Starting phenix.real_space_refine on Thu Sep 18 11:23:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bnm_44730/09_2025/9bnm_44730.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bnm_44730/09_2025/9bnm_44730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bnm_44730/09_2025/9bnm_44730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bnm_44730/09_2025/9bnm_44730.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bnm_44730/09_2025/9bnm_44730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bnm_44730/09_2025/9bnm_44730.map" } resolution = 3.97 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= 0.017 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 115 5.16 5 C 10270 2.51 5 N 2731 2.21 5 O 3334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16450 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3414 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 4 Chain: "B" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3416 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 4 Chain: "C" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3438 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Chain: "H" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1005 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 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: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102} Chain: "X" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "Y" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "Z" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: "A" 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: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "C" 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: "Y" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Z" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.55, per 1000 atoms: 0.22 Number of scatterers: 16450 At special positions: 0 Unit cell: (127.82, 122.01, 164.34, 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 115 16.00 O 3334 8.00 N 2731 7.00 C 10270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS X 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 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=2.04 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 Y 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS Z 605 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS X 598 " - pdb=" SG CYS X 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 598 " - pdb=" SG CYS Y 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 598 " - pdb=" SG CYS Z 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 M 3 " - " MAN M 4 " " BMA S 3 " - " MAN S 4 " " BMA k 3 " - " MAN k 7 " " MAN k 4 " - " MAN k 5 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA k 3 " - " MAN k 4 " " MAN k 4 " - " MAN k 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " 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-ASN " NAG A 601 " - " ASN A 448 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 88 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 234 " " NAG B 601 " - " ASN B 363 " " NAG B 602 " - " ASN B 355 " " NAG B 603 " - " ASN B 133 " " NAG B 604 " - " ASN B 339 " " NAG B 605 " - " ASN B 234 " " NAG C 601 " - " ASN C 448 " " NAG C 602 " - " ASN C 276 " " NAG C 603 " - " ASN C 355 " " NAG C 604 " - " ASN C 133 " " NAG C 605 " - " ASN C 88 " " NAG C 606 " - " ASN C 339 " " NAG D 1 " - " ASN A 363 " " NAG E 1 " - " ASN A 392 " " NAG F 1 " - " ASN A 386 " " NAG G 1 " - " ASN A 262 " " NAG I 1 " - " ASN A 276 " " NAG J 1 " - " ASN A 355 " " NAG K 1 " - " ASN A 295 " " NAG M 1 " - " ASN A 160 " " NAG N 1 " - " ASN A 156 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN A 332 " " NAG Q 1 " - " ASN B 392 " " NAG R 1 " - " ASN B 386 " " NAG S 1 " - " ASN B 262 " " NAG T 1 " - " ASN B 276 " " NAG U 1 " - " ASN B 295 " " NAG V 1 " - " ASN B 160 " " NAG W 1 " - " ASN B 156 " " NAG Y 701 " - " ASN Y 611 " " NAG Z 701 " - " ASN Z 618 " " NAG a 1 " - " ASN B 197 " " NAG b 1 " - " ASN B 88 " " NAG c 1 " - " ASN B 332 " " NAG d 1 " - " ASN B 301 " " NAG e 1 " - " ASN B 448 " " NAG f 1 " - " ASN C 363 " " NAG g 1 " - " ASN C 392 " " NAG h 1 " - " ASN C 386 " " NAG i 1 " - " ASN C 262 " " NAG j 1 " - " ASN C 295 " " NAG k 1 " - " ASN C 160 " " NAG l 1 " - " ASN C 156 " " NAG m 1 " - " ASN C 197 " " NAG n 1 " - " ASN C 332 " " NAG o 1 " - " ASN C 301 " " NAG p 1 " - " ASN C 234 " Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 456.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3566 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 28 sheets defined 25.6% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.575A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.720A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.574A pdb=" N PHE A 391 " --> pdb=" O SER A 388 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN A 392 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.786A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 484 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 117 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.628A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 335 through 354 removed outlier: 3.585A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.923A pdb=" N ARG B 429 " --> pdb=" O MET B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 Processing helix chain 'B' and resid 474 through 484 removed outlier: 4.359A pdb=" N ASN B 478 " --> pdb=" O ASP B 474 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 99 through 116 Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.810A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 335 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 475 through 484 removed outlier: 4.164A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'X' and resid 529 through 534 Processing helix chain 'X' and resid 536 through 544 removed outlier: 4.292A pdb=" N GLN X 540 " --> pdb=" O THR X 536 " (cutoff:3.500A) Processing helix chain 'X' and resid 569 through 595 Processing helix chain 'X' and resid 618 through 623 removed outlier: 3.559A pdb=" N TRP X 623 " --> pdb=" O LEU X 619 " (cutoff:3.500A) Processing helix chain 'X' and resid 627 through 635 Processing helix chain 'X' and resid 638 through 664 removed outlier: 3.507A pdb=" N LEU X 663 " --> pdb=" O ASP X 659 " (cutoff:3.500A) Processing helix chain 'Y' and resid 529 through 535 Processing helix chain 'Y' and resid 536 through 544 removed outlier: 4.185A pdb=" N GLN Y 540 " --> pdb=" O THR Y 536 " (cutoff:3.500A) Processing helix chain 'Y' and resid 569 through 596 removed outlier: 3.710A pdb=" N TRP Y 596 " --> pdb=" O LEU Y 592 " (cutoff:3.500A) Processing helix chain 'Y' and resid 618 through 625 Processing helix chain 'Y' and resid 627 through 636 Processing helix