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 82 TYR 0.011 0.001 TYR L 41 PHE 0.019 0.001 PHE H 84 TRP 0.015 0.001 TRP e 631 HIS 0.002 0.001 HIS c 564 Details of bonding type rmsd covalent geometry : bond 0.00271 (17500) covalent geometry : angle 0.62145 (23737) SS BOND : bond 0.00215 ( 38) SS BOND : angle 0.57112 ( 76) hydrogen bonds : bond 0.04093 ( 446) hydrogen bonds : angle 5.53878 ( 1206) link_ALPHA1-3 : bond 0.01668 ( 1) link_ALPHA1-3 : angle 3.36132 ( 3) link_ALPHA1-6 : bond 0.01214 ( 1) link_ALPHA1-6 : angle 1.26180 ( 3) link_BETA1-4 : bond 0.00626 ( 50) link_BETA1-4 : angle 2.93846 ( 150) link_NAG-ASN : bond 0.00333 ( 66) link_NAG-ASN : angle 2.45378 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 LYS cc_start: 0.9280 (mtpt) cc_final: 0.8930 (ttpp) REVERT: L 39 ASP cc_start: 0.8511 (m-30) cc_final: 0.8027 (p0) REVERT: L 43 GLN cc_start: 0.7931 (tp40) cc_final: 0.7610 (tp-100) REVERT: b 95 MET cc_start: 0.8979 (ptm) cc_final: 0.8675 (ptt) REVERT: b 320 MET cc_start: 0.7561 (mtp) cc_final: 0.7357 (mtp) REVERT: d 161 MET cc_start: 0.8451 (tpp) cc_final: 0.8183 (tpp) REVERT: e 530 MET cc_start: 0.8500 (mmt) cc_final: 0.7245 (tpp) REVERT: e 589 ASP cc_start: 0.9409 (OUTLIER) cc_final: 0.8858 (t0) REVERT: e 651 ASN cc_start: 0.9356 (t160) cc_final: 0.8973 (p0) REVERT: e 658 LYS cc_start: 0.8714 (mmmt) cc_final: 0.7915 (mtmm) REVERT: f 477 ASP cc_start: 0.9107 (m-30) cc_final: 0.8771 (m-30) REVERT: g 530 MET cc_start: 0.8026 (mmt) cc_final: 0.7315 (mmm) outliers start: 36 outliers final: 27 residues processed: 143 average time/residue: 0.1348 time to fit residues: 30.0585 Evaluate side-chains 131 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 606 THR Chi-restraints excluded: chain c residue 622 ILE Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 182 VAL Chi-restraints excluded: chain d residue 195 ASN Chi-restraints excluded: chain d residue 364 SER Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 589 ASP Chi-restraints excluded: chain e residue 599 SER Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain f residue 122 LEU Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 326 ILE Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain g residue 603 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 37 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 185 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 86 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 84 optimal weight: 0.2980 chunk 178 optimal weight: 7.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 425 ASN c 651 ASN f 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.046150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.035933 restraints weight = 104419.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.037221 restraints weight = 55091.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.038088 restraints weight = 36716.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.038671 restraints weight = 28269.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.039087 restraints weight = 23801.614| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17656 Z= 0.157 Angle : 0.708 14.311 24167 Z= 0.310 Chirality : 0.046 0.295 2983 Planarity : 0.003 0.042 2857 Dihedral : 7.796 58.452 4617 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.09 % Allowed : 11.18 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.19), residues: 1913 helix: 1.03 (0.28), residues: 382 sheet: -0.49 (0.25), residues: 452 loop : -0.42 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 82 TYR 0.011 0.001 TYR L 54 PHE 0.017 0.001 PHE H 84 TRP 0.012 0.001 TRP H 38 HIS 0.003 0.001 HIS c 564 Details of bonding type rmsd covalent geometry : bond 0.00346 (17500) covalent geometry : angle 0.63792 (23737) SS BOND : bond 0.00249 ( 38) SS BOND : angle 0.60169 ( 76) hydrogen bonds : bond 0.03994 ( 446) hydrogen bonds : angle 5.38733 ( 1206) link_ALPHA1-3 : bond 0.01787 ( 1) link_ALPHA1-3 : angle 3.44179 ( 3) link_ALPHA1-6 : bond 0.01285 ( 1) link_ALPHA1-6 : angle 1.33519 ( 