Starting phenix.real_space_refine on Thu Mar 5 08:59:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6opq_20153/03_2026/6opq_20153.cif Found real_map, /net/cci-nas-00/data/ceres_data/6opq_20153/03_2026/6opq_20153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6opq_20153/03_2026/6opq_20153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6opq_20153/03_2026/6opq_20153.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6opq_20153/03_2026/6opq_20153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6opq_20153/03_2026/6opq_20153.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.062 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 114 5.16 5 C 13074 2.51 5 N 3534 2.21 5 O 4155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20877 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3014 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 22, 'TRANS': 362} Chain breaks: 2 Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "B" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1027 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "C" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "D" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3014 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 22, 'TRANS': 362} Chain breaks: 2 Chain: "N" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "F" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1027 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "K" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "E" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3014 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 22, 'TRANS': 362} Chain breaks: 2 Chain: "O" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "G" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1027 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "J" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "M" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.56, per 1000 atoms: 0.22 Number of scatterers: 20877 At special positions: 0 Unit cell: (158.62, 157.59, 141.11, 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 114 16.00 O 4155 8.00 N 3534 7.00 C 13074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.06 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 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 B 605 " distance=2.14 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.08 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 84 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.06 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.02 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.02 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.14 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.08 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 16 " - pdb=" SG CYS I 84 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.06 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS G 605 " distance=2.14 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.08 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.02 Simple disulfide: pdb=" SG CYS J 16 " - pdb=" SG CYS J 84 " distance=2.02 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " 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 ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN Z 4 " - " MAN Z 5 " " MAN i 4 " - " MAN i 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA Z 3 " - " MAN Z 4 " " BMA i 3 " - " MAN i 4 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG 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 l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 615 " - " ASN A 339 " " NAG A 624 " - " ASN A 448 " " NAG D 601 " - " ASN D 234 " " NAG D 615 " - " ASN D 339 " " NAG D 624 " - " ASN D 448 " " NAG E 601 " - " ASN E 234 " " NAG E 615 " - " ASN E 339 " " NAG E 624 " - " ASN E 448 " " NAG P 1 " - " ASN A 241 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 295 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 362 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN A 413 " " NAG Y 1 " - " ASN D 241 " " NAG Z 1 " - " ASN D 262 " " NAG a 1 " - " ASN D 276 " " NAG b 1 " - " ASN D 295 " " NAG c 1 " - " ASN D 332 " " NAG d 1 " - " ASN D 362 " " NAG e 1 " - " ASN D 386 " " NAG f 1 " - " ASN D 392 " " NAG g 1 " - " ASN D 413 " " NAG h 1 " - " ASN E 241 " " NAG i 1 " - " ASN E 262 " " NAG j 1 " - " ASN E 276 " " NAG k 1 " - " ASN E 295 " " NAG l 1 " - " ASN E 332 " " NAG m 1 " - " ASN E 362 " " NAG n 1 " - " ASN E 386 " " NAG o 1 " - " ASN E 392 " " NAG p 1 " - " ASN E 413 " Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 943.0 milliseconds 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4698 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 42 sheets defined 23.8% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 64 through 74 removed outlier: 3.824A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.854A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 522 through 526 Processing helix chain 'B' and resid 529 through 546 Processing helix chain 'B' and resid 565 through 593 removed outlier: 4.628A pdb=" N TRP B 571 " --> pdb=" O GLN B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.620A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 58 through 65 removed outlier: 4.571A pdb=" N ASP C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 99 through 100C Processing helix chain 'D' and resid 64 through 74 removed outlier: 3.824A pdb=" N HIS D 72 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 114 Processing helix chain 'D' and resid 335 through 353 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 474 through 484 removed outlier: 3.854A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'F' and resid 522 through 526 Processing helix chain 'F' and resid 529 through 546 Processing helix chain 'F' and resid 565 through 593 removed outlier: 4.628A pdb=" N TRP F 571 " --> pdb=" O GLN F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 597 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.619A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'I' and resid 58 through 65 removed outlier: 4.571A pdb=" N ASP I 63 " --> pdb=" O SER I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 79 Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 99 through 100C Processing helix chain 'E' and resid 64 through 74 removed outlier: 3.824A pdb=" N HIS E 72 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 114 Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.854A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 Processing helix chain 'G' and resid 522 through 526 Processing helix chain 'G' and resid 529 through 546 Processing helix chain 'G' and resid 565 through 593 removed outlier: 4.628A pdb=" N TRP G 571 " --> pdb=" O GLN G 567 " (cutoff:3.500A) Processing helix chain 'G' and resid 594 through 597 Processing helix chain 'G' and resid 618 through 626 removed outlier: 3.619A pdb=" N MET G 626 " --> pdb=" O ILE G 622 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 635 Processing helix chain 'G' and resid 638 through 661 Processing helix chain 'J' and resid 58 through 65 removed outlier: 4.571A pdb=" N ASP J 63 " --> pdb=" O SER J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 79 Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 99 through 100C Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA5, first strand: chain 'A' and resid 197 through 202 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.694A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.411A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 394 through 395 removed outlier: 6.162A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.595A pdb=" N ALA L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N GLU L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N SER L 67 " --> pdb=" O GLU L 27 " (cutoff:3.500A) removed outlier: 11.556A pdb=" N VAL L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.681A pdb=" N SER L 65 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.938A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 2 through 5 removed outlier: 6.590A pdb=" N LYS C 2 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU C 96 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL C 4 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE C 26 " --> pdb=" O ASN C 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 12 through 14 Processing sheet with id=AB3, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.571A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N TYR H 32 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU H 46 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.571A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 494 through 499 Processing sheet with id=AB7, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB9, first strand: chain 'D' and resid 91 through 93 Processing sheet with id=AC1, first strand: chain 'D' and resid 197 through 202 Processing sheet with id=AC2, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.694A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY D 451 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.411A pdb=" N GLU D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLU D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER D 334 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 394 through 395 removed outlier: 6.162A pdb=" N THR D 357 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N PHE D 468 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE D 359 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 4 through 6 removed outlier: 5.594A pdb=" N ALA N 69 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N GLU N 27 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N SER N 67 " --> pdb=" O GLU N 27 " (cutoff:3.500A) removed outlier: 11.557A pdb=" N VAL N 29 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 11.681A pdb=" N SER N 65 " --> pdb=" O VAL N 29 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.938A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG N 45 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 2 through 5 removed