chain 'Y' and resid 638 through 664 removed outlier: 3.556A pdb=" N ILE Y 642 " --> pdb=" O TYR Y 638 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR Y 643 " --> pdb=" O THR Y 639 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY Y 644 " --> pdb=" O GLN Y 640 " (cutoff:3.500A) Processing helix chain 'Z' and resid 523 through 527 removed outlier: 4.537A pdb=" N GLY Z 527 " --> pdb=" O GLY Z 524 " (cutoff:3.500A) Processing helix chain 'Z' and resid 529 through 534 Processing helix chain 'Z' and resid 536 through 544 removed outlier: 4.221A pdb=" N GLN Z 540 " --> pdb=" O THR Z 536 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU Z 544 " --> pdb=" O GLN Z 540 " (cutoff:3.500A) Processing helix chain 'Z' and resid 569 through 596 removed outlier: 3.729A pdb=" N LYS Z 574 " --> pdb=" O VAL Z 570 " (cutoff:3.500A) Processing helix chain 'Z' and resid 618 through 623 removed outlier: 3.916A pdb=" N ILE Z 622 " --> pdb=" O ASN Z 618 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP Z 623 " --> pdb=" O LEU Z 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 618 through 623' Processing helix chain 'Z' and resid 628 through 636 Processing helix chain 'Z' and resid 638 through 664 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.355A pdb=" N VAL A 36 " --> pdb=" O THR X 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.348A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 7.176A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS A 218 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 4.171A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS A 239 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 93 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 176 removed outlier: 3.520A pdb=" N MET A 161 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 172 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN A 160 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR A 128 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.031A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 298 removed outlier: 7.127A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 297 " --> pdb=" O HIS A 330 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 330 through 334 current: chain 'A' and resid 383 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 413 through 420 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.190A pdb=" N SER A 306 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA A 319 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ARG A 308 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE A 317 " --> pdb=" O ARG A 308 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 312 " --> pdb=" O GLN A 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.302A pdb=" N VAL Y 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL B 38 " --> pdb=" O THR Y 606 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N THR Y 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N TYR B 40 " --> pdb=" O CYS Y 604 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N CYS Y 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.794A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AB3, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.603A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 169 through 176 removed outlier: 3.529A pdb=" N VAL B 182 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing sheet with id=AB5, 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 312 removed outlier: 7.367A pdb=" N ASN B 301 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ILE B 323 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 315 through 323A 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 470 Processing sheet with id=AB6, first strand: chain 'B' and resid 423 through 424 Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.238A pdb=" N VAL Z 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL C 38 " --> pdb=" O THR Z 606 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N THR Z 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TYR C 40 " --> pdb=" O CYS Z 604 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N CYS Z 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.906A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.156A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 56 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS C 218 " --> pdb=" O PHE C 53 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.688A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 170 through 176 removed outlier: 3.535A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 297 removed outlier: 7.261A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 330 through 334 current: chain 'C' and resid 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 382 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AC4, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AC5, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.620A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS H 22 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.512A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.989A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL H 37 " --> pdb=" O HIS H 91 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL H 94 " --> pdb=" O VAL H 102 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.187A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 13 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 469 hydrogen bonds defined for protein. 1308 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: 2.48 Time building geometry restraints manager: 2.35 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: 5102 1.34 - 1.47: 4085 1.47 - 1.59: 7416 1.59 - 1.72: 1 1.72 - 1.84: 152 Bond restraints: 16756 Sorted by residual: bond pdb=" OH TYS H 100F" pdb=" S TYS H 100F" ideal model delta sigma weight residual 1.679 1.595 0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" N VAL H 69 " pdb=" CA VAL H 69 " ideal model delta sigma weight residual 1.456 1.503 -0.047 1.15e-02 7.56e+03 1.71e+01 bond pdb=" N VAL H 100 " pdb=" CA VAL H 100 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.14e-02 7.69e+03 1.10e+01 bond pdb=" N VAL C 120 " pdb=" CA VAL C 120 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.17e-02 7.31e+03 1.09e+01 bond pdb=" N VAL H 32 " pdb=" CA VAL H 32 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.20e-02 6.94e+03 1.02e+01 ... (remaining 16751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 21995 2.40 - 4.81: 675 4.81 - 7.21: 52 7.21 - 9.62: 9 9.62 - 12.02: 1 Bond angle restraints: 22732 Sorted by residual: angle pdb=" CA ASP H 100A" pdb=" CB ASP H 100A" pdb=" CG ASP H 100A" ideal model delta sigma weight residual 112.60 118.55 -5.95 1.00e+00 1.00e+00 3.54e+01 