3) link_BETA1-4 : bond 0.00608 ( 50) link_BETA1-4 : angle 2.84575 ( 150) link_NAG-ASN : bond 0.00345 ( 66) link_NAG-ASN : angle 2.44520 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 LYS cc_start: 0.9272 (mtpt) cc_final: 0.8912 (ttpp) REVERT: L 39 ASP cc_start: 0.8504 (m-30) cc_final: 0.7937 (p0) REVERT: L 43 GLN cc_start: 0.7952 (tp40) cc_final: 0.7601 (tp-100) REVERT: L 54 TYR cc_start: 0.8666 (t80) cc_final: 0.8196 (t80) REVERT: L 99 LEU cc_start: 0.9353 (mm) cc_final: 0.9052 (tp) REVERT: b 95 MET cc_start: 0.9009 (ptm) cc_final: 0.8671 (ptt) REVERT: d 320 MET cc_start: 0.8630 (mpp) cc_final: 0.8337 (mpp) REVERT: e 530 MET cc_start: 0.8676 (mmt) cc_final: 0.7533 (tpp) REVERT: e 536 THR cc_start: 0.9359 (p) cc_final: 0.9147 (t) REVERT: e 589 ASP cc_start: 0.9438 (OUTLIER) cc_final: 0.8910 (t0) REVERT: e 651 ASN cc_start: 0.9381 (t160) cc_final: 0.9095 (p0) REVERT: f 477 ASP cc_start: 0.9119 (m-30) cc_final: 0.8801 (m-30) REVERT: g 530 MET cc_start: 0.8177 (mmt) cc_final: 0.7828 (tpp) outliers start: 36 outliers final: 32 residues processed: 136 average time/residue: 0.1385 time to fit residues: 28.9997 Evaluate side-chains 133 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain b residue 100 MET Chi-restraints excluded: chain b residue 123 THR Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 434 MET Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 606 THR Chi-restraints excluded: chain c residue 622 ILE Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 182 VAL Chi-restraints excluded: chain d residue 195 ASN Chi-restraints excluded: chain d residue 274 SER Chi-restraints excluded: chain d residue 364 SER Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 568 LEU Chi-restraints excluded: chain e residue 589 ASP Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 122 LEU Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 326 ILE Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain g residue 603 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 70 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 92 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.045968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.035746 restraints weight = 104615.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.037040 restraints weight = 54795.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.037910 restraints weight = 36482.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.038491 restraints weight = 28142.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.038874 restraints weight = 23709.543| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17656 Z= 0.146 Angle : 0.699 14.276 24167 Z= 0.307 Chirality : 0.046 0.290 2983 Planarity : 0.003 0.040 2857 Dihedral : 7.760 58.501 4617 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.09 % Allowed : 11.94 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -0.21 (0.19), residues: 1913 helix: 0.99 (0.28), residues: 382 sheet: -0.41 (0.25), residues: 458 loop : -0.36 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG g 520 TYR 0.024 0.001 TYR L 92 PHE 0.018 0.001 PHE H 84 TRP 0.013 0.001 TRP H 38 HIS 0.002 0.001 HIS d 72 Details of bonding type rmsd covalent geometry : bond 0.00320 (17500) covalent geometry : angle 0.63064 (23737) SS BOND : bond 0.00245 ( 38) SS BOND : angle 0.60059 ( 76) hydrogen bonds : bond 0.03893 ( 446) hydrogen bonds : angle 5.29317 ( 1206) link_ALPHA1-3 : bond 0.01716 ( 1) link_ALPHA1-3 : angle 3.39790 ( 3) link_ALPHA1-6 : bond 0.01262 ( 1) link_ALPHA1-6 : angle 1.38737 ( 3) link_BETA1-4 : bond 0.00584 ( 50) link_BETA1-4 : angle 2.78576 ( 150) link_NAG-ASN : bond 0.00342 ( 66) link_NAG-ASN : angle 2.38871 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 LYS cc_start: 0.9180 (mtpt) cc_final: 0.8818 (ttpp) REVERT: L 43 GLN cc_start: 0.7994 (tp40) cc_final: 0.7591 (tp-100) REVERT: L 54 TYR cc_start: 0.8679 (t80) cc_final: 0.8291 (t80) REVERT: L 99 LEU cc_start: 0.9368 (mm) cc_final: 0.9103 (tp) REVERT: b 95 MET cc_start: 0.9034 (ptm) cc_final: 0.8724 (ptt) REVERT: d 161 