Starting phenix.real_space_refine on Sun Sep 13 04:51:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6opq_20153/09_2026/6opq_20153.cif Found real_map, /net/cci-nas-00/data/ceres_data/6opq_20153/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6opq_20153/09_2026/6opq_20153.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6opq_20153/09_2026/6opq_20153.cif" model { file = "/net/cci-nas-00/data/ceres_data/6opq_20153/09_2026/6opq_20153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6opq_20153/09_2026/6opq_20153.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6opq_20153/09_2026/6opq_20153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6opq_20153/09_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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 4.83, per 1000 atoms: 0.23 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: 2.08 Conformation dependent library (CDL) restraints added in 828.9 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: 0.85 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: 3.75 Time building geometry restraints manager: 2.67 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 - 15.91: 11610 15.91 - 31.81: 438 31.81 - 47.72: 84 47.72 - 63.63: 72 63.63 - 79.53: 24 Dihedral angle restraints: 12228 sinusoidal: 4944 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 12225 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: 0.06 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.890 Find NCS groups from input model: 0.540 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 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 : 10.526 79.534 7413 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/Z covalent geometry : bond 0.02155 / 1.15 (21288) covalent geometry : angle 1.76200 / 1.15 (28893) SS BOND : bond 0.03635 / 2.42 ( 39) SS BOND : angle 2.56001 / 1.80 ( 78) hydrogen bonds : bond 0.16035 / 10.74 ( 825) hydrogen bonds : angle 7.50860 / 5.35 ( 2079) link_ALPHA1-2 : bond 0.03820 / 1.70 ( 3) link_ALPHA1-2 : angle 2.95754 / 1.87 ( 9) link_ALPHA1-3 : bond 0.03243 / 1.45 ( 3) link_ALPHA1-3 : angle 2.09850 / 1.32 ( 9) link_BETA1-4 : bond 0.02733 / 1.64 ( 30) link_BETA1-4 : angle 3.99407 / 2.77 ( 90) link_NAG-ASN : bond 0.03113 / 1.83 ( 36) link_NAG-ASN : angle 2.93961 / 2.00 ( 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 : 0.851 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: 0.1649 time to fit residues: 202.1059 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 : 0.832 ------------------------------------------------------------------------------- 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... ** 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 F 611 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 37 GLN ** 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.137477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.108190 restraints weight = 53947.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.112455 restraints weight = 28636.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.115400 restraints weight = 18527.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.117498 restraints weight = 13604.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.118913 restraints weight = 10891.393| |-----------------------------------------------------------------------------| r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 21399 Z= 0.206 Angle : 0.803 8.977 29187 Z= 0.420 Chirality : 0.049 0.280 3447 Planarity : 0.005 0.046 3606 Dihedral : 5.239 21.278 2697 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.57 % Favored : 97.31 % Rotamer: Outliers : 3.59 % Allowed : 12.10 % Favored : 84.31 % 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: 0.21 (0.16), residues: 2487 helix: 1.99 (0.25), residues: 411 sheet: 0.65 (0.20), residues: 660 loop : -0.69 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 103 TYR 0.028 0.002 TYR M 100E PHE 0.026 0.003 PHE K 100J TRP 0.021 0.002 TRP A 395 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (21288) covalent geometry : angle 0.78224 / 0.42 (28893) SS BOND : bond 0.00641 / 0.44 ( 39) SS BOND : angle 1.29881 / 0.89 ( 78) hydrogen bonds : bond 0.05897 / 3.93 ( 825) hydrogen bonds : angle 6.08242 / 4.35 ( 2079) link_ALPHA1-2 : bond 0.00088 / 0.04 ( 3) link_ALPHA1-2 : angle 1.80988 / 1.08 ( 9) link_ALPHA1-3 : bond 0.00538 / 0.22 ( 3) link_ALPHA1-3 : angle 1.25664 / 0.76 ( 9) link_BETA1-4 : bond 0.00318 / 0.17 ( 30) link_BETA1-4 : angle 2.20051 / 1.45 ( 90) link_NAG-ASN : bond 0.00400 / 0.24 ( 36) link_NAG-ASN : angle 2.20339 / 1.56 ( 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 586 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 507 time to evaluate : 0.695 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: A 100 MET cc_start: 0.7576 (mtm) cc_final: 0.7346 (mtm) REVERT: A 258 GLN cc_start: 0.7923 (mt0) cc_final: 0.7128 (mt0) REVERT: A 338 TRP cc_start: 0.8245 (t-100) cc_final: 0.7838 (t-100) REVERT: A 358 ILE cc_start: 0.8534 (mm) cc_final: 0.8197 (tp) REVERT: A 434 MET cc_start: 0.7816 (ttp) cc_final: 0.7470 (ttm) REVERT: A 475 MET cc_start: 0.6654 (mmm) cc_final: 0.5799 (mmm) REVERT: A 479 TRP cc_start: 0.6086 (m-90) cc_final: 0.5848 (m-90) REVERT: L 38 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7843 (tm-30) REVERT: L 49 TYR cc_start: 0.8462 (t80) cc_final: 0.7799 (t80) REVERT: L 79 GLN cc_start: 0.8539 (mm110) cc_final: 0.8300 (mm-40) REVERT: L 85 VAL cc_start: 0.7817 (t) cc_final: 0.7435 (t) REVERT: B 584 GLU cc_start: 0.7968 (pt0) cc_final: 0.7714 (tm-30) REVERT: B 629 MET cc_start: 0.7846 (mtt) cc_final: 0.7130 (mtt) REVERT: B 632 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8201 (tm-30) REVERT: B 647 GLU cc_start: 0.8569 (tt0) cc_final: 0.8009 (tt0) REVERT: C 51 LEU cc_start: 0.8519 (mt) cc_final: 0.8283 (mt) REVERT: C 67 PHE cc_start: 0.8410 (m-80) cc_final: 0.7441 (m-10) REVERT: C 73 ASN cc_start: 0.8353 (t0) cc_final: 0.7991 (p0) REVERT: C 82 TYR cc_start: 0.8278 (m-10) cc_final: 0.8006 (m-10) REVERT: H 23 LYS cc_start: 0.8019 (tmmt) cc_final: 0.7391 (tmmt) REVERT: H 25 SER cc_start: 0.8371 (t) cc_final: 0.7749 (m) REVERT: H 43 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7321 (mp10) REVERT: H 72 ASP cc_start: 0.7161 (t0) cc_final: 0.6726 (t0) REVERT: H 79 TYR cc_start: 0.7957 (m-80) cc_final: 0.7744 (m-80) REVERT: H 100 PHE cc_start: 0.6995 (m-80) cc_final: 0.6666 (m-80) REVERT: D 107 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.7052 (t70) REVERT: D 258 GLN cc_start: 0.8105 (mt0) cc_final: 0.7409 (mt0) REVERT: D 358 ILE cc_start: 0.8405 (mm) cc_final: 0.7997 (mm) REVERT: D 439 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7929 (tp) REVERT: D 475 MET cc_start: 0.6598 (mmm) cc_final: 0.5311 (mmm) REVERT: D 479 TRP cc_start: 0.6065 (m-90) cc_final: 0.5691 (m-90) REVERT: N 38 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7890 (tm-30) REVERT: N 42 GLN cc_start: 0.6479 (mm-40) cc_final: 0.6217 (mp10) REVERT: N 49 TYR cc_start: 0.8235 (t80) cc_final: 0.8024 (t80) REVERT: N 70 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8224 (mm-30) REVERT: N 79 GLN cc_start: 0.8689 (mm110) cc_final: 0.8456 (mm-40) REVERT: N 85 VAL cc_start: 0.8009 (t) cc_final: 0.7637 (t) REVERT: F 629 MET cc_start: 0.7919 (mtt) cc_final: 0.7653 (mtt) REVERT: I 33 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7552 (pp30) REVERT: I 34 ILE cc_start: 0.7944 (mm) cc_final: 0.7711 (mt) REVERT: I 73 ASN cc_start: 0.7861 (t0) cc_final: 0.7648 (p0) REVERT: I 80 ASP cc_start: 0.7695 (t0) cc_final: 0.7151 (t0) REVERT: I 81 THR cc_start: 0.8744 (m) cc_final: 0.8465 (t) REVERT: I 82 TYR cc_start: 0.8241 (m-10) cc_final: 0.7773 (m-10) REVERT: K 3 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8166 (mp10) REVERT: K 23 LYS cc_start: 0.8315 (tmmt) cc_final: 0.7795 (tmmt) REVERT: K 25 SER cc_start: 0.8266 (t) cc_final: 0.7652 (m) REVERT: K 43 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7498 (mp10) REVERT: E 209 SER cc_start: 0.7076 (t) cc_final: 0.6555 (p) REVERT: E 258 GLN cc_start: 0.8274 (mt0) cc_final: 0.8006 (mt0) REVERT: E 358 ILE cc_start: 0.8441 (mm) cc_final: 0.8131 (tp) REVERT: E 479 TRP cc_start: 0.6328 (m-90) cc_final: 0.5834 (m-90) REVERT: E 486 TYR cc_start: 0.8140 (m-80) cc_final: 0.7868 (m-80) REVERT: O 38 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7782 (tm-30) REVERT: O 42 GLN cc_start: 0.6563 (mm110) cc_final: 0.6334 (mp10) REVERT: O 58 VAL cc_start: 0.7604 (t) cc_final: 0.7250 (t) REVERT: O 70 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8281 (mm-30) REVERT: O 85 VAL cc_start: 0.7769 (t) cc_final: 0.7375 (t) REVERT: O 98 PHE cc_start: 0.6949 (p90) cc_final: 0.6691 (p90) REVERT: G 540 GLN cc_start: 0.9034 (mm110) cc_final: 