outlier: 6.590A pdb=" N LYS I 2 " --> pdb=" O GLN I 94 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU I 96 " --> pdb=" O LYS I 2 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL I 4 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE I 26 " --> pdb=" O ASN I 39 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 12 through 14 Processing sheet with id=AC8, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AC9, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.571A pdb=" N GLU K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N TYR K 32 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE K 52 " --> pdb=" O TYR K 32 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG K 50 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU K 46 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL K 56 " --> pdb=" O ILE K 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.571A pdb=" N GLU K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 494 through 499 Processing sheet with id=AD3, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AD4, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AD5, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AD6, first strand: chain 'E' and resid 197 through 202 Processing sheet with id=AD7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.694A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.411A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 394 through 395 removed outlier: 6.162A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N PHE E 468 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE E 359 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 4 through 6 removed outlier: 5.595A pdb=" N ALA O 69 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 9.680A pdb=" N GLU O 27 " --> pdb=" O SER O 67 " (cutoff:3.500A) removed outlier: 9.675A pdb=" N SER O 67 " --> pdb=" O GLU O 27 " (cutoff:3.500A) removed outlier: 11.556A pdb=" N VAL O 29 " --> pdb=" O SER O 65 " (cutoff:3.500A) removed outlier: 11.681A pdb=" N SER O 65 " --> pdb=" O VAL O 29 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 10 through 12 removed outlier: 5.938A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG O 45 " --> pdb=" O GLN O 37 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 2 through 5 removed outlier: 6.590A pdb=" N LYS J 2 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU J 96 " --> pdb=" O LYS J 2 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL J 4 " --> pdb=" O LEU J 96 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE J 26 " --> pdb=" O ASN J 39 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 12 through 14 Processing sheet with id=AE4, first strand: chain 'M' and resid 5 through 6 Processing sheet with id=AE5, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.570A pdb=" N GLU M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N TYR M 32 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE M 52 " --> pdb=" O TYR M 32 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE M 34 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG M 50 " --> pdb=" O PHE M 34 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU M 46 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.570A pdb=" N GLU M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) 837 hydrogen bonds defined for protein. 2079 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.97 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4095 1.32 - 1.44: 5730 1.44 - 1.57: 11253 1.57 - 1.70: 63 1.70 - 1.83: 147 Bond restraints: 21288 Sorted by residual: bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.380 0.117 1.40e-02 5.10e+03 6.98e+01 bond pdb=" CB HIS D 374 " pdb=" CG HIS D 374 " ideal model delta sigma weight residual 1.497 1.380 0.117 1.40e-02 5.10e+03 6.96e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.380 0.117 1.40e-02 5.10e+03 6.94e+01 bond pdb=" C1 NAG f 2 " pdb=" O5 NAG f 2 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" C1 NAG o 2 " pdb=" O5 NAG o 2 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.11e+01 ... (remaining 21283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 23694 2.17 - 4.33: 4405 4.33 - 6.50: 656 6.50 - 8.67: 111 8.67 - 10.84: 27 Bond angle restraints: 28893 Sorted by residual: angle pdb=" C PRO D 437 " pdb=" N PRO D 438 " pdb=" CA PRO D 438 " ideal model delta sigma weight residual 119.78 128.94 -9.16 1.03e+00 9.43e-01 7.91e+01 angle pdb=" C PRO A 437 " pdb=" N PRO A 438 " pdb=" CA PRO A 438 " ideal model delta sigma weight residual 119.78 128.93 -9.15 1.03e+00 9.43e-01 7.89e+01 angle pdb=" C PRO E 437 " pdb=" N PRO E 438 " pdb=" CA PRO E 438 " ideal model delta sigma weight residual 119.78 128.92 -9.14 1.03e+00 9.43e-01 7.88e+01 angle pdb=" C PHE E 353 " pdb=" N PRO E 354 " pdb=" CA PRO E 354 " ideal model delta sigma weight residual 119.56 127.71 -8.15 1.02e+00 9.61e-01 6.38e+01 angle pdb=" C PHE A 353 " pdb=" N PRO A 354 " pdb=" CA PRO A 354 " ideal model delta sigma weight residual 119.56 127.69 -8.13 1.02e+00 9.61e-01 6.36e+01 ... (remaining 28888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.93: 13152 21.93 - 43.86: 417 43.86 - 65.79: 105 65.79 - 87.72: 36 87.72 - 109.65: 12 Dihedral angle restraints: 13722 sinusoidal: 6438 harmonic: 7284 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 93.00 152.17 -59.17 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual 93.00 152.17 -59.17 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual 93.00 152.17 -59.17 1 1.00e+01 1.00e-02 4.68e+01 ... (remaining 13719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2607 0.114 - 0.228: 763 0.228 - 0.342: 50 0.342 - 0.456: 18 0.456 - 0.570: 9 Chirality restraints: 3447 Sorted by residual: chirality pdb=" C1 NAG b 2 " pdb=" O4 NAG b 1 " pdb=" C2 NAG b 2 " pdb=" O5 NAG b 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.90e+01 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 -2.58 0.18 2.00e-02 2.50e+03 7.86e+01 chirality pdb=" C1 NAG k 2 " pdb=" O4 NAG k 1 " pdb=" C2 NAG k 2 " pdb=" O5 NAG k 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.77e+01 ... (remaining 3444 not shown) Planarity restraints: 3642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.062 2.00e-02 2.50e+03 6.60e-02 5.44e+01 pdb=" CG ASN A 234 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.102 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 234 " -0.062 2.00e-02 2.50e+03 6.59e-02 5.43e+01 pdb=" CG ASN E 234 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN E 234 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN E 234 " 0.102 2.00e-02 2.50e+03 pdb=" C1 NAG E 601 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 234 " 0.062 2.00e-02 2.50e+03 6.58e-02 5.42e+01 pdb=" CG ASN D 234 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN D 234 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN D 234 " -0.102 2.00e-02 2.50e+03 pdb=" C1 NAG D 601 " 0.080 2.00e-02 2.50e+03 ... (remaining 3639 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5950 2.81 - 3.33: 18783 3.33 - 3.85: 35573 3.85 - 4.38: 42095 4.38 - 4.90: 67442 Nonbonded interactions: 169843 Sorted by model distance: nonbonded pdb=" O3 NAG D 601 " pdb=" O7 NAG D 601 " model vdw 2.284 3.040 nonbonded pdb=" O3 NAG A 601 " pdb=" O7 NAG A 601 " model vdw 2.284 3.040 nonbonded pdb=" O3 NAG E 601 " pdb=" O7 NAG E 601 " model vdw 2.284 3.040 nonbonded pdb=" O5 NAG f 1 " pdb=" O6 NAG f 1 " model vdw 2.336 2.432 nonbonded pdb=" O5 NAG o 1 " pdb=" O6 NAG o 1 " model vdw 2.336 2.432 ... (remaining 169838 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' 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 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'Q' selection = chain 'Z' selection = chain 'i' } 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.580 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 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 : 0.022 0.177 21399 Z= 1.149 Angle : 1.782 10.837 29187 Z= 1.149 Chirality : 0.103 0.570 3447 Planarity : 0.009 0.052 3606 Dihedral : 12.051 109.654 8907 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.17 % Favored : 97.71 % Rotamer: Outliers : 0.14 % Allowed : 0.82 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.16), residues: 2487 helix: 1.22 (0.23), residues: 423 sheet: 0.91 (0.20), residues: 654 loop : -0.12 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 327 TYR 0.060 0.008 TYR N 91 PHE 0.028 0.007 PHE E 233 TRP 0.065 0.010 TRP L 94 HIS 0.014 0.003 HIS E 308 Details of bonding type rmsd covalent geometry : bond 0.02155 (21288) covalent geometry : angle 1.76200 (28893) SS BOND : bond 0.03635 ( 39) SS BOND : angle 2.56001 ( 78) hydrogen bonds : bond 0.16035 ( 825) hydrogen bonds : angle 7.50860 ( 2079) link_ALPHA1-2 : bond 0.03820 ( 3) link_ALPHA1-2 : angle 2.95754 ( 9) link_ALPHA1-3 : bond 0.03243 ( 3) link_ALPHA1-3 : angle 2.09850 ( 9) link_BETA1-4 : bond 0.02733 ( 30) link_BETA1-4 : angle 3.99407 ( 90) link_NAG-ASN : bond 0.03113 ( 36) link_NAG-ASN : angle 2.93961 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 814 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 TRP cc_start: 0.8232 (t-100) cc_final: 0.7999 (t-100) REVERT: A 358 ILE cc_start: 0.8464 (mm) cc_final: 0.8226 (tp) REVERT: A 449 ILE cc_start: 0.8854 (mt) cc_final: 0.8577 (pt) REVERT: A 475 MET cc_start: 0.7355 (mmm) cc_final: 0.6650 (mmp) REVERT: L 102 THR cc_start: 0.4727 (p) cc_final: 0.4163 (t) REVERT: B 537 LEU cc_start: 0.8792 (tp) cc_final: 0.8560 (tt) REVERT: B 647 GLU cc_start: 0.8511 (tt0) cc_final: 0.8192 (tt0) REVERT: C 67 PHE cc_start: 0.8639 (m-80) cc_final: 0.8417 (m-80) REVERT: H 72 ASP cc_start: 0.8132 (t0) cc_final: 0.7918 (t0) REVERT: H 100 PHE cc_start: 0.7540 (m-80) cc_final: 0.7143 (m-80) REVERT: D 119 CYS cc_start: 0.6793 (m) cc_final: 0.6522 (m) REVERT: D 358 ILE cc_start: 0.8466 (mm) cc_final: 0.8159 (tp) REVERT: D 395 TRP cc_start: 0.8311 (m100) cc_final: 0.8095 (m100) REVERT: D 449 ILE cc_start: 0.8897 (mt) cc_final: 0.8580 (pt) REVERT: D 475 MET cc_start: 0.7403 (mmm) cc_final: 0.6793 (mmp) REVERT: D 478 ASN cc_start: 0.8596 (m-40) cc_final: 0.8124 (m110) REVERT: N 40 PRO cc_start: 0.7359 (Cg_exo) cc_final: 0.6992 (Cg_endo) REVERT: N 102 THR cc_start: 0.5024 (p) cc_final: 0.4424 (t) REVERT: F 537 LEU cc_start: 0.8930 (tp) cc_final: 0.8626 (tt) REVERT: F 647 GLU cc_start: 0.8658 (tt0) cc_final: 0.8226 (tt0) REVERT: I 34 ILE cc_start: 0.8133 (mm) cc_final: 0.7849 (mt) REVERT: E 258 GLN cc_start: 0.8401 (mt0) cc_final: 0.8186 (mt0) REVERT: E 338 TRP cc_start: 0.8298 (t-100) cc_final: 0.7814 (t-100) REVERT: E 358 ILE cc_start: 0.8380 (mm) cc_final: 0.8167 (tp) REVERT: E 395 TRP cc_start: 0.8250 (m100) cc_final: 0.7407 (m100) REVERT: E 449 ILE cc_start: 0.8801 (mt) cc_final: 0.8499 (pt) REVERT: E 475 MET cc_start: 0.7336 (mmm) cc_final: 0.6714 (mmp) REVERT: O 40 PRO cc_start: 0.7558 (Cg_exo) cc_final: 0.7173 (Cg_endo) REVERT: O 49 TYR cc_start: 0.7311 (t80) cc_final: 0.7050 (t80) REVERT: G 537 LEU cc_start: 0.8807 (tp) cc_final: 0.8553 (tt) REVERT: G 647 GLU cc_start: 0.8643 (tt0) cc_final: 0.8021 (tt0) REVERT: J 69 LEU cc_start: 0.9052 (tp) cc_final: 0.8739 (tt) REVERT: M 100 PHE cc_start: 0.7771 (m-80) cc_final: 0.7189 (m-80) outliers start: 3 outliers final: 0 residues processed: 817 average time/residue: 0.1581 time to fit residues: 192.8412 Evaluate side-chains 422 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 325 ASN L 37 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN B 611 ASN C 25 GLN C 27 HIS C 66 ASN C 73 ASN H 82BASN ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS N 92 ASN I 25 GLN I 27 HIS I 73 ASN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN G 611 ASN J 25 GLN J 27 HIS M 82BASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.137860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.108740 restraints weight = 53834.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.112916 restraints weight = 29014.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.115864 restraints weight = 18908.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.117933 restraints weight = 13934.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.119330 restraints weight = 11156.004| |-----------------------------------------------------------------------------| r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 21399 Z= 0.186 Angle : 0.802 9.125 29187 Z= 0.411 Chirality : 0.050 0.290 3447 Planarity : 0.005 0.042 3606 Dihedral : 8.402 60.146 4191 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.41 % Favored : 97.47 % Rotamer: Outliers : 3.77 % Allowed : 11.51 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.16), residues: 2487 helix: 1.83 (0.25), residues: 411 sheet: 0.49 (0.20), residues: 684 loop : -0.73 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 103 TYR 0.031 0.003 TYR M 100E PHE 0.024 0.003 PHE A 376 TRP 0.022 0.002 TRP A 395 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00434 (21288) covalent geometry : angle 0.78167 (28893) SS BOND : bond 0.00444 ( 39) SS BOND : angle 1.22726 ( 78) hydrogen bonds : bond 0.05515 ( 825) hydrogen bonds : angle 6.08584 ( 2079) link_ALPHA1-2 : bond 0.00075 ( 3) link_ALPHA1-2 : angle 1.97346 ( 9) link_ALPHA1-3 : bond 0.00402 ( 3) link_ALPHA1-3 : angle 2.43411 ( 9) link_BETA1-4 : bond 0.00308 ( 30) link_BETA1-4 : angle 2.32340 ( 90) link_NAG-ASN : bond 0.00311 ( 36) link_NAG-ASN : angle 2.02242 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 517 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 GLN cc_start: 0.7941 (mt0) cc_final: 0.7037 (mt0) REVERT: A 338 TRP cc_start: 0.8220 (t-100) cc_final: 0.7829 (t-100) REVERT: A 358 ILE cc_start: 0.8541 (mm) cc_final: 0.8222 (mm) REVERT: A 434 MET cc_start: 0.7774 (ttp) cc_final: 0.7428 (ttm) REVERT: A 475 MET cc_start: 0.6450 (mmm) cc_final: 0.5446 (mmm) REVERT: A 479 TRP cc_start: 0.6152 (m-90) cc_final: 0.5865 (m-90) REVERT: L 38 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7802 (tm-30) REVERT: L 49 TYR cc_start: 0.8499 (t80) cc_final: 0.8275 (t80) REVERT: L 79 GLN cc_start: 0.8530 (mm110) cc_final: 0.8280 (mm-40) REVERT: L 85 VAL cc_start: 0.7850 (t) cc_final: 0.7453 (t) REVERT: L 98 PHE cc_start: 0.6847 (p90) cc_final: 0.6579 (p90) REVERT: B 584 GLU cc_start: 0.7993 (pt0) cc_final: 0.7650 (tm-30) REVERT: B 629 MET cc_start: 0.7914 (mtt) cc_final: 0.7149 (mtt) REVERT: B 632 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8261 (tm-30) REVERT: B 647 GLU cc_start: 0.8715 (tt0) cc_final: 0.8468 (tt0) REVERT: C 33 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7580 (pp30) REVERT: C 34 ILE cc_start: 0.7571 (mt) cc_final: 0.7351 (mt) REVERT: C 51 LEU cc_start: 0.8512 (mt) cc_final: 0.8256 (mt) REVERT: C 67 PHE cc_start: 0.8344 (m-80) cc_final: 0.7370 (m-10) REVERT: C 73 ASN cc_start: 0.8360 (t0) cc_final: 0.7968 (p0) REVERT: H 23 LYS cc_start: 0.8042 (tmmt) cc_final: 0.7435 (tmmt) REVERT: H 25 SER cc_start: 0.8390 (t) cc_final: 0.7743 (m) REVERT: H 53 ILE cc_start: 0.8630 (tp) cc_final: 0.8318 (tp) REVERT: H 72 ASP cc_start: 0.7070 (t0) cc_final: 0.6619 (t0) REVERT: H 79 TYR cc_start: 0.7954 (m-80) cc_final: 0.7690 (m-80) REVERT: D 107 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6981 (t70) REVERT: D 258 GLN cc_start: 0.8084 (mt0) cc_final: 0.7340 (mt0) REVERT: D 358 ILE cc_start: 0.8421 (mm) cc_final: 0.8010 (mm) REVERT: D 439 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7923 (tp) REVERT: D 475 MET cc_start: 0.6506 (mmm) cc_final: 0.6052 (mmm) REVERT: N 38 GLN cc_start: 0.8290 (tm-30) cc_final: 0.8016 (tm-30) REVERT: N 42 GLN cc_start: 0.6529 (mm-40) cc_final: 0.6287 (mp10) REVERT: N 49 TYR cc_start: 0.8263 (t80) cc_final: 0.8041 (t80) REVERT: N 70 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8253 (mm-30) REVERT: N 79 GLN cc_start: 0.8705 (mm110) cc_final: 0.8464 (mm-40) REVERT: F 584 GLU cc_start: 0.8130 (pt0) cc_final: 0.7630 (tm-30) REVERT: F 629 MET cc_start: 0.7981 (mtt) cc_final: 0.7673 (mtt) REVERT: I 33 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7533 (pp30) REVERT: I 34 ILE cc_start: 0.7935 (mm) cc_final: 0.7716 (mt) REVERT: I 66 ASN cc_start: 0.8239 (t0) cc_final: 0.8031 (m-40) REVERT: I 73 ASN cc_start: 0.7918 (t0) cc_final: 0.7664 (p0) REVERT: I 80 ASP cc_start: 0.7736 (t0) cc_final: 0.7143 (t0) REVERT: I 81 THR cc_start: 0.8858 (m) cc_final: 0.8570 (t) REVERT: I 82 TYR cc_start: 0.8285 (m-10) cc_final: 0.7781 (m-10) REVERT: I 85 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7402 (tm-30) REVERT: K 3 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8157 (mp10) REVERT: K 23 LYS cc_start: 0.8266 (tmmt) cc_final: 0.7749 (tmmt) REVERT: K 25 SER cc_start: 0.8312 (t) cc_final: 0.7664 (m) REVERT: E 209 SER cc_start: 0.7018 (t) cc_final: 0.6649 (p) REVERT: E 338 TRP cc_start: 0.8173 (t-100) cc_final: 0.7967 (t-100) REVERT: E 358 ILE cc_start: 0.8453 (mm) cc_final: 0.8137 (tp) REVERT: E 479 TRP cc_start: 0.6379 (m-90) cc_final: 0.6020 (m-90) REVERT: E 486 TYR cc_start: 0.8190 (m-80) cc_final: 0.7907 (m-80) REVERT: O 38 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7984 (tm-30) REVERT: O 42 GLN cc_start: 0.6603 (mm110) cc_final: 0.6387 (mp10) REVERT: O 49 TYR cc_start: 0.7945 (t80) cc_final: 0.7474 (t80) REVERT: O 58 VAL cc_start: 0.7525 (t) cc_final: 0.7142 (t) REVERT: O 70 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8428 (mm-30) REVERT: O 79 GLN cc_start: 0.8666 (mm110) cc_final: 0.8459 (mm-40) REVERT: G 540 GLN cc_start: 0.9063 (mm110) cc_final: 0.8345 (tt0) REVERT: G 626 MET cc_start: 0.7387 (mtt) cc_final: 0.7070 (ttm) REVERT: J 25 GLN cc_start: 0.7960 (tt0) cc_final: 0.7710 (tm-30) REVERT: J 33 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7646 (pp30) REVERT: J 66 ASN cc_start: 0.8454 (t0) cc_final: 0.8088 (m-40) REVERT: J 73 ASN cc_start: 0.8104 (t0) cc_final: 0.7777 (p0) REVERT: J 85 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7597 (tm-30) REVERT: M 3 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8305 (mp10) REVERT: M 23 LYS cc_start: 0.8099 (tmmt) cc_final: 0.7492 (tmmt) REVERT: M 25 SER cc_start: 0.8291 (t) cc_final: 0.7747 (m) REVERT: M 53 ILE cc_start: 0.8476 (tp) cc_final: 0.8233 (tp) REVERT: M 100 PHE cc_start: 0.6874 (m-80) cc_final: 0.6251 (m-80) outliers start: 83 outliers final: 46 residues processed: 559 average time/residue: 0.1422 time to fit residues: 123.4561 Evaluate side-chains 485 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 437 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 611 ASN Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 91 PHE Chi-restraints excluded: chain M residue 105 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 70 optimal weight: 10.0000 chunk 234 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 218 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN L 37 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN B 607 ASN C 20 GLN D 67 ASN D 478 ASN F 590 GLN F 607 ASN I 20 GLN E 67 ASN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 590 GLN G 607 ASN G 611 ASN G 656 ASN J 20 GLN M 58 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.128676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.100484 restraints weight = 52571.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.104250 restraints weight = 28673.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.106914 restraints weight = 19018.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.108573 restraints weight = 14309.