MET cc_start: 0.8513 (tpp) cc_final: 0.8218 (tpp) REVERT: e 530 MET cc_start: 0.8725 (mmt) cc_final: 0.7561 (tpp) REVERT: e 589 ASP cc_start: 0.9421 (OUTLIER) cc_final: 0.8891 (t0) REVERT: f 477 ASP cc_start: 0.9143 (m-30) cc_final: 0.8805 (m-30) REVERT: g 530 MET cc_start: 0.8167 (mmt) cc_final: 0.7819 (tpp) outliers start: 36 outliers final: 29 residues processed: 132 average time/residue: 0.1301 time to fit residues: 26.7570 Evaluate side-chains 126 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain b residue 123 THR Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 434 MET Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 535 ILE Chi-restraints excluded: chain c residue 606 THR Chi-restraints excluded: chain c residue 622 ILE Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 182 VAL Chi-restraints excluded: chain d residue 195 ASN Chi-restraints excluded: chain d residue 364 SER Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 589 ASP Chi-restraints excluded: chain e residue 599 SER Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 122 LEU Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain g residue 603 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 118 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.045233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.035065 restraints weight = 105606.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.036313 restraints weight = 56250.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.037161 restraints weight = 37953.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.037723 restraints weight = 29477.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.038098 restraints weight = 24949.429| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17656 Z= 0.188 Angle : 0.727 14.244 24167 Z= 0.319 Chirality : 0.046 0.305 2983 Planarity : 0.003 0.037 2857 Dihedral : 7.870 60.179 4617 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.26 % Allowed : 12.46 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -0.22 (0.19), residues: 1913 helix: 1.00 (0.27), residues: 379 sheet: -0.41 (0.24), residues: 481 loop : -0.36 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 66 TYR 0.013 0.001 TYR b 302 PHE 0.021 0.002 PHE d 382 TRP 0.011 0.001 TRP H 38 HIS 0.003 0.001 HIS f 85 Details of bonding type rmsd covalent geometry : bond 0.00415 (17500) covalent geometry : angle 0.66227 (23737) SS BOND : bond 0.00278 ( 38) SS BOND : angle 0.64834 ( 76) hydrogen bonds : bond 0.03922 ( 446) hydrogen bonds : angle 5.26052 ( 1206) link_ALPHA1-3 : bond 0.01788 ( 1) link_ALPHA1-3 : angle 3.32437 ( 3) link_ALPHA1-6 : bond 0.01244 ( 1) link_ALPHA1-6 : angle 1.30043 ( 3) link_BETA1-4 : bond 0.00569 ( 50) link_BETA1-4 : angle 2.74118 ( 150) link_NAG-ASN : bond 0.00388 ( 66) link_NAG-ASN : angle 2.41637 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 95 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.8530 (mmm-85) cc_final: 0.8284 (mmm-85) REVERT: L 43 GLN cc_start: 0.8037 (tp40) cc_final: 0.7639 (tp-100) REVERT: L 54 TYR cc_start: 0.8752 (t80) cc_final: 0.8371 (t80) REVERT: L 99 LEU cc_start: 0.9330 (mm) cc_final: 0.9093 (tp) REVERT: b 95 MET cc_start: 0.9044 (ptm) cc_final: 0.8786 (ptm) REVERT: f 477 ASP cc_start: 0.9110 (m-30) cc_final: 0.8781 (m-30) REVERT: g 530 MET cc_start: 0.8376 (mmt) cc_final: 0.8033 (tpp) outliers start: 39 outliers final: 36 residues processed: 126 average time/residue: 0.1317 time to fit residues: 26.0360 Evaluate side-chains 128 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain b residue 100 MET Chi-restraints excluded: chain b residue 123 THR Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 434 MET Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 606 THR Chi-restraints excluded: chain c residue 622 ILE Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 182 VAL Chi-restraints excluded: chain d residue 195 ASN Chi-restraints excluded: chain d residue 364 SER Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 589 ASP Chi-restraints excluded: chain e residue 599 SER Chi-restraints excluded: chain e residue 605 CYS Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 122 LEU Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 195 ASN Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain g residue 603 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 122 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 182 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 152 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.045754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.035475 restraints weight = 105633.