angle pdb=" N ARG H 71 " pdb=" CA ARG H 71 " pdb=" CB ARG H 71 " ideal model delta sigma weight residual 111.05 119.49 -8.44 1.50e+00 4.44e-01 3.16e+01 angle pdb=" CG LYS A 169 " pdb=" CD LYS A 169 " pdb=" CE LYS A 169 " ideal model delta sigma weight residual 111.30 123.32 -12.02 2.30e+00 1.89e-01 2.73e+01 angle pdb=" C ASP H 100A" pdb=" CA ASP H 100A" pdb=" CB ASP H 100A" ideal model delta sigma weight residual 112.09 119.83 -7.74 1.54e+00 4.22e-01 2.53e+01 angle pdb=" C ARG H 71 " pdb=" CA ARG H 71 " pdb=" CB ARG H 71 " ideal model delta sigma weight residual 110.24 100.81 9.43 1.88e+00 2.83e-01 2.52e+01 ... (remaining 22727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 10549 21.67 - 43.34: 632 43.34 - 65.01: 121 65.01 - 86.68: 60 86.68 - 108.35: 28 Dihedral angle restraints: 11390 sinusoidal: 5881 harmonic: 5509 Sorted by residual: dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual 93.00 174.08 -81.08 1 1.00e+01 1.00e-02 8.11e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS Z 605 " pdb=" CB CYS Z 605 " ideal model delta sinusoidal sigma weight residual -86.00 -6.96 -79.04 1 1.00e+01 1.00e-02 7.77e+01 dihedral pdb=" CB CYS B 119 " pdb=" SG CYS B 119 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual -86.00 -154.21 68.21 1 1.00e+01 1.00e-02 6.04e+01 ... (remaining 11387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.246: 2837 0.246 - 0.492: 15 0.492 - 0.738: 1 0.738 - 0.984: 1 0.984 - 1.231: 1 Chirality restraints: 2855 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 -2.07 -0.33 2.00e-02 2.50e+03 2.68e+02 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.42e+02 chirality pdb=" C1 NAG m 2 " pdb=" O4 NAG m 1 " pdb=" C2 NAG m 2 " pdb=" O5 NAG m 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.17e+02 ... (remaining 2852 not shown) Planarity restraints: 2809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.276 2.00e-02 2.50e+03 2.37e-01 7.01e+02 pdb=" C7 NAG M 1 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.414 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " 0.261 2.00e-02 2.50e+03 2.26e-01 6.39e+02 pdb=" C7 NAG M 2 " -0.053 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.007 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " -0.387 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " 0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG k 2 " 0.147 2.00e-02 2.50e+03 1.23e-01 1.88e+02 pdb=" C7 NAG k 2 " -0.037 2.00e-02 2.50e+03 pdb=" C8 NAG k 2 " 0.107 2.00e-02 2.50e+03 pdb=" N2 NAG k 2 " -0.202 2.00e-02 2.50e+03 pdb=" O7 NAG k 2 " -0.014 2.00e-02 2.50e+03 ... (remaining 2806 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 110 2.55 - 3.14: 13334 3.14 - 3.73: 23585 3.73 - 4.31: 32793 4.31 - 4.90: 54072 Nonbonded interactions: 123894 Sorted by model distance: nonbonded pdb=" O LYS H 75 " pdb=" OD1 ASN H 76 " model vdw 1.963 3.040 nonbonded pdb=" OG SER H 7 " pdb=" OG SER H 21 " model vdw 2.111 3.040 nonbonded pdb=" OG1 THR C 163 " pdb=" OE1 GLU C 164 " model vdw 2.160 3.040 nonbonded pdb=" OD1 ASN B 276 " pdb=" OG1 THR B 278 " model vdw 2.170 3.040 nonbonded pdb=" O3 NAG K 1 " pdb=" O5 NAG K 2 " model vdw 2.179 3.040 ... (remaining 123889 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 135 or resid 151 through 184 or resid 188 throu \ gh 605)) selection = (chain 'B' and (resid 33 through 135 or resid 151 through 605)) selection = (chain 'C' and (resid 33 through 135 or resid 151 through 184 or resid 188 throu \ gh 397 or resid 412 through 605)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'G' selection = chain 'W' selection = chain 'i' selection = chain 'l' } ncs_group { reference = chain 'X' selection = (chain 'Y' and resid 520 through 664) selection = (chain 'Z' and resid 520 through 664) } 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: 5.160 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.460 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 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 : 0.007 0.312 16895 Z= 0.371 Angle : 1.043 39.083 23111 Z= 0.518 Chirality : 0.065 1.231 2855 Planarity : 0.009 0.237 2756 Dihedral : 15.230 108.349 7710 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.19), residues: 1866 helix: 0.92 (0.27), residues: 421 sheet: -0.91 (0.24), residues: 484 loop : -1.22 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 19 TYR 0.065 0.001 TYR L 49 PHE 0.012 0.001 PHE C 376 TRP 0.027 0.001 TRP A 479 HIS 0.007 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00597 (16756) covalent geometry : angle 0.89040 (22732) SS BOND : bond 0.00458 ( 38) SS BOND : angle 2.24732 ( 76) hydrogen bonds : bond 0.19815 ( 469) hydrogen bonds : angle 7.82170 ( 1308) link_ALPHA1-3 : bond 0.04620 ( 4) link_ALPHA1-3 : angle 4.00522 ( 12) link_ALPHA1-6 : bond 0.03665 ( 3) link_ALPHA1-6 : angle 3.30839 ( 9) link_BETA1-4 : bond 0.03103 ( 41) link_BETA1-4 : angle 4.76560 ( 123) link_NAG-ASN : bond 0.04747 ( 53) link_NAG-ASN : angle 4.78232 ( 159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.541 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: A 104 MET cc_start: 0.8033 (ttt) cc_final: 0.7827 (ttt) REVERT: A 271 MET cc_start: 0.7448 (mmt) cc_final: 0.7215 (mmm) REVERT: A 475 MET cc_start: 0.8486 (tpp) cc_final: 0.8151 (tpt) REVERT: B 104 MET cc_start: 0.8815 (tpp) cc_final: 0.8411 (tpt) REVERT: H 82 LEU cc_start: 0.6961 (mm) cc_final: 0.6734 (mm) REVERT: L 82 ASP cc_start: 0.6126 (m-30) cc_final: 0.5620 (t70) REVERT: Z 581 LEU cc_start: 0.9234 (tp) cc_final: 0.8788 (pp) REVERT: Z 586 TYR cc_start: 0.9123 (t80) cc_final: 0.8821 (t80) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.1246 time to fit residues: 58.9132 Evaluate side-chains 219 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 656 ASN ** Z 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.085344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.066075 restraints weight = 54382.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.068242 restraints weight = 30689.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.069704 restraints weight = 21284.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.070691 restraints weight = 16670.