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.109925 restraints weight = 11802.914| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 21399 Z= 0.249 Angle : 0.777 8.917 29187 Z= 0.398 Chirality : 0.049 0.266 3447 Planarity : 0.005 0.041 3606 Dihedral : 7.367 46.071 4191 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.38 % Favored : 96.50 % Rotamer: Outliers : 5.14 % Allowed : 12.78 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2487 helix: 1.56 (0.25), residues: 438 sheet: 0.65 (0.20), residues: 690 loop : -1.20 (0.15), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 327 TYR 0.029 0.003 TYR K 100E PHE 0.037 0.003 PHE H 100J TRP 0.027 0.002 TRP D 395 HIS 0.013 0.002 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00581 (21288) covalent geometry : angle 0.76040 (28893) SS BOND : bond 0.00439 ( 39) SS BOND : angle 1.16267 ( 78) hydrogen bonds : bond 0.05172 ( 825) hydrogen bonds : angle 5.85429 ( 2079) link_ALPHA1-2 : bond 0.00315 ( 3) link_ALPHA1-2 : angle 2.13869 ( 9) link_ALPHA1-3 : bond 0.01604 ( 3) link_ALPHA1-3 : angle 1.79281 ( 9) link_BETA1-4 : bond 0.00284 ( 30) link_BETA1-4 : angle 1.95148 ( 90) link_NAG-ASN : bond 0.00517 ( 36) link_NAG-ASN : angle 1.87881 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 439 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8116 (mmmm) REVERT: A 209 SER cc_start: 0.7286 (t) cc_final: 0.6925 (p) REVERT: A 258 GLN cc_start: 0.8262 (mt0) cc_final: 0.7610 (mt0) REVERT: A 358 ILE cc_start: 0.8526 (mm) cc_final: 0.8284 (mm) REVERT: A 475 MET cc_start: 0.6833 (mmm) cc_final: 0.5895 (mmm) REVERT: A 479 TRP cc_start: 0.6408 (m-90) cc_final: 0.6169 (m-90) REVERT: L 30 SER cc_start: 0.8781 (t) cc_final: 0.8557 (t) REVERT: L 38 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7655 (tm-30) REVERT: L 42 GLN cc_start: 0.6707 (mm110) cc_final: 0.6456 (mp10) REVERT: L 79 GLN cc_start: 0.8754 (mm110) cc_final: 0.8546 (mm-40) REVERT: L 85 VAL cc_start: 0.7762 (t) cc_final: 0.7389 (t) REVERT: L 98 PHE cc_start: 0.6688 (p90) cc_final: 0.6389 (p90) REVERT: B 540 GLN cc_start: 0.9014 (mm110) cc_final: 0.8131 (tt0) REVERT: B 584 GLU cc_start: 0.8033 (pt0) cc_final: 0.7420 (tm-30) REVERT: B 629 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.6637 (mtm) REVERT: B 632 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8124 (tm-30) REVERT: C 33 GLN cc_start: 0.8047 (mm-40) cc_final: 0.6891 (tm-30) REVERT: C 51 LEU cc_start: 0.8580 (mt) cc_final: 0.8374 (mt) REVERT: C 80 ASP cc_start: 0.8473 (t0) cc_final: 0.8007 (t70) REVERT: C 82 TYR cc_start: 0.8379 (m-10) cc_final: 0.8139 (m-10) REVERT: C 94 GLN cc_start: 0.7448 (tp40) cc_final: 0.7221 (tp40) REVERT: H 30 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8081 (tt) REVERT: H 72 ASP cc_start: 0.7088 (t0) cc_final: 0.6629 (t0) REVERT: H 83 ARG cc_start: 0.8200 (ptp-170) cc_final: 0.7928 (ptt-90) REVERT: D 33 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8254 (mmmm) REVERT: D 209 SER cc_start: 0.7068 (t) cc_final: 0.6835 (p) REVERT: D 358 ILE cc_start: 0.8322 (mm) cc_final: 0.7993 (mm) REVERT: N 21 LEU cc_start: 0.8726 (tp) cc_final: 0.8477 (mp) REVERT: N 38 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7878 (tm-30) REVERT: N 42 GLN cc_start: 0.6593 (mm-40) cc_final: 0.6277 (mp10) REVERT: N 83 PHE cc_start: 0.8398 (m-10) cc_final: 0.8188 (m-10) REVERT: F 629 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7586 (mtm) REVERT: I 33 GLN cc_start: 0.7982 (mm-40) cc_final: 0.6770 (tm-30) REVERT: I 34 ILE cc_start: 0.8182 (mm) cc_final: 0.7929 (mt) REVERT: I 66 ASN cc_start: 0.8425 (t0) cc_final: 0.8136 (m-40) REVERT: K 3 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8249 (mp10) REVERT: K 5 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8304 (mp) REVERT: K 23 LYS cc_start: 0.8436 (tmmt) cc_final: 0.7944 (tmmt) REVERT: K 25 SER cc_start: 0.8277 (t) cc_final: 0.7523 (p) REVERT: K 81 GLU cc_start: 0.8677 (tt0) cc_final: 0.8069 (tm-30) REVERT: E 33 LYS cc_start: 0.8587 (mmtt) cc_final: 0.8201 (mmmm) REVERT: E 209 SER cc_start: 0.7332 (t) cc_final: 0.6956 (p) REVERT: E 258 GLN cc_start: 0.7926 (mt0) cc_final: 0.7340 (mt0) REVERT: E 338 TRP cc_start: 0.8081 (t-100) cc_final: 0.7852 (t-100) REVERT: E 358 ILE cc_start: 0.8425 (mm) cc_final: 0.8175 (mm) REVERT: E 475 MET cc_start: 0.6768 (mmm) cc_final: 0.4854 (mmm) REVERT: E 479 TRP cc_start: 0.6420 (m-90) cc_final: 0.6095 (m-90) REVERT: O 38 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7978 (tm-30) REVERT: O 42 GLN cc_start: 0.6625 (mm110) cc_final: 0.6387 (mp-120) REVERT: O 47 LEU cc_start: 0.8991 (pp) cc_final: 0.8148 (mm) REVERT: O 49 TYR cc_start: 0.7891 (t80) cc_final: 0.7647 (t80) REVERT: O 58 VAL cc_start: 0.7631 (t) cc_final: 0.5291 (t) REVERT: O 70 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8060 (mm-30) REVERT: O 79 GLN cc_start: 0.8819 (mm110) cc_final: 0.8615 (mm-40) REVERT: G 540 GLN cc_start: 0.9051 (mm110) cc_final: 0.8373 (tt0) REVERT: G 657 GLU cc_start: 0.9093 (tt0) cc_final: 0.8875 (tm-30) REVERT: M 3 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8243 (mp10) REVERT: M 23 LYS cc_start: 0.8351 (tmmt) cc_final: 0.7831 (tmmt) REVERT: M 25 SER cc_start: 0.8213 (t) cc_final: 0.7648 (m) REVERT: M 66 ARG cc_start: 0.8474 (mtm-85) cc_final: 0.8246 (mtm-85) REVERT: M 85 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8005 (t0) REVERT: M 100 PHE cc_start: 0.7193 (m-80) cc_final: 0.6461 (m-80) outliers start: 113 outliers final: 68 residues processed: 507 average time/residue: 0.1499 time to fit residues: 116.3165 Evaluate side-chains 470 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 397 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 82 ASN Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 91 PHE Chi-restraints excluded: chain M residue 105 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 170 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 234 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 232 optimal weight: 0.0770 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN B 611 ASN B 620 ASN ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN E 67 ASN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 607 ASN G 620 ASN ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.134156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.105331 restraints weight = 54240.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.109446 restraints weight = 29197.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.113001 restraints weight = 17617.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.113936 restraints weight = 12059.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.114448 restraints weight = 10844.453| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 21399 Z= 0.157 Angle : 0.701 8.983 29187 Z= 0.354 Chirality : 0.047 0.250 3447 Planarity : 0.005 0.045 3606 Dihedral : 6.803 57.100 4191 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.46 % Favored : 96.42 % Rotamer: Outliers : 3.77 % Allowed : 14.78 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.16), residues: 2487 helix: 1.77 (0.25), residues: 420 sheet: 0.47 (0.20), residues: 711 loop : -1.19 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 18 TYR 0.031 0.002 TYR M 100E PHE 0.021 0.002 PHE E 53 TRP 0.020 0.001 TRP N 94 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00364 (21288) covalent geometry : angle 0.68718 (28893) SS BOND : bond 0.00312 ( 39) SS BOND : angle 1.36097 ( 78) hydrogen bonds : bond 0.04361 ( 825) hydrogen bonds : angle 5.49160 ( 2079) link_ALPHA1-2 : bond 0.00151 ( 3) link_ALPHA1-2 : angle 1.91578 ( 9) link_ALPHA1-3 : bond 0.01316 ( 3) link_ALPHA1-3 : angle 1.48696 ( 9) link_BETA1-4 : bond 0.00347 ( 30) link_BETA1-4 : angle 1.62962 ( 90) link_NAG-ASN : bond 0.00333 ( 36) link_NAG-ASN : angle 1.55071 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 463 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8347 (mmtt) cc_final: 0.8129 (mmmm) REVERT: A 111 LEU cc_start: 0.8520 (tt) cc_final: 0.8288 (tp) REVERT: A 341 THR cc_start: 0.8549 (m) cc_final: 0.8287 (p) REVERT: A 358 ILE cc_start: 0.8444 (mm) cc_final: 0.8216 (mm) REVERT: L 36 TYR cc_start: 0.6871 (m-80) cc_final: 0.6476 (m-80) REVERT: L 38 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7843 (tm-30) REVERT: L 42 GLN cc_start: 0.6725 (mm110) cc_final: 0.6519 (mp10) REVERT: L 46 LEU cc_start: 0.8582 (tp) cc_final: 0.8368 (tp) REVERT: L 85 VAL cc_start: 0.7569 (t) cc_final: 0.7181 (t) REVERT: B 540 GLN cc_start: 0.8929 (mm110) cc_final: 0.8192 (tt0) REVERT: B 584 GLU cc_start: 0.8153 (pt0) cc_final: 0.7579 (tm-30) REVERT: B 592 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7526 (mm) REVERT: B 629 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.6459 (mtm) REVERT: B 632 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8033 (tm-30) REVERT: C 51 LEU cc_start: 0.8600 (mt) cc_final: 0.8376 (mt) REVERT: C 80 ASP cc_start: 0.8568 (t0) cc_final: 0.8019 (t70) REVERT: C 82 TYR cc_start: 0.8396 (m-10) cc_final: 0.8129 (m-10) REVERT: H 36 TRP cc_start: 0.8050 (m100) cc_final: 0.7019 (m100) REVERT: H 72 ASP cc_start: 0.7112 (t0) cc_final: 0.6642 (t0) REVERT: H 83 ARG cc_start: 0.8279 (ptp-170) cc_final: 0.7967 (ptt-90) REVERT: H 100 PHE cc_start: 0.6874 (m-80) cc_final: 0.6654 (m-80) REVERT: D 33 LYS cc_start: 0.8289 (mmtt) cc_final: 0.8080 (mmmm) REVERT: D 107 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7523 (t70) REVERT: D 209 SER cc_start: 0.7072 (t) cc_final: 0.6712 (p) REVERT: D 258 GLN cc_start: 0.8059 (mt0) cc_final: 0.7473 (mt0) REVERT: D 358 ILE cc_start: 0.8222 (mm) cc_final: 0.7981 (mm) REVERT: D 475 MET cc_start: 0.6487 (mmm) cc_final: 0.5375 (mmm) REVERT: D 479 TRP cc_start: 0.6155 (m-10) cc_final: 0.5892 (m-90) REVERT: D 482 GLU cc_start: 0.7578 (tp30) cc_final: 0.7333 (tp30) REVERT: N 38 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7890 (tm-30) REVERT: N 42 GLN cc_start: 0.6581 (mm-40) cc_final: 0.6246 (mp10) REVERT: N 48 ILE cc_start: 0.9263 (mm) cc_final: 0.9000 (mm) REVERT: N 58 VAL cc_start: 0.7772 (t) cc_final: 0.7310 (t) REVERT: F 584 GLU cc_start: 0.8229 (pt0) cc_final: 0.7548 (tm-30) REVERT: F 629 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7811 (mtt) REVERT: F 657 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8453 (tm-30) REVERT: I 33 GLN cc_start: 0.7987 (mm-40) cc_final: 0.6889 (tm-30) REVERT: I 34 ILE cc_start: 0.8229 (mm) cc_final: 0.8008 (mt) REVERT: I 76 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9128 (pt) REVERT: I 80 ASP cc_start: 0.8218 (t0) cc_final: 0.7657 (t0) REVERT: K 5 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8322 (mp) REVERT: K 23 LYS cc_start: 0.8449 (tmmt) cc_final: 0.8136 (tmmt) REVERT: K 25 SER cc_start: 0.8135 (t) cc_final: 0.7826 (m) REVERT: E 33 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8169 (mmmm) REVERT: E 111 LEU cc_start: 0.8462 (tt) cc_final: 0.8250 (tp) REVERT: E 209 SER cc_start: 0.7272 (t) cc_final: 0.6893 (p) REVERT: E 258 GLN cc_start: 0.7912 (mt0) cc_final: 0.7188 (mt0) REVERT: E 358 ILE cc_start: 0.8350 (mm) cc_final: 0.8143 (mm) REVERT: E 