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.036756 restraints weight = 55619.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.037634 restraints weight = 37280.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.038190 restraints weight = 28777.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.038598 restraints weight = 24334.160| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17656 Z= 0.121 Angle : 0.688 14.226 24167 Z= 0.301 Chirality : 0.046 0.289 2983 Planarity : 0.003 0.034 2857 Dihedral : 7.768 59.806 4617 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.91 % Allowed : 12.98 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -0.03 (0.19), residues: 1913 helix: 1.13 (0.28), residues: 375 sheet: -0.32 (0.24), residues: 501 loop : -0.20 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG g 520 TYR 0.014 0.001 TYR L 92 PHE 0.019 0.001 PHE H 84 TRP 0.021 0.001 TRP H 38 HIS 0.004 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00265 (17500) covalent geometry : angle 0.62302 (23737) SS BOND : bond 0.00229 ( 38) SS BOND : angle 0.53521 ( 76) hydrogen bonds : bond 0.03742 ( 446) hydrogen bonds : angle 5.15122 ( 1206) link_ALPHA1-3 : bond 0.01760 ( 1) link_ALPHA1-3 : angle 3.29371 ( 3) link_ALPHA1-6 : bond 0.01264 ( 1) link_ALPHA1-6 : angle 1.23670 ( 3) link_BETA1-4 : bond 0.00607 ( 50) link_BETA1-4 : angle 2.71454 ( 150) link_NAG-ASN : bond 0.00338 ( 66) link_NAG-ASN : angle 2.31385 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 43 GLN cc_start: 0.7941 (tp40) cc_final: 0.7522 (tp-100) REVERT: L 54 TYR cc_start: 0.8681 (t80) cc_final: 0.8294 (t80) REVERT: L 86 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7560 (pm20) REVERT: L 99 LEU cc_start: 0.9340 (mm) cc_final: 0.9108 (tp) REVERT: b 95 MET cc_start: 0.9066 (ptm) cc_final: 0.8754 (ptm) REVERT: d 95 MET cc_start: 0.8021 (ptt) cc_final: 0.7691 (ptt) REVERT: d 161 MET cc_start: 0.8424 (tpp) cc_final: 0.8104 (tpp) REVERT: e 530 MET cc_start: 0.8756 (mmt) cc_final: 0.7495 (tpp) REVERT: f 477 ASP cc_start: 0.9175 (m-30) cc_final: 0.8844 (m-30) REVERT: g 530 MET cc_start: 0.8172 (mmt) cc_final: 0.7835 (tpp) outliers start: 33 outliers final: 32 residues processed: 129 average time/residue: 0.1347 time to fit residues: 27.1995 Evaluate side-chains 128 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain b residue 123 THR Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 434 MET Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 606 THR Chi-restraints excluded: chain c residue 622 ILE Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 195 ASN Chi-restraints excluded: chain d residue 364 SER Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 589 ASP Chi-restraints excluded: chain e residue 599 SER Chi-restraints excluded: chain e residue 605 CYS Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 122 LEU Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 195 ASN Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain g residue 603 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 80 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.044813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.034625 restraints weight = 106393.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.035870 restraints weight = 56856.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.036707 restraints weight = 38304.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.037266 restraints weight = 29758.