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.071293 restraints weight = 14124.486| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 16895 Z= 0.283 Angle : 0.819 14.602 23111 Z= 0.384 Chirality : 0.049 0.378 2855 Planarity : 0.005 0.052 2756 Dihedral : 10.711 74.816 4128 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.66 % Allowed : 10.30 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.19), residues: 1866 helix: 1.12 (0.27), residues: 411 sheet: -0.75 (0.22), residues: 550 loop : -1.00 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG X 585 TYR 0.024 0.002 TYR L 49 PHE 0.014 0.002 PHE A 53 TRP 0.019 0.002 TRP A 479 HIS 0.007 0.002 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00642 (16756) covalent geometry : angle 0.76523 (22732) SS BOND : bond 0.00424 ( 38) SS BOND : angle 1.20977 ( 76) hydrogen bonds : bond 0.04826 ( 469) hydrogen bonds : angle 5.72448 ( 1308) link_ALPHA1-3 : bond 0.00701 ( 4) link_ALPHA1-3 : angle 2.10460 ( 12) link_ALPHA1-6 : bond 0.00890 ( 3) link_ALPHA1-6 : angle 2.42427 ( 9) link_BETA1-4 : bond 0.00564 ( 41) link_BETA1-4 : angle 2.64184 ( 123) link_NAG-ASN : bond 0.00523 ( 53) link_NAG-ASN : angle 2.66766 ( 159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.8057 (mmt) cc_final: 0.7587 (mmm) REVERT: B 69 TRP cc_start: 0.7472 (m-90) cc_final: 0.7270 (m-90) REVERT: B 116 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8792 (tp) REVERT: C 95 MET cc_start: 0.8887 (ppp) cc_final: 0.8176 (ppp) REVERT: C 377 ASN cc_start: 0.8763 (t0) cc_final: 0.8494 (t0) REVERT: H 75 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.7758 (pttm) REVERT: H 77 THR cc_start: 0.7154 (p) cc_final: 0.6864 (p) REVERT: H 79 TYR cc_start: 0.6968 (m-10) cc_final: 0.6522 (m-80) REVERT: L 87 TYR cc_start: 0.7862 (m-10) cc_final: 0.7082 (m-80) REVERT: X 584 GLU cc_start: 0.8518 (tt0) cc_final: 0.7656 (tm-30) REVERT: X 654 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8489 (mt-10) REVERT: Y 584 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8181 (tm-30) REVERT: Y 588 ARG cc_start: 0.8310 (ttm170) cc_final: 0.8070 (ttm110) REVERT: Z 586 TYR cc_start: 0.9315 (t80) cc_final: 0.9113 (t80) outliers start: 28 outliers final: 16 residues processed: 227 average time/residue: 0.1139 time to fit residues: 40.3027 Evaluate side-chains 196 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain Y residue 539 VAL Chi-restraints excluded: chain Y residue 637 ASN Chi-restraints excluded: chain Z residue 570 VAL Chi-restraints excluded: chain Z residue 613 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 428 GLN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 630 GLN ** Z 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.086982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.067599 restraints weight = 54321.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.069834 restraints weight = 30632.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.071370 restraints weight = 21120.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.072372 restraints weight = 16525.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.072937 restraints weight = 13970.641| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16895 Z= 0.141 Angle : 0.665 14.211 23111 Z= 0.310 Chirality : 0.046 0.350 2855 Planarity : 0.003 0.046 2756 Dihedral : 9.247 70.313 4128 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.07 % Allowed : 12.72 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.20), residues: 1866 helix: 1.41 (0.27), residues: 413 sheet: -0.64 (0.22), residues: 576 loop : -0.90 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 151 TYR 0.022 0.002 TYR X 586 PHE 0.024 0.001 PHE H 29 TRP 0.023 0.002 TRP X 631 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00317 (16756) covalent geometry : angle 0.61000 (22732) SS BOND : bond 0.00285 ( 38) SS BOND : angle 0.76660 ( 76) hydrogen bonds : bond 0.04040 ( 469) hydrogen bonds : angle 5.22810 ( 1308) link_ALPHA1-3 : bond 0.01212 ( 4) link_ALPHA1-3 : angle 2.07420 ( 12) link_ALPHA1-6 : bond 0.01004 ( 3) link_ALPHA1-6 : angle 2.10472 ( 9) link_BETA1-4 : bond 0.00505 ( 41) link_BETA1-4 : angle 2.25998 ( 123) link_NAG-ASN : bond 0.00366 ( 53) link_NAG-ASN : angle 2.52021 ( 159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8656 (ppp) cc_final: 0.7911 (ppp) REVERT: B 69 TRP cc_start: 0.7568 (m-90) cc_final: 0.7216 (m-90) REVERT: B 116 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8646 (tp) REVERT: B 279 ASN cc_start: 0.9321 (t0) cc_final: 0.9069 (t0) REVERT: C 95 MET cc_start: 0.8821 (ppp) cc_final: 0.8066 (ppp) REVERT: C 424 ILE cc_start: 0.9360 (pt) cc_final: 0.9043 (mt) REVERT: H 75 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7988 (pttm) REVERT: L 5 THR cc_start: 0.9019 (p) cc_final: 0.8770 (t) REVERT: L 87 TYR cc_start: 0.7899 (m-10) cc_final: 0.7076 (m-80) REVERT: X 584 GLU cc_start: 0.8463 (tt0) cc_final: 0.7573 (tm-30) REVERT: X 654 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8548 (mt-10) REVERT: Y 584 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8194 (tm-30) REVERT: Y 586 TYR cc_start: 0.9429 (t80) cc_final: 0.9223 (t80) REVERT: Y 588 ARG cc_start: 0.8300 (ttm170) cc_final: 0.8014 (ttm110) REVERT: Z 581 LEU cc_start: 0.9263 (tt) cc_final: 0.8822 (pp) REVERT: Z 630 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8748 (pm20) outliers start: 35 outliers final: 21 residues processed: 216 average time/residue: 0.1119 time to fit residues: 37.6404 Evaluate side-chains 204 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain X residue 544 LEU Chi-restraints excluded: chain X residue 589 ASP Chi-restraints excluded: chain Y residue 544 LEU Chi-restraints excluded: chain Z residue 570 VAL Chi-restraints excluded: chain Z residue 630 GLN Chi-restraints excluded: chain Z residue 635 ILE Chi-restraints excluded: chain Z residue 639 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 144 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.086238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.066916 restraints weight = 54097.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.069128 restraints weight = 30516.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.070631 restraints weight = 21038.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.071634 restraints weight = 16493.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.072168 restraints weight = 13972.658| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16895 Z= 0.147 Angle : 0.649 14.343 23111 Z= 0.303 Chirality : 0.045 0.338 2855 Planarity : 0.003 0.039 2756 Dihedral : 8.271 64.272 4128 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.54 % Allowed : 14.56 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.20), residues: 1866 helix: 1.51 (0.27), residues: 407 sheet: -0.46 (0.22), residues: 558 loop : -0.85 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 151 TYR 0.029 0.002 TYR Z 586 PHE 0.014 0.001 PHE H 29 TRP 0.023 0.002 TRP X 631 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00338 (16756) covalent geometry : angle 0.59575 (22732) SS BOND : bond 0.00221 ( 38) SS BOND : angle 0.75783 ( 76) hydrogen bonds : bond 0.03721 ( 469) hydrogen bonds : angle 5.04014 ( 1308) link_ALPHA1-3 : bond 0.01030 ( 4) link_ALPHA1-3 : angle 2.17532 ( 12) link_ALPHA1-6 : bond 0.01006 ( 3) link_ALPHA1-6 : angle 2.23301 ( 9) link_BETA1-4 : bond 0.00458 ( 41) link_BETA1-4 : angle 2.12621 ( 123) link_NAG-ASN : bond 0.00325 ( 