475 MET cc_start: 0.6265 (mmm) cc_final: 0.4834 (tpp) REVERT: E 479 TRP cc_start: 0.6245 (m-90) cc_final: 0.5740 (m-90) REVERT: O 70 GLU cc_start: 0.8704 (mm-30) cc_final: 0.7981 (mm-30) REVERT: G 530 MET cc_start: 0.8471 (mmm) cc_final: 0.8196 (mmt) REVERT: G 540 GLN cc_start: 0.8970 (mm110) cc_final: 0.8393 (tt0) REVERT: J 66 ASN cc_start: 0.8480 (t0) cc_final: 0.8108 (m-40) REVERT: J 73 ASN cc_start: 0.8193 (t0) cc_final: 0.7921 (p0) REVERT: J 82 TYR cc_start: 0.8197 (m-10) cc_final: 0.7979 (m-10) REVERT: M 3 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8232 (mp10) REVERT: M 5 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8098 (mp) REVERT: M 12 LYS cc_start: 0.9057 (mttp) cc_final: 0.8693 (mtpp) REVERT: M 23 LYS cc_start: 0.8343 (tmmt) cc_final: 0.7901 (tmmt) REVERT: M 25 SER cc_start: 0.8202 (t) cc_final: 0.7733 (m) REVERT: M 36 TRP cc_start: 0.7922 (m100) cc_final: 0.7362 (m100) REVERT: M 81 GLU cc_start: 0.8692 (tt0) cc_final: 0.7931 (tm-30) REVERT: M 100 PHE cc_start: 0.7116 (m-80) cc_final: 0.6492 (m-80) outliers start: 83 outliers final: 56 residues processed: 513 average time/residue: 0.1436 time to fit residues: 113.4170 Evaluate side-chains 463 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 400 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 82 ASN Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 91 PHE Chi-restraints excluded: chain M residue 105 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 178 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 138 optimal weight: 0.0030 chunk 10 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 187 optimal weight: 0.3980 chunk 227 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 overall best weight: 1.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN L 89 GLN B 607 ASN B 611 ASN C 66 ASN D 67 ASN D 478 ASN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN O 42 GLN G 607 ASN G 611 ASN G 620 ASN ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.132171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.104671 restraints weight = 52287.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.108539 restraints weight = 28274.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.111257 restraints weight = 18601.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.113143 restraints weight = 13785.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.114334 restraints weight = 11107.931| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21399 Z= 0.140 Angle : 0.675 9.160 29187 Z= 0.340 Chirality : 0.046 0.246 3447 Planarity : 0.004 0.046 3606 Dihedral : 6.501 58.251 4191 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.22 % Favored : 95.66 % Rotamer: Outliers : 4.14 % Allowed : 16.42 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.16), residues: 2487 helix: 1.89 (0.25), residues: 417 sheet: 0.58 (0.21), residues: 645 loop : -1.33 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 18 TYR 0.030 0.002 TYR K 100E PHE 0.021 0.002 PHE K 100J TRP 0.018 0.001 TRP N 94 HIS 0.005 0.001 HIS I 27 Details of bonding type rmsd covalent geometry : bond 0.00323 (21288) covalent geometry : angle 0.66003 (28893) SS BOND : bond 0.00274 ( 39) SS BOND : angle 1.54950 ( 78) hydrogen bonds : bond 0.04059 ( 825) hydrogen bonds : angle 5.35213 ( 2079) link_ALPHA1-2 : bond 0.00071 ( 3) link_ALPHA1-2 : angle 1.87922 ( 9) link_ALPHA1-3 : bond 0.01370 ( 3) link_ALPHA1-3 : angle 1.23823 ( 9) link_BETA1-4 : bond 0.00318 ( 30) link_BETA1-4 : angle 1.55915 ( 90) link_NAG-ASN : bond 0.00326 ( 36) link_NAG-ASN : angle 1.49450 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 425 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8329 (mmtt) cc_final: 0.8103 (mmmm) REVERT: A 258 GLN cc_start: 0.8004 (mt0) cc_final: 0.7252 (mt0) REVERT: A 341 THR cc_start: 0.8522 (m) cc_final: 0.8281 (p) REVERT: A 358 ILE cc_start: 0.8401 (mm) cc_final: 0.8196 (mm) REVERT: A 475 MET cc_start: 0.7098 (mmm) cc_final: 0.6258 (mmm) REVERT: L 36 TYR cc_start: 0.6823 (m-80) cc_final: 0.6435 (m-10) REVERT: L 38 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7851 (tm-30) REVERT: L 46 LEU cc_start: 0.8591 (tp) cc_final: 0.8365 (tp) REVERT: L 85 VAL cc_start: 0.7628 (t) cc_final: 0.7248 (t) REVERT: L 90 GLN cc_start: 0.6516 (mt0) cc_final: 0.6268 (tp-100) REVERT: B 540 GLN cc_start: 0.8905 (mm110) cc_final: 0.8174 (tt0) REVERT: B 584 GLU cc_start: 0.8172 (pt0) cc_final: 0.7604 (tm-30) REVERT: B 629 MET cc_start: 0.7500 (mtt) cc_final: 0.6799 (mtt) REVERT: B 632 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8089 (tm-30) REVERT: C 80 ASP cc_start: 0.8595 (t0) cc_final: 0.8121 (t70) REVERT: H 23 LYS cc_start: 0.8124 (tmmt) cc_final: 0.7701 (mmtm) REVERT: H 30 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8062 (tt) REVERT: H 72 ASP cc_start: 0.7079 (t0) cc_final: 0.6620 (t0) REVERT: H 83 ARG cc_start: 0.8227 (ptp-170) cc_final: 0.7910 (ptt-90) REVERT: H 100 PHE cc_start: 0.6880 (m-80) cc_final: 0.6472 (m-10) REVERT: D 33 LYS cc_start: 0.8310 (mmtt) cc_final: 0.8089 (mmmm) REVERT: D 107 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7543 (t70) REVERT: D 209 SER cc_start: 0.7091 (t) cc_final: 0.6729 (p) REVERT: D 258 GLN cc_start: 0.8085 (mt0) cc_final: 0.7618 (mt0) REVERT: D 358 ILE cc_start: 0.8319 (mm) cc_final: 0.8085 (mm) REVERT: D 475 MET cc_start: 0.6394 (mmm) cc_final: 0.4391 (mmm) REVERT: D 479 TRP cc_start: 0.6128 (m-10) cc_final: 0.5807 (m-90) REVERT: N 27 GLU cc_start: 0.9147 (tp30) cc_final: 0.8668 (tp30) REVERT: N 38 GLN cc_start: 0.8288 (tm-30) cc_final: 0.8083 (tm-30) REVERT: N 42 GLN cc_start: 0.6664 (mm-40) cc_final: 0.6399 (mp10) REVERT: N 48 ILE cc_start: 0.9246 (mm) cc_final: 0.8976 (mm) REVERT: F 584 GLU cc_start: 0.8245 (pt0) cc_final: 0.7574 (tm-30) REVERT: F 629 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7252 (mtm) REVERT: F 647 GLU cc_start: 0.8400 (tt0) cc_final: 0.7867 (tt0) REVERT: F 657 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8497 (tm-30) REVERT: I 66 ASN cc_start: 0.8357 (t0) cc_final: 0.8036 (m-40) REVERT: I 76 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9118 (pt) REVERT: I 80 ASP cc_start: 0.8085 (t0) cc_final: 0.7844 (t0) REVERT: K 23 LYS cc_start: 0.8459 (tmmt) cc_final: 0.8110 (tmmt) REVERT: E 33 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8187 (mmmm) REVERT: E 209 SER cc_start: 0.7234 (t) cc_final: 0.6881 (p) REVERT: E 258 GLN cc_start: 0.7902 (mt0) cc_final: 0.7672 (mt0) REVERT: E 475 MET cc_start: 0.6321 (mmm) cc_final: 0.5528 (mmp) REVERT: O 38 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7751 (tm-30) REVERT: O 49 TYR cc_start: 0.8382 (t80) cc_final: 0.8158 (t80) REVERT: O 70 GLU cc_start: 0.8694 (mm-30) cc_final: 0.7967 (mm-30) REVERT: O 83 PHE cc_start: 0.8566 (m-10) cc_final: 0.8349 (m-80) REVERT: G 530 MET cc_start: 0.8480 (mmm) cc_final: 0.8271 (mmt) REVERT: G 540 GLN cc_start: 0.8937 (mm110) cc_final: 0.8383 (tt0) REVERT: M 3 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8212 (mp10) REVERT: M 12 LYS cc_start: 0.9052 (mttp) cc_final: 0.8703 (mtpp) REVERT: M 13 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8521 (mmmt) REVERT: M 23 LYS cc_start: 0.8398 (tmmt) cc_final: 0.8072 (tmmt) REVERT: M 81 GLU cc_start: 0.8685 (tt0) cc_final: 0.8079 (tm-30) REVERT: M 83 ARG cc_start: 0.8084 (ptp-170) cc_final: 0.7560 (ptt-90) REVERT: M 100 PHE cc_start: 0.7388 (m-80) cc_final: 0.6814 (m-80) outliers start: 91 outliers final: 57 residues processed: 482 average time/residue: 0.1458 time to fit residues: 108.5324 Evaluate side-chains 449 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 388 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 91 PHE Chi-restraints excluded: chain M residue 108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 31 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 206 optimal weight: 40.0000 chunk 89 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 212 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 chunk 193 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN B 607 ASN B 658 GLN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN G 607 ASN G 620 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.130686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.103036 restraints weight = 52826.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.106821 restraints weight = 28795.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.109472 restraints weight = 19036.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.111327 restraints weight = 14174.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.112638 restraints weight = 11483.619| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21399 Z= 0.163 Angle : 0.674 11.035 29187 Z= 0.341 Chirality : 0.047 0.248 3447 Planarity : 0.005 0.049 3606 Dihedral : 6.458 56.733 4191 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.91 % Favored : 94.97 % Rotamer: Outliers : 4.23 % Allowed : 17.42 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.16), residues: 2487 helix: 1.74 (0.25), residues: 423 sheet: 0.47 (0.21), residues: 651 loop : -1.35 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 18 TYR 0.029 0.002 TYR K 100E PHE 0.019 0.002 PHE E 376 TRP 0.033 0.002 TRP E 479 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00380 (21288) covalent geometry : angle 0.65888 (28893) SS BOND : bond 0.00363 ( 39) SS BOND : angle 1.62308 ( 78) hydrogen bonds : bond 0.04072 ( 825) hydrogen bonds : angle 5.33216 ( 2079) link_ALPHA1-2 : bond 0.00294 ( 3) link_ALPHA1-2 : angle 1.94840 ( 9) link_ALPHA1-3 : bond 0.01145 ( 3) link_ALPHA1-3 : angle 1.30277 ( 9) link_BETA1-4 : bond 0.00274 ( 30) link_BETA1-4 : angle 1.55930 ( 90) link_NAG-ASN : bond 0.00308 ( 36) link_NAG-ASN : angle 1.52110 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 395 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8377 (mmtt) cc_final: 0.8043 (mmmm) REVERT: A 358 ILE cc_start: 0.8284 (mm) cc_final: 0.8060 (mm) REVERT: A 475 MET cc_start: 0.7191 (mmm) cc_final: 0.6433 (mmm) REVERT: A 478 ASN cc_start: 0.8346 (m-40) cc_final: 0.8131 (m110) REVERT: L 38 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7788 (tm-30) REVERT: B 540 GLN