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.037657 restraints weight = 25218.630| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17656 Z= 0.200 Angle : 0.739 14.244 24167 Z= 0.326 Chirality : 0.046 0.312 2983 Planarity : 0.003 0.038 2857 Dihedral : 7.938 60.604 4617 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.20 % Allowed : 13.04 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -0.19 (0.19), residues: 1913 helix: 1.04 (0.27), residues: 378 sheet: -0.42 (0.24), residues: 489 loop : -0.33 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 82 TYR 0.014 0.001 TYR b 302 PHE 0.018 0.002 PHE H 84 TRP 0.015 0.001 TRP H 38 HIS 0.005 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00437 (17500) covalent geometry : angle 0.67736 (23737) SS BOND : bond 0.00308 ( 38) SS BOND : angle 0.69853 ( 76) hydrogen bonds : bond 0.03940 ( 446) hydrogen bonds : angle 5.20522 ( 1206) link_ALPHA1-3 : bond 0.01561 ( 1) link_ALPHA1-3 : angle 3.23450 ( 3) link_ALPHA1-6 : bond 0.01206 ( 1) link_ALPHA1-6 : angle 1.25003 ( 3) link_BETA1-4 : bond 0.00571 ( 50) link_BETA1-4 : angle 2.69445 ( 150) link_NAG-ASN : bond 0.00415 ( 66) link_NAG-ASN : angle 2.41682 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 43 GLN cc_start: 0.7912 (tp40) cc_final: 0.7577 (tp40) REVERT: L 54 TYR cc_start: 0.8724 (t80) cc_final: 0.8311 (t80) REVERT: L 99 LEU cc_start: 0.9288 (mm) cc_final: 0.9083 (tp) REVERT: b 95 MET cc_start: 0.9075 (ptm) cc_final: 0.8770 (ptm) REVERT: d 95 MET cc_start: 0.8023 (ptt) cc_final: 0.7735 (ptt) REVERT: d 161 MET cc_start: 0.8640 (tpp) cc_final: 0.8321 (tpp) REVERT: e 530 MET cc_start: 0.8724 (mmt) cc_final: 0.7541 (tpp) REVERT: f 477 ASP cc_start: 0.9170 (m-30) cc_final: 0.8842 (m-30) REVERT: g 530 MET cc_start: 0.8480 (mmt) cc_final: 0.7401 (tpp) outliers start: 38 outliers final: 36 residues processed: 124 average time/residue: 0.1332 time to fit residues: 25.8102 Evaluate side-chains 127 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain b residue 100 MET Chi-restraints excluded: chain b residue 123 THR Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 434 MET Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 606 THR Chi-restraints excluded: chain c residue 622 ILE Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 195 ASN Chi-restraints excluded: chain d residue 274 SER Chi-restraints excluded: chain d residue 364 SER Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 589 ASP Chi-restraints excluded: chain e residue 599 SER Chi-restraints excluded: chain e residue 605 CYS Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 122 LEU Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 195 ASN Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain g residue 603 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 91 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 167 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 181 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.044743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.034568 restraints weight = 111109.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.035811 restraints weight = 60262.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.036644 restraints weight = 40843.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.037189 restraints weight = 31798.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.037584 restraints weight = 27010.374| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17656 Z= 0.136 Angle : 0.701 14.261 24167 Z= 0.308 Chirality : 0.046 0.295 2983 Planarity : 0.003 0.042 2857 Dihedral : 7.855 59.835 4617 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.03 % Allowed : 13.44 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -0.06 (0.19), residues: 1913 helix: 1.15 (0.28), residues: 375 sheet: -0.34 (0.24), residues: 503 loop : -0.22 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 82 TYR 0.012 0.001 TYR L 92 PHE 0.021 0.001 PHE H 84 TRP 0.017 0.001 TRP H 38 HIS 0.004 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00299 (17500) covalent