53) link_NAG-ASN : angle 2.46162 ( 159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8720 (ppp) cc_final: 0.7820 (ppp) REVERT: A 271 MET cc_start: 0.8212 (mmt) cc_final: 0.7798 (mmm) REVERT: B 69 TRP cc_start: 0.7759 (m-90) cc_final: 0.7243 (m-90) REVERT: B 96 TRP cc_start: 0.8806 (m100) cc_final: 0.8539 (m100) REVERT: B 116 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8449 (tp) REVERT: C 95 MET cc_start: 0.8848 (ppp) cc_final: 0.8158 (ppp) REVERT: C 116 LEU cc_start: 0.9064 (mm) cc_final: 0.8344 (tp) REVERT: C 424 ILE cc_start: 0.9384 (pt) cc_final: 0.9102 (mt) REVERT: L 5 THR cc_start: 0.9018 (p) cc_final: 0.8767 (t) REVERT: L 87 TYR cc_start: 0.7927 (m-80) cc_final: 0.7094 (m-80) REVERT: X 584 GLU cc_start: 0.8487 (tt0) cc_final: 0.7625 (tm-30) REVERT: X 654 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8590 (mt-10) REVERT: Y 584 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8165 (tm-30) REVERT: Y 588 ARG cc_start: 0.8370 (ttm170) cc_final: 0.8076 (ttm110) REVERT: Z 581 LEU cc_start: 0.9275 (tt) cc_final: 0.8865 (pp) REVERT: Z 586 TYR cc_start: 0.9129 (t80) cc_final: 0.8820 (t80) REVERT: Z 638 TYR cc_start: 0.8100 (m-80) cc_final: 0.7846 (m-10) REVERT: Z 648 GLU cc_start: 0.8910 (tp30) cc_final: 0.8361 (tm-30) outliers start: 43 outliers final: 29 residues processed: 228 average time/residue: 0.1141 time to fit residues: 40.5458 Evaluate side-chains 211 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain X residue 589 ASP Chi-restraints excluded: chain Y residue 539 VAL Chi-restraints excluded: chain Y residue 592 LEU Chi-restraints excluded: chain Y residue 619 LEU Chi-restraints excluded: chain Y residue 637 ASN Chi-restraints excluded: chain Z residue 570 VAL Chi-restraints excluded: chain Z residue 639 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.085040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.065822 restraints weight = 54209.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.068010 restraints weight = 30497.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.069491 restraints weight = 21099.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.070478 restraints weight = 16495.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.071138 restraints weight = 13977.005| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16895 Z= 0.166 Angle : 0.654 14.044 23111 Z= 0.306 Chirality : 0.045 0.326 2855 Planarity : 0.003 0.037 2756 Dihedral : 7.984 58.871 4128 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.90 % Allowed : 15.92 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.20), residues: 1866 helix: 1.54 (0.27), residues: 408 sheet: -0.43 (0.22), residues: 566 loop : -0.88 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 151 TYR 0.017 0.002 TYR Z 586 PHE 0.012 0.001 PHE H 100O TRP 0.016 0.002 TRP C 69 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00382 (16756) covalent geometry : angle 0.60322 (22732) SS BOND : bond 0.00242 ( 38) SS BOND : angle 0.76747 ( 76) hydrogen bonds : bond 0.03697 ( 469) hydrogen bonds : angle 4.93160 ( 1308) link_ALPHA1-3 : bond 0.00983 ( 4) link_ALPHA1-3 : angle 2.30779 ( 12) link_ALPHA1-6 : bond 0.00998 ( 3) link_ALPHA1-6 : angle 2.17205 ( 9) link_BETA1-4 : bond 0.00445 ( 41) link_BETA1-4 : angle 2.02562 ( 123) link_NAG-ASN : bond 0.00343 ( 53) link_NAG-ASN : angle 2.45225 ( 159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 192 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8670 (ppp) cc_final: 0.7821 (ppp) REVERT: A 271 MET cc_start: 0.8200 (mmt) cc_final: 0.7876 (mmm) REVERT: A 434 MET cc_start: 0.8856 (tmm) cc_final: 0.8340 (tmm) REVERT: B 69 TRP cc_start: 0.7915 (m-90) cc_final: 0.7384 (m-90) REVERT: B 96 TRP cc_start: 0.8775 (m100) cc_final: 0.8508 (m100) REVERT: B 116 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8528 (tp) REVERT: B 279 ASN cc_start: 0.9360 (t0) cc_final: 0.9070 (t0) REVERT: C 95 MET cc_start: 0.8878 (ppp) cc_final: 0.8253 (ppp) REVERT: C 161 MET cc_start: 0.8438 (tpp) cc_final: 0.8119 (mmt) REVERT: C 377 ASN cc_start: 0.8706 (t0) cc_final: 0.8412 (t0) REVERT: C 424 ILE cc_start: 0.9435 (pt) cc_final: 0.9148 (mt) REVERT: H 82 MET cc_start: 0.6005 (ptt) cc_final: 0.5699 (ptp) REVERT: H 82 LEU cc_start: 0.8358 (mm) cc_final: 0.8056 (tp) REVERT: L 5 THR cc_start: 0.9056 (p) cc_final: 0.8549 (t) REVERT: L 42 ARG cc_start: 0.7318 (ptp-170) cc_final: 0.7087 (ptp90) REVERT: L 87 TYR cc_start: 0.7867 (m-80) cc_final: 0.7124 (m-80) REVERT: X 584 GLU cc_start: 0.8513 (tt0) cc_final: 0.7653 (tm-30) REVERT: X 603 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.8757 (mm) REVERT: Y 584 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8038 (tm-30) REVERT: Y 587 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9372 (mm) REVERT: Y 588 ARG cc_start: 0.8365 (ttm170) cc_final: 0.8032 (ttm110) REVERT: Y 654 GLU cc_start: 0.8608 (tt0) cc_final: 0.8251 (pt0) REVERT: Z 581 LEU cc_start: 0.9239 (tt) cc_final: 0.8899 (pp) REVERT: Z 586 TYR cc_start: 0.9158 (t80) cc_final: 0.8861 (t80) outliers start: 49 outliers final: 32 residues processed: 225 average time/residue: 0.1143 time to fit residues: 39.7433 Evaluate side-chains 210 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain X residue 544 LEU Chi-restraints excluded: chain X residue 589 ASP Chi-restraints excluded: chain X residue 603 ILE Chi-restraints excluded: chain X residue 626 MET Chi-restraints excluded: chain Y residue 544 LEU Chi-restraints excluded: chain Y residue 587 LEU Chi-restraints excluded: chain Y residue 592 LEU Chi-restraints excluded: chain Y residue 612 SER Chi-restraints excluded: chain Y residue 619 LEU Chi-restraints excluded: chain Y residue 637 ASN Chi-restraints excluded: chain Z residue 570 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 186 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 176 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.085981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.066618 restraints weight = 53573.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.068882 restraints weight = 29609.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.070403 restraints weight = 20294.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.071431 restraints weight = 15805.