cc_start: 0.8888 (mm110) cc_final: 0.8189 (tt0) REVERT: B 584 GLU cc_start: 0.8137 (pt0) cc_final: 0.7424 (tm-30) REVERT: B 629 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6872 (mtt) REVERT: B 632 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8068 (tm-30) REVERT: C 66 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.8025 (t0) REVERT: C 80 ASP cc_start: 0.8659 (t0) cc_final: 0.8202 (t70) REVERT: H 3 GLN cc_start: 0.8387 (mp10) cc_final: 0.8110 (mp10) REVERT: H 23 LYS cc_start: 0.8279 (tmmt) cc_final: 0.7791 (mmtm) REVERT: H 30 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8064 (tt) REVERT: H 72 ASP cc_start: 0.7092 (t0) cc_final: 0.6653 (t0) REVERT: H 83 ARG cc_start: 0.8214 (ptp-170) cc_final: 0.7896 (ptt-90) REVERT: D 107 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7615 (t70) REVERT: D 209 SER cc_start: 0.7154 (t) cc_final: 0.6807 (p) REVERT: D 258 GLN cc_start: 0.8317 (mt0) cc_final: 0.7688 (mt0) REVERT: D 358 ILE cc_start: 0.8210 (mm) cc_final: 0.7991 (mm) REVERT: D 475 MET cc_start: 0.6543 (mmm) cc_final: 0.5308 (mmm) REVERT: N 27 GLU cc_start: 0.9154 (tp30) cc_final: 0.8686 (tp30) REVERT: N 38 GLN cc_start: 0.8217 (tm-30) cc_final: 0.8017 (tm-30) REVERT: N 42 GLN cc_start: 0.6679 (mm-40) cc_final: 0.6462 (mp-120) REVERT: N 48 ILE cc_start: 0.9197 (mm) cc_final: 0.8912 (mm) REVERT: F 629 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7304 (mtm) REVERT: I 66 ASN cc_start: 0.8386 (t0) cc_final: 0.8057 (m-40) REVERT: I 76 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.9121 (pt) REVERT: I 80 ASP cc_start: 0.8152 (t0) cc_final: 0.7914 (t0) REVERT: K 12 LYS cc_start: 0.8705 (mttp) cc_final: 0.8432 (mttt) REVERT: K 23 LYS cc_start: 0.8596 (tmmt) cc_final: 0.8173 (mmtm) REVERT: E 33 LYS cc_start: 0.8535 (mmtt) cc_final: 0.8256 (mmmm) REVERT: E 104 MET cc_start: 0.7448 (tpt) cc_final: 0.7242 (tpp) REVERT: E 209 SER cc_start: 0.7304 (t) cc_final: 0.6960 (p) REVERT: E 258 GLN cc_start: 0.8025 (mt0) cc_final: 0.7724 (mt0) REVERT: O 38 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7717 (tm-30) REVERT: O 46 LEU cc_start: 0.8506 (tp) cc_final: 0.8297 (tp) REVERT: O 49 TYR cc_start: 0.8416 (t80) cc_final: 0.8157 (t80) REVERT: O 83 PHE cc_start: 0.8562 (m-10) cc_final: 0.8338 (m-80) REVERT: G 540 GLN cc_start: 0.8902 (mm110) cc_final: 0.8358 (tt0) REVERT: G 657 GLU cc_start: 0.9062 (tp30) cc_final: 0.8719 (tp30) REVERT: J 76 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.9117 (pt) REVERT: J 94 GLN cc_start: 0.7121 (tp40) cc_final: 0.6732 (tp40) REVERT: M 12 LYS cc_start: 0.9028 (mttp) cc_final: 0.8606 (mtpp) REVERT: M 13 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8501 (mmmt) REVERT: M 23 LYS cc_start: 0.8632 (tmmt) cc_final: 0.8037 (mmtm) REVERT: M 81 GLU cc_start: 0.8684 (tt0) cc_final: 0.8070 (tm-30) REVERT: M 84 SER cc_start: 0.9383 (OUTLIER) cc_final: 0.9144 (p) REVERT: M 100 PHE cc_start: 0.7511 (m-80) cc_final: 0.6881 (m-80) outliers start: 93 outliers final: 64 residues processed: 449 average time/residue: 0.1510 time to fit residues: 103.0086 Evaluate side-chains 443 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 371 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 617 LYS Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 82 ASN Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 91 PHE Chi-restraints excluded: chain M residue 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 151 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 154 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 234 optimal weight: 3.9990 chunk 241 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN B 607 ASN B 620 ASN C 66 ASN D 308 HIS ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 607 ASN G 620 ASN G 656 ASN M 64 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.129988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.102102 restraints weight = 53330.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.105885 restraints weight = 29084.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.108510 restraints weight = 19275.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.110337 restraints weight = 14447.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.111654 restraints weight = 11747.208| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21399 Z= 0.163 Angle : 0.687 11.730 29187 Z= 0.347 Chirality : 0.047 0.247 3447 Planarity : 0.005 0.050 3606 Dihedral : 6.399 59.498 4191 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.27 % Favored : 94.61 % Rotamer: Outliers : 4.27 % Allowed : 17.83 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 2487 helix: 1.66 (0.24), residues: 423 sheet: 0.65 (0.21), residues: 630 loop : -1.43 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 66 TYR 0.029 0.002 TYR K 100E PHE 0.025 0.002 PHE L 83 TRP 0.045 0.002 TRP D 479 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00379 (21288) covalent geometry : angle 0.67203 (28893) SS BOND : bond 0.00352 ( 39) SS BOND : angle 1.72963 ( 78) hydrogen bonds : bond 0.04037 ( 825) hydrogen bonds : angle 5.27470 ( 2079) link_ALPHA1-2 : bond 0.00147 ( 3) link_ALPHA1-2 : angle 2.00317 ( 9) link_ALPHA1-3 : bond 0.00994 ( 3) link_ALPHA1-3 : angle 1.16795 ( 9) link_BETA1-4 : bond 0.00266 ( 30) link_BETA1-4 : angle 1.52681 ( 90) link_NAG-ASN : bond 0.00305 ( 36) link_NAG-ASN : angle 1.49104 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 392 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8155 (mmmm) REVERT: A 258 GLN cc_start: 0.7968 (mt0) cc_final: 0.7353 (mt0) REVERT: A 358 ILE cc_start: 0.8284 (mm) cc_final: 0.8034 (mm) REVERT: A 475 MET cc_start: 0.7193 (mmm) cc_final: 0.6423 (mmm) REVERT: A 478 ASN cc_start: 0.8378 (m-40) cc_final: 0.8118 (m110) REVERT: B 540 GLN cc_start: 0.8897 (mm110) cc_final: 0.8234 (tt0) REVERT: B 584 GLU cc_start: 0.8108 (pt0) cc_final: 0.7424 (tm-30) REVERT: B 592 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7600 (mm) REVERT: B 629 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.5803 (mtm) REVERT: B 632 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8015 (tm-30) REVERT: C 80 ASP cc_start: 0.8757 (t0) cc_final: 0.8504 (t0) REVERT: C 85 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7763 (tm-30) REVERT: H 3 GLN cc_start: 0.8418 (mp10) cc_final: 0.8129 (mp10) REVERT: H 23 LYS cc_start: 0.8337 (tmmt) cc_final: 0.7813 (mmtm) REVERT: H 30 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8018 (tt) REVERT: H 72 ASP cc_start: 0.7063 (t0) cc_final: 0.6614 (t0) REVERT: H 83 ARG cc_start: 0.8207 (ptp-170) cc_final: 0.7895 (ptt-90) REVERT: D 107 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7627 (t70) REVERT: D 209 SER cc_start: 0.7133 (t) cc_final: 0.6757 (p) REVERT: D 358 ILE cc_start: 0.8219 (mm) cc_final: 0.8014 (mm) REVERT: N 27 GLU cc_start: 0.9158 (tp30) cc_final: 0.8687 (tp30) REVERT: N 48 ILE cc_start: 0.9180 (mm) cc_final: 0.8918 (mm) REVERT: N 58 VAL cc_start: 0.7872 (t) cc_final: 0.7409 (t) REVERT: N 105 GLU cc_start: 0.7117 (pt0) cc_final: 0.6699 (pm20) REVERT: F 629 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7272 (mtm) REVERT: F 654 GLU cc_start: 0.8958 (tp30) cc_final: 0.8749 (tp30) REVERT: I 80 ASP cc_start: 0.8267 (t0) cc_final: 0.7813 (t0) REVERT: I 94 GLN cc_start: 0.7178 (tp40) cc_final: 0.6701 (tp40) REVERT: K 23 LYS cc_start: 0.8597 (tmmt) cc_final: 0.8149 (mmtm) REVERT: E 33 LYS cc_start: 0.8526 (mmtt) cc_final: 0.8296 (mmmm) REVERT: E 209 SER cc_start: 0.7297 (t) cc_final: 0.6993 (p) REVERT: E 231 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.9000 (mptt) REVERT: E 258 GLN cc_start: 0.8063 (mt0) cc_final: 0.7554 (mt0) REVERT: E 479 TRP cc_start: 0.6024 (m-90) cc_final: 0.5747 (m-90) REVERT: O 27 GLU cc_start: 0.9088 (tp30) cc_final: 0.8678 (tp30) REVERT: O 49 TYR cc_start: 0.8376 (t80) cc_final: 0.8093 (t80) REVERT: O 70 GLU cc_start: 0.8735 (mm-30) cc_final: 0.7963 (mm-30) REVERT: O 83 PHE cc_start: 0.8620 (m-10) cc_final: 0.8382 (m-80) REVERT: G 540 GLN cc_start: 0.8898 (mm110) cc_final: 0.8421 (tt0) REVERT: G 626 MET cc_start: 0.7740 (ttm) cc_final: 0.7438 (mtp) REVERT: G 629 MET cc_start: 0.7502 (mtt) cc_final: 0.7247 (mtt) REVERT: G 657 GLU cc_start: 0.9089 (tp30) cc_final: 0.8736 (tp30) REVERT: J 66 ASN cc_start: 0.8593 (t0) cc_final: 0.8102 (m-40) REVERT: J 73 ASN cc_start: 0.8071 (t0) cc_final: 0.7815 (p0) REVERT: M 12 LYS cc_start: 0.8884 (mttp) cc_final: 0.8515 (mtpp) REVERT: M 13 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8509 (mmmt) REVERT: M 23 LYS cc_start: 0.8745 (tmmt) cc_final: 0.8146 (mmtm) REVERT: M 81 GLU cc_start: 0.8670 (tt0) cc_final: 0.8008 (tm-30) REVERT: M 100 PHE cc_start: 0.7602 (m-80) cc_final: 0.6792 (m-80) outliers start: 94 outliers final: 74 residues processed: 450 average time/residue: 0.1450 time to fit residues: 100.2942 Evaluate side-chains 453 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 373 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain G residue 543 LEU Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 607 ASN Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain M residue 91 PHE Chi-restraints excluded: chain M residue 108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 192 optimal weight: 0.0980 chunk 165 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 55 optimal weight: 0.0770 chunk 135 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN B 607 ASN B 620 ASN C 66 ASN H 64 GLN F 620 ASN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 607 ASN G 620 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.131532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.103780 restraints weight = 52863.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.107577 restraints weight = 29020.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.110214 restraints weight = 19150.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.111936 restraints weight = 14285.