geometry : angle 0.63857 (23737) SS BOND : bond 0.00258 ( 38) SS BOND : angle 0.54420 ( 76) hydrogen bonds : bond 0.03741 ( 446) hydrogen bonds : angle 5.09819 ( 1206) link_ALPHA1-3 : bond 0.01658 ( 1) link_ALPHA1-3 : angle 3.17983 ( 3) link_ALPHA1-6 : bond 0.01232 ( 1) link_ALPHA1-6 : angle 1.20365 ( 3) link_BETA1-4 : bond 0.00597 ( 50) link_BETA1-4 : angle 2.68244 ( 150) link_NAG-ASN : bond 0.00340 ( 66) link_NAG-ASN : angle 2.30854 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 39 ASP cc_start: 0.8510 (m-30) cc_final: 0.7910 (p0) REVERT: L 43 GLN cc_start: 0.7907 (tp40) cc_final: 0.7521 (tp40) REVERT: L 54 TYR cc_start: 0.8719 (t80) cc_final: 0.8234 (t80) REVERT: L 86 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7571 (pm20) REVERT: L 99 LEU cc_start: 0.9281 (mm) cc_final: 0.9071 (tp) REVERT: b 95 MET cc_start: 0.9059 (ptm) cc_final: 0.8795 (ptm) REVERT: b 161 MET cc_start: 0.9248 (tpp) cc_final: 0.8674 (tpp) REVERT: d 95 MET cc_start: 0.7936 (ptt) cc_final: 0.7584 (ptt) REVERT: d 161 MET cc_start: 0.8460 (tpp) cc_final: 0.8168 (tpp) REVERT: e 530 MET cc_start: 0.8721 (mmt) cc_final: 0.7550 (tpp) REVERT: f 477 ASP cc_start: 0.9175 (m-30) cc_final: 0.8850 (m-30) REVERT: g 530 MET cc_start: 0.8289 (mmt) cc_final: 0.7268 (tpp) outliers start: 35 outliers final: 35 residues processed: 126 average time/residue: 0.1303 time to fit residues: 25.6795 Evaluate side-chains 128 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain b residue 123 THR Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 339 ASN Chi-restraints excluded: chain b residue 434 MET Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 606 THR Chi-restraints excluded: chain c residue 622 ILE Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 195 ASN Chi-restraints excluded: chain d residue 274 SER Chi-restraints excluded: chain d residue 364 SER Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 589 ASP Chi-restraints excluded: chain e residue 599 SER Chi-restraints excluded: chain e residue 605 CYS Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 122 LEU Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 195 ASN Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain g residue 603 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 181 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 171 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.044512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.034336 restraints weight = 111880.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.035557 restraints weight = 60579.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.036380 restraints weight = 41405.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.036927 restraints weight = 32340.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.037321 restraints weight = 27504.112| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17656 Z= 0.160 Angle : 0.713 14.279 24167 Z= 0.314 Chirality : 0.045 0.301 2983 Planarity : 0.003 0.035 2857 Dihedral : 7.888 59.942 4617 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.20 % Allowed : 13.33 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -0.06 (0.19), residues: 1913 helix: 1.13 (0.27), residues: 375 sheet: -0.32 (0.24), residues: 494 loop : -0.23 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.011 0.001 TYR L 92 PHE 0.021 0.001 PHE H 84 TRP 0.016 0.001 TRP H 38 HIS 0.005 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00351 (17500) covalent geometry : angle 0.65164 (23737) SS BOND : bond 0.00279 ( 38) SS BOND : angle 0.58362 ( 76) hydrogen bonds : bond 0.03771 ( 446) hydrogen bonds : angle 5.09324 ( 1206) link_ALPHA1-3 : bond 0.01728 ( 1) link_ALPHA1-3 : angle 3.09095 ( 3) link_ALPHA1-6 : bond 0.01090 ( 1) link_ALPHA1-6 : angle 1.12456 ( 3) link_BETA1-4 : bond 0.00578 ( 50) link_BETA1-4 : angle 2.64930 ( 150) link_NAG-ASN : bond 0.00368 ( 66) link_NAG-ASN : angle 2.33818 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2438.53 seconds wall clock time: 43 minutes 23.04 seconds (2603.04 seconds total)