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.071996 restraints weight = 13324.519| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16895 Z= 0.121 Angle : 0.623 13.575 23111 Z= 0.292 Chirality : 0.044 0.324 2855 Planarity : 0.003 0.050 2756 Dihedral : 7.721 58.881 4128 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.14 % Allowed : 16.75 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.20), residues: 1866 helix: 1.56 (0.27), residues: 409 sheet: -0.33 (0.22), residues: 560 loop : -0.86 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 151 TYR 0.020 0.001 TYR L 49 PHE 0.012 0.001 PHE C 288 TRP 0.018 0.001 TRP X 631 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00276 (16756) covalent geometry : angle 0.57435 (22732) SS BOND : bond 0.00216 ( 38) SS BOND : angle 0.75666 ( 76) hydrogen bonds : bond 0.03509 ( 469) hydrogen bonds : angle 4.86962 ( 1308) link_ALPHA1-3 : bond 0.00981 ( 4) link_ALPHA1-3 : angle 2.26509 ( 12) link_ALPHA1-6 : bond 0.01059 ( 3) link_ALPHA1-6 : angle 2.00340 ( 9) link_BETA1-4 : bond 0.00449 ( 41) link_BETA1-4 : angle 1.89594 ( 123) link_NAG-ASN : bond 0.00320 ( 53) link_NAG-ASN : angle 2.37729 ( 159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 196 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8761 (ppp) cc_final: 0.7782 (ppp) REVERT: A 271 MET cc_start: 0.8208 (mmt) cc_final: 0.7897 (mmm) REVERT: A 434 MET cc_start: 0.8762 (tmm) cc_final: 0.8210 (tmm) REVERT: B 69 TRP cc_start: 0.7888 (m-90) cc_final: 0.7370 (m-90) REVERT: B 96 TRP cc_start: 0.8793 (m100) cc_final: 0.8558 (m100) REVERT: B 116 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8455 (tp) REVERT: B 279 ASN cc_start: 0.9366 (t0) cc_final: 0.9147 (t0) REVERT: C 95 MET cc_start: 0.8856 (ppp) cc_final: 0.8211 (ppp) REVERT: C 161 MET cc_start: 0.8374 (tpp) cc_final: 0.8054 (mmt) REVERT: C 424 ILE cc_start: 0.9349 (pt) cc_final: 0.9126 (mt) REVERT: H 73 GLU cc_start: 0.7516 (pm20) cc_final: 0.7261 (pm20) REVERT: H 82 MET cc_start: 0.5987 (ptt) cc_final: 0.5418 (ptp) REVERT: H 82 LEU cc_start: 0.8353 (mm) cc_final: 0.8089 (tp) REVERT: L 77 ARG cc_start: 0.7688 (tpp80) cc_final: 0.7410 (tpp80) REVERT: L 87 TYR cc_start: 0.7874 (m-80) cc_final: 0.7196 (m-80) REVERT: X 584 GLU cc_start: 0.8468 (tt0) cc_final: 0.7569 (tm-30) REVERT: X 603 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.8691 (mm) REVERT: X 657 GLU cc_start: 0.9052 (pp20) cc_final: 0.8119 (pp20) REVERT: Y 584 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8164 (tm-30) REVERT: Y 588 ARG cc_start: 0.8382 (ttm170) cc_final: 0.8073 (ttm110) REVERT: Y 654 GLU cc_start: 0.8784 (tt0) cc_final: 0.8322 (pt0) REVERT: Z 537 LEU cc_start: 0.9060 (mp) cc_final: 0.8786 (mm) REVERT: Z 581 LEU cc_start: 0.9251 (tt) cc_final: 0.8877 (pp) REVERT: Z 586 TYR cc_start: 0.9064 (t80) cc_final: 0.8789 (t80) REVERT: Z 638 TYR cc_start: 0.8128 (m-80) cc_final: 0.7919 (m-10) outliers start: 53 outliers final: 40 residues processed: 231 average time/residue: 0.1108 time to fit residues: 39.7473 Evaluate side-chains 223 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain X residue 544 LEU Chi-restraints excluded: chain X residue 589 ASP Chi-restraints excluded: chain X residue 603 ILE Chi-restraints excluded: chain Y residue 539 VAL Chi-restraints excluded: chain Y residue 544 LEU Chi-restraints excluded: chain Y residue 612 SER Chi-restraints excluded: chain Y residue 619 LEU Chi-restraints excluded: chain Y residue 637 ASN Chi-restraints excluded: chain Z residue 570 VAL Chi-restraints excluded: chain Z residue 635 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 145 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 178 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 154 optimal weight: 0.3980 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Z 630 GLN ** Z 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.083652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.064177 restraints weight = 54083.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.066365 restraints weight = 30262.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.067831 restraints weight = 20907.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.068804 restraints weight = 16380.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.069412 restraints weight = 13905.847| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16895 Z= 0.206 Angle : 0.700 14.096 23111 Z= 0.330 Chirality : 0.046 0.333 2855 Planarity : 0.004 0.037 2756 Dihedral : 7.753 58.511 4128 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.61 % Allowed : 16.80 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.20), residues: 1866 helix: 1.51 (0.26), residues: 405 sheet: -0.38 (0.22), residues: 550 loop : -0.88 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 151 TYR 0.024 0.002 TYR Z 643 PHE 0.016 0.002 PHE H 100O TRP 0.035 0.002 TRP Y 571 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00470 (16756) covalent geometry : angle 0.65197 (22732) SS BOND : bond 0.00416 ( 38) SS BOND : angle 1.04096 ( 76) hydrogen bonds : bond 0.03822 ( 469) hydrogen bonds : angle 4.97705 ( 1308) link_ALPHA1-3 : bond 0.00804 ( 4) link_ALPHA1-3 : angle 2.39500 ( 12) link_ALPHA1-6 : bond 0.00770 ( 3) link_ALPHA1-6 : angle 2.04412 ( 9) link_BETA1-4 : bond 0.00417 ( 41) link_BETA1-4 : angle 1.97846 ( 123) link_NAG-ASN : bond 0.00413 ( 53) link_NAG-ASN : angle 2.49818 ( 159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 191 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8805 (ppp) cc_final: 0.7978 (ppp) REVERT: A 271 MET cc_start: 0.8266 (mmt) cc_final: 0.8030 (mmm) REVERT: A 434 MET cc_start: 0.8935 (tmm) cc_final: 0.8378 (tmm) REVERT: B 69 TRP cc_start: 0.7976 (m-90) cc_final: 0.7527 (m-10) REVERT: B 96 TRP cc_start: 0.8828 (m100) cc_final: 0.8620 (m100) REVERT: B 116 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8511 (tp) REVERT: C 95 MET cc_start: 0.8860 (ppp) cc_final: 0.8288 (ppp) REVERT: C 104 MET cc_start: 0.9281 (tpp) cc_final: 0.8714 (tpp) REVERT: C 377 ASN cc_start: 0.8827 (t0) cc_final: 0.8595 (t0) REVERT: C 424 ILE cc_start: 0.9462 (pt) cc_final: 0.9219 (mt) REVERT: H 82 ASN cc_start: 0.8454 (m110) cc_final: 0.8248 (m-40) REVERT: H 82 LEU cc_start: 0.8418 (mm) cc_final: 0.8099 (tp) REVERT: L 87 TYR cc_start: 0.7816 (m-80) cc_final: 0.7137 (m-80) REVERT: X 584 GLU cc_start: 0.8559 (tt0) cc_final: 0.7679 (tm-30) REVERT: Y 571 TRP cc_start: 0.7204 (m100) cc_final: 0.6993 (m100) REVERT: Y 574 LYS cc_start: 0.7964 (pttt) cc_final: 0.7231 (mmtp) REVERT: Y 584 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8002 (tm-30) REVERT: Y 588 ARG cc_start: 0.8435 (ttm170) cc_final: 0.8103 (ttm110) REVERT: Z 535 MET cc_start: 0.8605 (mmp) cc_final: 0.8387 (mmp) REVERT: Z 581 LEU cc_start: 0.9251 (tt) cc_final: 0.8955 (pp) REVERT: Z 586 TYR cc_start: 0.9161 (t80) cc_final: 0.8920 (t80) REVERT: Z 648 GLU cc_start: 0.8848 (tp30) cc_final: 0.8281 (tm-30) outliers start: 61 outliers final: 42 residues processed: 234 average time/residue: 0.1101 time to fit residues: 40.2317 Evaluate side-chains 217 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain X residue 544 LEU Chi-restraints excluded: chain Y residue 539 VAL Chi-restraints excluded: chain Y residue 544 LEU Chi-restraints excluded: chain Y residue 592 LEU Chi-restraints excluded: chain Y residue 612 SER Chi-restraints excluded: chain Y residue 619 LEU Chi-restraints excluded: chain Y residue 637 ASN Chi-restraints excluded: chain Z residue 570 VAL Chi-restraints excluded: chain Z residue 624 ASP Chi-restraints excluded: chain Z residue 635 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 119 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN ** Z 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.085198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.065771 restraints weight = 53694.