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.113316 restraints weight = 11675.406| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21399 Z= 0.142 Angle : 0.685 12.328 29187 Z= 0.346 Chirality : 0.046 0.238 3447 Planarity : 0.005 0.053 3606 Dihedral : 6.215 55.653 4191 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.11 % Favored : 94.77 % Rotamer: Outliers : 4.23 % Allowed : 18.74 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.16), residues: 2487 helix: 1.73 (0.25), residues: 423 sheet: 0.68 (0.21), residues: 630 loop : -1.42 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 66 TYR 0.028 0.002 TYR H 100E PHE 0.021 0.002 PHE K 100J TRP 0.037 0.001 TRP D 479 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00332 (21288) covalent geometry : angle 0.67091 (28893) SS BOND : bond 0.00272 ( 39) SS BOND : angle 1.77423 ( 78) hydrogen bonds : bond 0.03842 ( 825) hydrogen bonds : angle 5.18973 ( 2079) link_ALPHA1-2 : bond 0.00128 ( 3) link_ALPHA1-2 : angle 1.93608 ( 9) link_ALPHA1-3 : bond 0.01069 ( 3) link_ALPHA1-3 : angle 1.08597 ( 9) link_BETA1-4 : bond 0.00286 ( 30) link_BETA1-4 : angle 1.47351 ( 90) link_NAG-ASN : bond 0.00294 ( 36) link_NAG-ASN : angle 1.42969 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 398 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8218 (mmmm) REVERT: A 258 GLN cc_start: 0.7917 (mt0) cc_final: 0.7243 (mt0) REVERT: A 358 ILE cc_start: 0.8325 (mm) cc_final: 0.8071 (mm) REVERT: A 475 MET cc_start: 0.7086 (mmm) cc_final: 0.6321 (mmm) REVERT: A 478 ASN cc_start: 0.8347 (m-40) cc_final: 0.8122 (m110) REVERT: B 530 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7142 (mmm) REVERT: B 540 GLN cc_start: 0.8928 (mm110) cc_final: 0.8215 (tt0) REVERT: B 584 GLU cc_start: 0.8175 (pt0) cc_final: 0.7467 (tm-30) REVERT: B 629 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.5833 (mtm) REVERT: B 632 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8092 (tp30) REVERT: C 33 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7580 (tp-100) REVERT: C 76 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.9221 (pt) REVERT: C 80 ASP cc_start: 0.8756 (t0) cc_final: 0.8449 (t0) REVERT: C 85 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7584 (tm-30) REVERT: C 94 GLN cc_start: 0.7327 (tp40) cc_final: 0.6996 (tp40) REVERT: H 3 GLN cc_start: 0.8314 (mp10) cc_final: 0.8003 (mp10) REVERT: H 23 LYS cc_start: 0.8418 (tmmt) cc_final: 0.7923 (mmtm) REVERT: H 72 ASP cc_start: 0.6910 (t0) cc_final: 0.6483 (t0) REVERT: H 83 ARG cc_start: 0.8240 (ptp-170) cc_final: 0.7872 (ptt-90) REVERT: D 107 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7557 (t70) REVERT: D 202 THR cc_start: 0.9548 (m) cc_final: 0.9320 (p) REVERT: D 209 SER cc_start: 0.7136 (t) cc_final: 0.6746 (p) REVERT: D 258 GLN cc_start: 0.8169 (mt0) cc_final: 0.7428 (mt0) REVERT: N 36 TYR cc_start: 0.6428 (m-80) cc_final: 0.6139 (m-80) REVERT: N 58 VAL cc_start: 0.7826 (t) cc_final: 0.7421 (t) REVERT: N 105 GLU cc_start: 0.7180 (pt0) cc_final: 0.6750 (pm20) REVERT: F 629 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7272 (mtm) REVERT: F 654 GLU cc_start: 0.9063 (tp30) cc_final: 0.8820 (tp30) REVERT: I 33 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7370 (tp40) REVERT: I 66 ASN cc_start: 0.8441 (t0) cc_final: 0.7996 (m-40) REVERT: I 80 ASP cc_start: 0.8333 (t0) cc_final: 0.8014 (t0) REVERT: I 94 GLN cc_start: 0.7298 (tp40) cc_final: 0.6888 (tp40) REVERT: K 23 LYS cc_start: 0.8535 (tmmt) cc_final: 0.8133 (mmtm) REVERT: E 33 LYS cc_start: 0.8635 (mmtt) cc_final: 0.8325 (mmmm) REVERT: E 114 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8044 (mt0) REVERT: E 209 SER cc_start: 0.7273 (t) cc_final: 0.6964 (p) REVERT: E 231 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8993 (mptt) REVERT: E 258 GLN cc_start: 0.7992 (mt0) cc_final: 0.7406 (mt0) REVERT: E 475 MET cc_start: 0.6170 (mmm) cc_final: 0.4943 (mmm) REVERT: E 479 TRP cc_start: 0.6092 (m-90) cc_final: 0.5642 (m-90) REVERT: O 27 GLU cc_start: 0.9141 (tp30) cc_final: 0.8705 (tp30) REVERT: O 38 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7669 (tm-30) REVERT: O 49 TYR cc_start: 0.8375 (t80) cc_final: 0.8134 (t80) REVERT: O 70 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8121 (mm-30) REVERT: O 83 PHE cc_start: 0.8550 (m-10) cc_final: 0.8303 (m-80) REVERT: G 540 GLN cc_start: 0.8999 (mm110) cc_final: 0.8482 (tt0) REVERT: G 581 LEU cc_start: 0.7170 (tp) cc_final: 0.6310 (tp) REVERT: G 584 GLU cc_start: 0.8304 (pt0) cc_final: 0.7614 (tm-30) REVERT: G 626 MET cc_start: 0.7756 (ttm) cc_final: 0.7363 (mtp) REVERT: G 629 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7330 (mtt) REVERT: G 657 GLU cc_start: 0.9179 (tp30) cc_final: 0.8830 (tp30) REVERT: J 66 ASN cc_start: 0.8514 (t0) cc_final: 0.8060 (m-40) REVERT: J 73 ASN cc_start: 0.8136 (t0) cc_final: 0.7878 (p0) REVERT: J 94 GLN cc_start: 0.7171 (tp40) cc_final: 0.6890 (tp40) REVERT: M 12 LYS cc_start: 0.8905 (mttp) cc_final: 0.8521 (mtpp) REVERT: M 13 LYS cc_start: 0.8820 (mmtt) cc_final: 0.8517 (mmmt) REVERT: M 23 LYS cc_start: 0.8729 (tmmt) cc_final: 0.8119 (mmtm) REVERT: M 30 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.7960 (tt) REVERT: M 81 GLU cc_start: 0.8748 (tt0) cc_final: 0.8469 (tm-30) REVERT: M 100 PHE cc_start: 0.7683 (m-80) cc_final: 0.6870 (m-80) outliers start: 93 outliers final: 73 residues processed: 448 average time/residue: 0.1458 time to fit residues: 100.9214 Evaluate side-chains 455 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 374 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain G residue 543 LEU Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 629 MET Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain M residue 91 PHE Chi-restraints excluded: chain M residue 110 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 133 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 219 optimal weight: 0.8980 chunk 187 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 208 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 226 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 607 ASN B 620 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN F 620 ASN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 607 ASN G 611 ASN G 620 ASN ** M 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.130219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.102421 restraints weight = 53367.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.106168 restraints weight = 29315.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.108757 restraints weight = 19353.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.110593 restraints weight = 14482.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.111877 restraints weight = 11747.451| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21399 Z= 0.171 Angle : 0.720 12.657 29187 Z= 0.363 Chirality : 0.047 0.254 3447 Planarity : 0.005 0.055 3606 Dihedral : 6.233 59.453 4191 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.63 % Favored : 94.25 % Rotamer: Outliers : 4.23 % Allowed : 18.69 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.16), residues: 2487 helix: 1.74 (0.25), residues: 420 sheet: 0.70 (0.21), residues: 615 loop : -1.48 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 103 TYR 0.031 0.002 TYR M 100E PHE 0.019 0.002 PHE E 376 TRP 0.030 0.002 TRP D 479 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00403 (21288) covalent geometry : angle 0.70560 (28893) SS BOND : bond 0.00330 ( 39) SS BOND : angle 1.88902 ( 78) hydrogen bonds : bond 0.03979 ( 825) hydrogen bonds : angle 5.23996 ( 2079) link_ALPHA1-2 : bond 0.00224 ( 3) link_ALPHA1-2 : angle 1.95026 ( 9) link_ALPHA1-3 : bond 0.01050 ( 3) link_ALPHA1-3 : angle 1.17262 ( 9) link_BETA1-4 : bond 0.00259 ( 30) link_BETA1-4 : angle 1.50240 ( 90) link_NAG-ASN : bond 0.00291 ( 36) link_NAG-ASN : angle 1.48173 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 377 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8189 (mmmm) REVERT: A 258 GLN cc_start: 0.8021 (mt0) cc_final: 0.7316 (mt0) REVERT: A 358 ILE cc_start: 0.8284 (mm) cc_final: 0.8041 (mm) REVERT: A 475 MET cc_start: 0.7204 (mmm) cc_final: 0.6457 (mmm) REVERT: A 478 ASN cc_start: 0.8393 (m-40) cc_final: 0.8087 (m110) REVERT: B 530 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7164 (mmm) REVERT: B 540 GLN cc_start: 0.8863 (mm110) cc_final: 0.8217 (tt0) REVERT: B 584 GLU cc_start: 0.8108 (pt0) cc_final: 0.7395 (tm-30) REVERT: B 629 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6444 (mtm) REVERT: C 33 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7576 (tp-100) REVERT: C 76 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9183 (pt) REVERT: C 80 ASP cc_start: 0.8768 (t0) cc_final: 0.8337 (t0) REVERT: C 94 GLN cc_start: 0.7180 (tp40) cc_final: 0.6740 (tp40) REVERT: H 3 GLN cc_start: 0.8281 (mp10) cc_final: 0.7964 (mp10) REVERT: H 23 LYS cc_start: 0.8443 (tmmt) cc_final: 0.7962 (mmtm) REVERT: H 30 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.7984 (tt) REVERT: H 72 ASP cc_start: 0.7082 (t0) cc_final: 0.6634 (t0) REVERT: H 83 ARG cc_start: 0.8106 (ptp-170) cc_final: 0.7769 (ptt-90) REVERT: H 100 PHE cc_start: 0.7292 (m-80) cc_final: 0.6662 (m-10) REVERT: D 107 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7710 (t70) REVERT: D 202 THR cc_start: 0.9507 (m) cc_final: 0.9255 (p) REVERT: D 209 SER cc_start: 0.7180 (t) cc_final: 0.6800 (p) REVERT: D 258 GLN cc_start: 0.8333 (mt0) cc_final: 0.7798 (mt0) REVERT: N 48 ILE cc_start: 0.9054 (mm) cc_final: 0.8834 (mm) REVERT: N 58 VAL cc_start: 0.7898 (t) cc_final: 0.7449 (t) REVERT: N 105 GLU cc_start: 0.7257 (pt0) cc_final: 0.6819 (pm20) REVERT: F 629 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7322 (mtm) REVERT: I 33 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7379 (tp40) REVERT: I 66 ASN cc_start: 0.8405 (t0) cc_final: 0.8071 (m-40) REVERT: K 3 GLN cc_start: 0.8306 (mp10) cc_final: 0.7990 (mp10) REVERT: K 23 LYS cc_start: 0.8577 (tmmt) cc_final: 0.8147 (mmtm) REVERT: K 85 ASP cc_start: 0.8455 (m-30) cc_final: 0.8077 (t0) REVERT: E 33 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8250 (mmmm) REVERT: E 114 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8023 (mt0) REVERT: E 209 SER cc_start: 0.7325 (t) cc_final: 0.7038 (p) REVERT: E 231 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8997 (mptt) REVERT: E 258 GLN cc_start: 0.8099 (mt0) cc_final: 0.7728 (mt0) REVERT: E 475 