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.068001 restraints weight = 29821.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.069509 restraints weight = 20516.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.070497 restraints weight = 15994.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.071180 restraints weight = 13541.125| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16895 Z= 0.129 Angle : 0.642 13.818 23111 Z= 0.303 Chirality : 0.045 0.328 2855 Planarity : 0.004 0.070 2756 Dihedral : 7.470 58.982 4128 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.78 % Allowed : 18.22 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.20), residues: 1866 helix: 1.63 (0.27), residues: 403 sheet: -0.25 (0.23), residues: 555 loop : -0.81 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 151 TYR 0.029 0.002 TYR Z 638 PHE 0.027 0.001 PHE H 29 TRP 0.023 0.002 TRP H 103 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00294 (16756) covalent geometry : angle 0.59551 (22732) SS BOND : bond 0.00195 ( 38) SS BOND : angle 0.87439 ( 76) hydrogen bonds : bond 0.03662 ( 469) hydrogen bonds : angle 4.87881 ( 1308) link_ALPHA1-3 : bond 0.00923 ( 4) link_ALPHA1-3 : angle 2.40173 ( 12) link_ALPHA1-6 : bond 0.01072 ( 3) link_ALPHA1-6 : angle 1.85862 ( 9) link_BETA1-4 : bond 0.00436 ( 41) link_BETA1-4 : angle 1.83123 ( 123) link_NAG-ASN : bond 0.00329 ( 53) link_NAG-ASN : angle 2.38517 ( 159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 0.514 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: A 95 MET cc_start: 0.8727 (ppp) cc_final: 0.7839 (ppp) REVERT: A 271 MET cc_start: 0.8210 (mmt) cc_final: 0.7997 (mmm) REVERT: A 282 LYS cc_start: 0.6467 (pttp) cc_final: 0.6256 (pttp) REVERT: A 434 MET cc_start: 0.8959 (tmm) cc_final: 0.8400 (tmm) REVERT: B 69 TRP cc_start: 0.8010 (m-90) cc_final: 0.7634 (m-10) REVERT: B 116 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8543 (tp) REVERT: C 95 MET cc_start: 0.8846 (ppp) cc_final: 0.8293 (ppp) REVERT: C 104 MET cc_start: 0.9259 (tpp) cc_final: 0.8655 (tpp) REVERT: C 424 ILE cc_start: 0.9420 (pt) cc_final: 0.9210 (mt) REVERT: H 75 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8113 (pttp) REVERT: H 82 LEU cc_start: 0.8428 (mm) cc_final: 0.8170 (tp) REVERT: L 77 ARG cc_start: 0.8010 (tpp80) cc_final: 0.7797 (tpp80) REVERT: L 87 TYR cc_start: 0.7767 (m-80) cc_final: 0.7117 (m-80) REVERT: X 584 GLU cc_start: 0.8486 (tt0) cc_final: 0.7530 (tm-30) REVERT: Y 574 LYS cc_start: 0.7856 (pttt) cc_final: 0.7567 (ptpt) REVERT: Y 584 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8138 (tm-30) REVERT: Y 588 ARG cc_start: 0.8387 (ttm170) cc_final: 0.8184 (ttm110) REVERT: Y 654 GLU cc_start: 0.8592 (tt0) cc_final: 0.8128 (pt0) REVERT: Z 581 LEU cc_start: 0.9245 (tt) cc_final: 0.8951 (pp) REVERT: Z 586 TYR cc_start: 0.9090 (t80) cc_final: 0.8860 (t80) outliers start: 47 outliers final: 36 residues processed: 224 average time/residue: 0.1184 time to fit residues: 40.8406 Evaluate side-chains 215 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain X residue 544 LEU Chi-restraints excluded: chain Y residue 539 VAL Chi-restraints excluded: chain Y residue 544 LEU Chi-restraints excluded: chain Y residue 592 LEU Chi-restraints excluded: chain Y residue 612 SER Chi-restraints excluded: chain Y residue 619 LEU Chi-restraints excluded: chain Y residue 637 ASN Chi-restraints excluded: chain Z residue 570 VAL Chi-restraints excluded: chain Z residue 635 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 94 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.085454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.066274 restraints weight = 53708.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.068475 restraints weight = 30188.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.069948 restraints weight = 20894.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.070959 restraints weight = 16364.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.071602 restraints weight = 13836.484| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16895 Z= 0.127 Angle : 0.640 13.768 23111 Z= 0.303 Chirality : 0.045 0.330 2855 Planarity : 0.003 0.040 2756 Dihedral : 7.265 58.090 4128 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.60 % Allowed : 18.46 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.20), residues: 1866 helix: 1.63 (0.27), residues: 403 sheet: -0.11 (0.23), residues: 537 loop : -0.76 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG L 24 TYR 0.036 0.002 TYR C 486 PHE 0.021 0.001 PHE H 29 TRP 0.046 0.002 TRP B 96 HIS 0.004 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00292 (16756) covalent geometry : angle 0.59508 (22732) SS BOND : bond 0.00162 ( 38) SS BOND : angle 0.81093 ( 76) hydrogen bonds : bond 0.03583 ( 469) hydrogen bonds : angle 4.83486 ( 1308) link_ALPHA1-3 : bond 0.00992 ( 4) link_ALPHA1-3 : angle 2.39684 ( 12) link_ALPHA1-6 : bond 0.01143 ( 3) link_ALPHA1-6 : angle 1.80191 ( 9) link_BETA1-4 : bond 0.00433 ( 41) link_BETA1-4 : angle 1.76522 ( 123) link_NAG-ASN : bond 0.00325 ( 53) link_NAG-ASN : angle 2.36147 ( 159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8702 (ppp) cc_final: 0.7768 (ppp) REVERT: A 217 TYR cc_start: 0.7811 (m-10) cc_final: 0.7554 (m-10) REVERT: A 282 LYS cc_start: 0.6521 (pttp) cc_final: 0.6262 (pttp) REVERT: A 434 MET cc_start: 0.8951 (tmm) cc_final: 0.8394 (tmm) REVERT: B 69 TRP cc_start: 0.8033 (m-90) cc_final: 0.7757 (m-10) REVERT: B 116 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8597 (tp) REVERT: C 95 MET cc_start: 0.8935 (ppp) cc_final: 0.8313 (ppp) REVERT: C 104 MET cc_start: 0.9268 (tpp) cc_final: 0.8661 (tpp) REVERT: C 161 MET cc_start: 0.8343 (mmm) cc_final: 0.8018 (mmt) REVERT: C 320 THR cc_start: 0.9046 (m) cc_final: 0.8815 (m) REVERT: C 424 ILE cc_start: 0.9428 (pt) cc_final: 0.9205 (mt) REVERT: H 75 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8262 (pttp) REVERT: H 82 ASN cc_start: 0.8515 (m-40) cc_final: 0.8112 (t0) REVERT: H 82 LEU cc_start: 0.8371 (mm) cc_final: 0.8040 (tp) REVERT: L 87 TYR cc_start: 0.7912 (m-80) cc_final: 0.7192 (m-80) REVERT: X 543 ASN cc_start: 0.8717 (t0) cc_final: 0.8455 (t0) REVERT: X 584 GLU cc_start: 0.8486 (tt0) cc_final: 0.7554 (tm-30) REVERT: Y 574 LYS cc_start: 0.7868 (pttt) cc_final: 0.7644 (ptpt) REVERT: Y 584 