MET cc_start: 0.6407 (mmm) cc_final: 0.5214 (mmm) REVERT: E 479 TRP cc_start: 0.6219 (m-90) cc_final: 0.5827 (m-90) REVERT: O 27 GLU cc_start: 0.9094 (tp30) cc_final: 0.8717 (tp30) REVERT: O 36 TYR cc_start: 0.6769 (m-80) cc_final: 0.6305 (m-80) REVERT: O 38 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7736 (tm-30) REVERT: O 46 LEU cc_start: 0.8520 (tp) cc_final: 0.8107 (tp) REVERT: O 70 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8323 (mm-30) REVERT: O 83 PHE cc_start: 0.8561 (m-10) cc_final: 0.8286 (m-80) REVERT: G 540 GLN cc_start: 0.8887 (mm110) cc_final: 0.8425 (tt0) REVERT: G 626 MET cc_start: 0.7765 (ttm) cc_final: 0.7446 (mtp) REVERT: G 629 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.7271 (mtt) REVERT: G 657 GLU cc_start: 0.9124 (tp30) cc_final: 0.8815 (tp30) REVERT: J 66 ASN cc_start: 0.8541 (t0) cc_final: 0.8152 (m-40) REVERT: J 94 GLN cc_start: 0.7091 (tp40) cc_final: 0.6698 (tp40) REVERT: M 12 LYS cc_start: 0.8787 (mttp) cc_final: 0.8445 (mtpp) REVERT: M 13 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8509 (mmmt) REVERT: M 23 LYS cc_start: 0.8728 (tmmt) cc_final: 0.8083 (mmtm) REVERT: M 30 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.7937 (tt) REVERT: M 81 GLU cc_start: 0.8647 (tt0) cc_final: 0.8409 (tm-30) outliers start: 93 outliers final: 76 residues processed: 430 average time/residue: 0.1474 time to fit residues: 97.8943 Evaluate side-chains 454 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 369 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain G residue 543 LEU Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 607 ASN Chi-restraints excluded: chain G residue 629 MET Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 91 PHE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 239 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 242 optimal weight: 3.9990 chunk 55 optimal weight: 0.0670 chunk 81 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 189 optimal weight: 6.9990 overall best weight: 1.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 607 ASN B 620 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN F 620 ASN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 607 ASN G 620 ASN ** M 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.130479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.102957 restraints weight = 53354.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.106715 restraints weight = 29235.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.109338 restraints weight = 19245.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.111153 restraints weight = 14303.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.112307 restraints weight = 11618.568| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21399 Z= 0.156 Angle : 0.716 12.811 29187 Z= 0.362 Chirality : 0.047 0.238 3447 Planarity : 0.005 0.054 3606 Dihedral : 6.124 54.856 4191 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.59 % Favored : 94.33 % Rotamer: Outliers : 4.00 % Allowed : 19.55 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.16), residues: 2487 helix: 1.84 (0.25), residues: 420 sheet: 0.75 (0.21), residues: 615 loop : -1.50 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 542 TYR 0.031 0.002 TYR M 100E PHE 0.019 0.002 PHE E 376 TRP 0.024 0.001 TRP E 479 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00367 (21288) covalent geometry : angle 0.70182 (28893) SS BOND : bond 0.00296 ( 39) SS BOND : angle 1.91040 ( 78) hydrogen bonds : bond 0.03859 ( 825) hydrogen bonds : angle 5.18897 ( 2079) link_ALPHA1-2 : bond 0.00163 ( 3) link_ALPHA1-2 : angle 1.94389 ( 9) link_ALPHA1-3 : bond 0.00954 ( 3) link_ALPHA1-3 : angle 1.13917 ( 9) link_BETA1-4 : bond 0.00268 ( 30) link_BETA1-4 : angle 1.46638 ( 90) link_NAG-ASN : bond 0.00286 ( 36) link_NAG-ASN : angle 1.43618 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 381 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8196 (mmmm) REVERT: A 258 GLN cc_start: 0.8001 (mt0) cc_final: 0.7247 (mt0) REVERT: A 358 ILE cc_start: 0.8270 (mm) cc_final: 0.8025 (mm) REVERT: A 475 MET cc_start: 0.7141 (mmm) cc_final: 0.6450 (mmm) REVERT: A 478 ASN cc_start: 0.8331 (m-40) cc_final: 0.8054 (m110) REVERT: B 530 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7120 (mmm) REVERT: B 540 GLN cc_start: 0.8863 (mm110) cc_final: 0.8255 (tt0) REVERT: B 584 GLU cc_start: 0.8166 (pt0) cc_final: 0.7432 (tm-30) REVERT: B 629 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.6514 (mtm) REVERT: B 647 GLU cc_start: 0.8300 (tt0) cc_final: 0.7972 (tt0) REVERT: C 76 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9172 (pt) REVERT: C 80 ASP cc_start: 0.8789 (t0) cc_final: 0.8538 (t0) REVERT: H 23 LYS cc_start: 0.8447 (tmmt) cc_final: 0.7962 (mmtm) REVERT: H 30 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.7981 (tt) REVERT: H 72 ASP cc_start: 0.7054 (t0) cc_final: 0.6596 (t0) REVERT: H 83 ARG cc_start: 0.8131 (ptp-170) cc_final: 0.7800 (ptt-90) REVERT: H 100 PHE cc_start: 0.7249 (m-80) cc_final: 0.6519 (m-10) REVERT: D 107 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7702 (t70) REVERT: D 202 THR cc_start: 0.9488 (m) cc_final: 0.9227 (p) REVERT: D 209 SER cc_start: 0.7160 (t) cc_final: 0.6782 (p) REVERT: D 258 GLN cc_start: 0.8264 (mt0) cc_final: 0.7725 (mt0) REVERT: N 48 ILE cc_start: 0.8987 (mm) cc_final: 0.8781 (mm) REVERT: N 105 GLU cc_start: 0.7218 (pt0) cc_final: 0.6689 (pm20) REVERT: F 542 ARG cc_start: 0.8767 (tpp80) cc_final: 0.8336 (tpp80) REVERT: F 629 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7311 (mtm) REVERT: I 66 ASN cc_start: 0.8373 (t0) cc_final: 0.8098 (m-40) REVERT: K 3 GLN cc_start: 0.8353 (mp10) cc_final: 0.8037 (mp10) REVERT: K 23 LYS cc_start: 0.8588 (tmmt) cc_final: 0.8145 (mmtm) REVERT: E 33 LYS cc_start: 0.8503 (mmtt) cc_final: 0.8261 (mmmm) REVERT: E 107 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7441 (t0) REVERT: E 114 GLN cc_start: 0.8872 (tm-30) cc_final: 0.7983 (mt0) REVERT: E 202 THR cc_start: 0.9362 (m) cc_final: 0.9010 (p) REVERT: E 209 SER cc_start: 0.7306 (t) cc_final: 0.7022 (p) REVERT: E 231 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.9014 (mptt) REVERT: E 258 GLN cc_start: 0.8093 (mt0) cc_final: 0.7725 (mt0) REVERT: E 475 MET cc_start: 0.6321 (mmm) cc_final: 0.5160 (mmm) REVERT: E 479 TRP cc_start: 0.6243 (m-90) cc_final: 0.5800 (m-90) REVERT: O 27 GLU cc_start: 0.9134 (tp30) cc_final: 0.8771 (tp30) REVERT: O 36 TYR cc_start: 0.6749 (m-80) cc_final: 0.6326 (m-80) REVERT: O 38 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7757 (tm-30) REVERT: O 46 LEU cc_start: 0.8479 (tp) cc_final: 0.8122 (tp) REVERT: O 70 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8364 (mm-30) REVERT: G 540 GLN cc_start: 0.8908 (mm110) cc_final: 0.8390 (tt0) REVERT: G 626 MET cc_start: 0.7770 (ttm) cc_final: 0.7446 (mtp) REVERT: G 629 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7216 (mtt) REVERT: G 647 GLU cc_start: 0.8153 (tt0) cc_final: 0.7470 (tt0) REVERT: G 657 GLU cc_start: 0.9131 (tp30) cc_final: 0.8819 (tp30) REVERT: J 66 ASN cc_start: 0.8447 (t0) cc_final: 0.8173 (m-40) REVERT: J 80 ASP cc_start: 0.8231 (t70) cc_final: 0.7936 (t0) REVERT: J 94 GLN cc_start: 0.7126 (tp40) cc_final: 0.6724 (tp40) REVERT: M 12 LYS cc_start: 0.8837 (mttp) cc_final: 0.8491 (mtpp) REVERT: M 13 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8525 (mmmt) REVERT: M 23 LYS cc_start: 0.8701 (tmmt) cc_final: 0.8058 (mmtm) REVERT: M 30 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8022 (tt) REVERT: M 81 GLU cc_start: 0.8653 (tt0) cc_final: 0.8394 (tm-30) REVERT: M 100 PHE cc_start: 0.7433 (m-80) cc_final: 0.7128 (m-80) outliers start: 88 outliers final: 72 residues processed: 429 average time/residue: 0.1412 time to fit residues: 94.0924 Evaluate side-chains 448 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 366 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain G residue 543 LEU Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 629 MET Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 91 PHE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 26 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 168 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 607 ASN B 620 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN D 478 ASN F 620 ASN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 607 ASN G 620 ASN ** M 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.129996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.100333 restraints weight = 56429.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.103992 restraints weight = 31164.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.106547 restraints weight = 20851.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.108360 restraints weight = 15760.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.109609 restraints weight = 12902.228| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21399 Z= 0.199 Angle : 0.740 12.968 29187 Z= 0.375 Chirality : 0.048 0.250 3447 Planarity : 0.005 0.055 3606 Dihedral : 6.267 57.485 4191 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.71 % Favored : 93.24 % Rotamer: Outliers : 4.23 % Allowed : 19.37 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.16), residues: 2487 helix: 1.70 (0.25), residues: 417 sheet: 0.62 (0.21), residues: 615 loop : -1.64 (0.15), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG O 103 TYR 0.030 0.002 TYR M 100E PHE 0.033 0.002 PHE O 83 TRP 0.023 0.002 TRP N 94 HIS 0.007 0.001 HIS H 62 Details of bonding type rmsd covalent geometry : bond 0.00470 (21288) covalent geometry : angle 0.72485 (28893) SS BOND : bond 0.00379 ( 39) SS BOND : angle 1.95631 ( 78) hydrogen bonds : bond 0.04168 ( 825) hydrogen bonds : angle 5.33972 ( 2079) link_ALPHA1-2 : bond 0.00328 ( 3) link_ALPHA1-2 : angle 2.04950 ( 9) link_ALPHA1-3 : bond 0.00846 ( 3) link_ALPHA1-3 : angle 1.33582 ( 9) link_BETA1-4 : bond 0.00252 ( 30) link_BETA1-4 : angle 1.54055 ( 90) link_NAG-ASN : bond 0.00337 ( 36) link_NAG-ASN : angle 1.54358 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4011.43 seconds wall clock time: 70 minutes 0.36 seconds (4200.36 seconds total)