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8099 (tm-30) REVERT: Y 588 ARG cc_start: 0.8371 (ttm170) cc_final: 0.8168 (ttm110) REVERT: Y 654 GLU cc_start: 0.8500 (tt0) cc_final: 0.8090 (pt0) REVERT: Z 581 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8961 (pp) outliers start: 44 outliers final: 37 residues processed: 223 average time/residue: 0.1160 time to fit residues: 40.1182 Evaluate side-chains 225 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain X residue 544 LEU Chi-restraints excluded: chain Y residue 539 VAL Chi-restraints excluded: chain Y residue 544 LEU Chi-restraints excluded: chain Y residue 592 LEU Chi-restraints excluded: chain Y residue 612 SER Chi-restraints excluded: chain Y residue 619 LEU Chi-restraints excluded: chain Y residue 637 ASN Chi-restraints excluded: chain Z residue 570 VAL Chi-restraints excluded: chain Z residue 581 LEU Chi-restraints excluded: chain Z residue 635 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 92 optimal weight: 0.3980 chunk 182 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** Z 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.086488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.067367 restraints weight = 53440.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.069606 restraints weight = 30028.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.071085 restraints weight = 20712.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.072108 restraints weight = 16206.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.072659 restraints weight = 13673.568| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16895 Z= 0.116 Angle : 0.639 13.704 23111 Z= 0.303 Chirality : 0.045 0.327 2855 Planarity : 0.003 0.038 2756 Dihedral : 7.054 57.926 4128 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.54 % Allowed : 18.70 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.20), residues: 1866 helix: 1.58 (0.27), residues: 403 sheet: 0.00 (0.23), residues: 546 loop : -0.79 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 77 TYR 0.044 0.002 TYR Z 586 PHE 0.020 0.001 PHE H 29 TRP 0.052 0.002 TRP Y 571 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00266 (16756) covalent geometry : angle 0.59726 (22732) SS BOND : bond 0.00249 ( 38) SS BOND : angle 0.68450 ( 76) hydrogen bonds : bond 0.03434 ( 469) hydrogen bonds : angle 4.77826 ( 1308) link_ALPHA1-3 : bond 0.00912 ( 4) link_ALPHA1-3 : angle 2.34743 ( 12) link_ALPHA1-6 : bond 0.01133 ( 3) link_ALPHA1-6 : angle 1.68239 ( 9) link_BETA1-4 : bond 0.00450 ( 41) link_BETA1-4 : angle 1.68502 ( 123) link_NAG-ASN : bond 0.00321 ( 53) link_NAG-ASN : angle 2.30269 ( 159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 0.512 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: A 95 MET cc_start: 0.8684 (ppp) cc_final: 0.7692 (ppp) REVERT: A 434 MET cc_start: 0.8922 (tmm) cc_final: 0.8373 (tmm) REVERT: B 69 TRP cc_start: 0.8033 (m-90) cc_final: 0.7760 (m-10) REVERT: B 116 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8597 (tp) REVERT: C 95 MET cc_start: 0.8947 (ppp) cc_final: 0.8299 (ppp) REVERT: C 104 MET cc_start: 0.9272 (tpp) cc_final: 0.8682 (tpp) REVERT: C 161 MET cc_start: 0.8349 (mmm) cc_final: 0.8060 (mmt) REVERT: C 381 GLU cc_start: 0.8136 (pm20) cc_final: 0.7035 (pt0) REVERT: H 75 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8339 (pttp) REVERT: H 82 ASN cc_start: 0.8521 (m-40) cc_final: 0.8080 (t0) REVERT: H 82 LEU cc_start: 0.8356 (mm) cc_final: 0.8079 (tp) REVERT: L 5 THR cc_start: 0.8830 (p) cc_final: 0.8601 (t) REVERT: L 87 TYR cc_start: 0.7931 (m-80) cc_final: 0.7349 (m-80) REVERT: X 543 ASN cc_start: 0.8670 (t0) cc_final: 0.8436 (t0) REVERT: X 584 GLU cc_start: 0.8493 (tt0) cc_final: 0.7492 (tm-30) REVERT: X 661 LEU cc_start: 0.8643 (mm) cc_final: 0.8380 (mm) REVERT: Y 574 LYS cc_start: 0.7989 (pttt) cc_final: 0.7571 (mmtp) REVERT: Y 584 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8068 (tm-30) REVERT: Y 588 ARG cc_start: 0.8353 (ttm170) cc_final: 0.7938 (ttm-80) REVERT: Y 654 GLU cc_start: 0.8494 (tt0) cc_final: 0.8172 (pt0) REVERT: Z 581 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8965 (pp) outliers start: 43 outliers final: 35 residues processed: 227 average time/residue: 0.1115 time to fit residues: 38.9061 Evaluate side-chains 218 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain X residue 544 LEU Chi-restraints excluded: chain Y residue 539 VAL Chi-restraints excluded: chain Y residue 544 LEU Chi-restraints excluded: chain Y residue 592 LEU Chi-restraints excluded: chain Y residue 612 SER Chi-restraints excluded: chain Y residue 619 LEU Chi-restraints excluded: chain Y residue 637 ASN Chi-restraints excluded: chain Z residue 570 VAL Chi-restraints excluded: chain Z residue 581 LEU Chi-restraints excluded: chain Z residue 635 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 39 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 134 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 177 optimal weight: 0.6980 chunk 68 optimal weight: 0.0970 chunk 17 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** Z 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.085945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.066786 restraints weight = 54082.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.069007 restraints weight = 30502.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.070514 restraints weight = 21102.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.071535 restraints weight = 16487.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.072204 restraints weight = 13921.502| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16895 Z= 0.129 Angle : 0.650 14.073 23111 Z= 0.309 Chirality : 0.044 0.339 2855 Planarity : 0.003 0.037 2756 Dihedral : 7.020 57.395 4128 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.37 % Allowed : 19.05 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.20), residues: 1866 helix: 1.49 (0.27), residues: 403 sheet: 0.03 (0.23), residues: 531 loop : -0.77 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 151 TYR 0.027 0.002 TYR Z 638 PHE 0.019 0.001 PHE H 29 TRP 0.061 0.002 TRP X 631 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00298 (16756) covalent geometry : angle 0.60823 (22732) SS BOND : bond 0.00208 ( 38) SS BOND : angle 0.85628 ( 76) hydrogen bonds : bond 0.03495 ( 469) hydrogen bonds : angle 4.79380 ( 1308) link_ALPHA1-3 : bond 0.00878 ( 4) link_ALPHA1-3 : angle 2.29651 ( 12) link_ALPHA1-6 : bond 0.01091 ( 3) link_ALPHA1-6 : angle 1.64906 ( 9) link_BETA1-4 : bond 0.00435 ( 41) link_BETA1-4 : angle 1.68863 ( 123) link_NAG-ASN : bond 0.00310 ( 53) link_NAG-ASN : angle 2.32012 ( 159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2285.18 seconds wall clock time: 40 minutes 34.07 seconds (2434.07 seconds total)