0.8261 (tt0) REVERT: G 626 MET cc_start: 0.7414 (mtt) cc_final: 0.7065 (ttm) REVERT: G 647 GLU cc_start: 0.8106 (tt0) cc_final: 0.7657 (tt0) REVERT: J 33 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7568 (pp30) REVERT: J 66 ASN cc_start: 0.8466 (t0) cc_final: 0.8112 (m-40) REVERT: J 73 ASN cc_start: 0.7996 (t0) cc_final: 0.7717 (p0) REVERT: M 3 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8295 (mp10) REVERT: M 23 LYS cc_start: 0.8156 (tmmt) cc_final: 0.7628 (tmmt) REVERT: M 25 SER cc_start: 0.8248 (t) cc_final: 0.7725 (m) REVERT: M 53 ILE cc_start: 0.8475 (tp) cc_final: 0.8236 (tp) outliers start: 79 outliers final: 41 residues processed: 544 average time/residue: 0.1500 time to fit residues: 126.3094 Evaluate side-chains 489 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 444 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 402 ASP 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 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR 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 43 GLN 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 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 43 GLN 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 373 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain O residue 104 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 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: 7.9990 chunk 234 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 34 optimal weight: 0.0570 chunk 100 optimal weight: 9.9990 chunk 178 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN A 325 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN C 20 GLN D 67 ASN D 478 ASN F 607 ASN I 20 GLN ** I 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 ASN ** I 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 607 ASN G 656 ASN J 20 GLN ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.131706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.103409 restraints weight = 52090.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.107376 restraints weight = 28217.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.110107 restraints weight = 18629.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.112080 restraints weight = 13916.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.113262 restraints weight = 11234.368| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 21399 Z= 0.192 Angle : 0.717 7.939 29187 Z= 0.369 Chirality : 0.047 0.246 3447 Planarity : 0.005 0.040 3606 Dihedral : 5.157 22.750 2697 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.02 % Favored : 96.86 % Rotamer: Outliers : 4.96 % Allowed : 13.14 % Favored : 81.90 % 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: 0.11 (0.16), residues: 2487 helix: 2.02 (0.25), residues: 408 sheet: 0.74 (0.20), residues: 714 loop : -0.94 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 24 TYR 0.032 0.002 TYR K 100E PHE 0.028 0.002 PHE K 100J TRP 0.017 0.002 TRP G 610 HIS 0.014 0.001 HIS I 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (21288) covalent geometry : angle 0.70286 / 0.37 (28893) SS BOND : bond 0.00387 / 0.24 ( 39) SS BOND : angle 0.99559 / 0.67 ( 78) hydrogen bonds : bond 0.04822 / 3.20 ( 825) hydrogen bonds : angle 5.72278 / 4.10 ( 2079) link_ALPHA1-2 : bond 0.00154 / 0.06 ( 3) link_ALPHA1-2 : angle 1.92282 / 1.16 ( 9) link_ALPHA1-3 : bond 0.00513 / 0.24 ( 3) link_ALPHA1-3 : angle 1.12487 / 0.67 ( 9) link_BETA1-4 : bond 0.00297 / 0.15 ( 30) link_BETA1-4 : angle 1.61968 / 1.07 ( 90) link_NAG-ASN : bond 0.00422 / 0.25 ( 36) link_NAG-ASN : angle 1.81451 / 1.26 ( 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 564 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 455 time to evaluate : 0.859 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 209 SER cc_start: 0.7158 (t) cc_final: 0.6814 (p) REVERT: A 258 GLN cc_start: 0.8122 (mt0) cc_final: 0.7447 (mt0) REVERT: A 358 ILE cc_start: 0.8504 (mm) cc_final: 0.8215 (mm) REVERT: A 475 MET cc_start: 0.6511 (mmm) cc_final: 0.5965 (mmm) REVERT: A 479 TRP cc_start: 0.6306 (m-90) cc_final: 0.6064 (m-90) REVERT: L 30 SER cc_start: 0.8669 (t) cc_final: 0.8323 (t) REVERT: L 38 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7776 (tm-30) REVERT: L 42 GLN cc_start: 0.6589 (mm110) cc_final: 0.6348 (mp10) REVERT: L 49 TYR cc_start: 0.8257 (t80) cc_final: 0.7799 (t80) REVERT: L 85 VAL cc_start: 0.7675 (t) cc_final: 0.7261 (t) REVERT: B 540 GLN cc_start: 0.9000 (mm110) cc_final: 0.8118 (tt0) REVERT: B 584 GLU cc_start: 0.8170 (pt0) cc_final: 0.7540 (tm-30) REVERT: B 592 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7596 (mm) REVERT: B 632 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8134 (tm-30) REVERT: C 33 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7004 (tm-30) REVERT: C 51 LEU cc_start: 0.8522 (mt) cc_final: 0.8306 (mt) REVERT: C 56 ASP cc_start: 0.8375 (t70) cc_final: 0.8148 (t0) REVERT: C 67 PHE cc_start: 0.8317 (m-80) cc_final: 0.8086 (m-80) REVERT: C 94 GLN cc_start: 0.7389 (tp40) cc_final: 0.7186 (tp40) REVERT: H 72 ASP cc_start: 0.7050 (t0) cc_final: 0.6593 (t0) REVERT: H 83 ARG cc_start: 0.8245 (ptp-170) cc_final: 0.7990 (ptt-90) REVERT: H 100 PHE cc_start: 0.7072 (m-80) cc_final: 0.6476 (m-80) REVERT: D 258 GLN cc_start: 0.8310 (mt0) cc_final: 0.7491 (mt0) REVERT: D 358 ILE cc_start: 0.8288 (mm) cc_final: 0.7975 (mm) REVERT: D 439 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7993 (tp) REVERT: N 38 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7864 (tm-30) REVERT: N 42 GLN cc_start: 0.6643 (mm-40) cc_final: 0.6340 (mp10) REVERT: N 85 VAL cc_start: 0.7933 (t) cc_final: 0.7585 (t) REVERT: F 530 MET cc_start: 0.8077 (mtm) cc_final: 0.7708 (mtt) REVERT: F 629 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7295 (mtm) REVERT: I 81 THR cc_start: 0.8939 (m) cc_final: 0.8711 (t) REVERT: K 3 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8258 (mp10) REVERT: K 5 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8261 (mp) REVERT: K 23 LYS cc_start: 0.8377 (tmmt) cc_final: 0.7865 (tmmt) REVERT: K 25 SER cc_start: 0.8205 (t) cc_final: 0.7414 (p) REVERT: K 81 GLU cc_start: 0.8676 (tt0) cc_final: 0.8073 (tm-30) REVERT: E 33 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8201 (mmmm) REVERT: E 209 SER cc_start: 0.7180 (t) cc_final: 0.6928 (p) REVERT: E 258 GLN cc_start: 0.8406 (mt0) cc_final: 0.8078 (mt0) REVERT: E 358 ILE cc_start: 0.8406 (mm) cc_final: 0.8164 (mm) REVERT: E 475 MET cc_start: 0.6632 (mmm) cc_final: 0.4593 (mmm) REVERT: E 479 TRP cc_start: 0.6314 (m-90) cc_final: 0.6010 (m-90) REVERT: O 38 GLN cc_start: 0.8259 (tm-30) cc_final: 0.8014 (tm-30) REVERT: O 42 GLN cc_start: 0.6574 (mm110) cc_final: 0.6352 (mp-120) REVERT: O 49 TYR cc_start: 0.8293 (t80) cc_final: 0.7943 (t80) REVERT: O 58 VAL cc_start: 0.7634 (t) cc_final: 0.5238 (t) REVERT: O 70 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8069 (mm-30) REVERT: G 540 GLN cc_start: 0.9040 (mm110) cc_final: 0.8351 (tt0) REVERT: G 626 MET cc_start: 0.7493 (mtt) cc_final: 0.7247 (ttm) REVERT: G 657 GLU cc_start: 0.9078 (tt0) cc_final: 0.8873 (tm-30) REVERT: J 33 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7663 (pp30) REVERT: J 66 ASN cc_start: 0.8436 (t0) cc_final: 0.8126 (m-40) REVERT: M 3 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8280 (mp10) REVERT: M 5 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8104 (mp) REVERT: M 23 LYS cc_start: 0.8291 (tmmt) cc_final: 0.7823 (tmmt) REVERT: M 25 SER cc_start: 0.8226 (t) cc_final: 0.7716 (m) REVERT: M 85 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8062 (t0) REVERT: M 100 PHE cc_start: 0.7201 (m-80) cc_final: 0.6513 (m-80) outliers start: 109 outliers final: 65 residues processed: 521 average time/residue: 0.1491 time to fit residues: 120.3910 Evaluate side-chains 463 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 392 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 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 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 592 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain H residue 19 LYS 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 111 LEU 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 D residue 439 ILE 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 F residue 629 MET Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 66 ASN 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 107 ASP Chi-restraints excluded: chain E residue 108 ILE 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 368 ASP Chi-restraints excluded: chain E residue 373 THR 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 5 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 30 ILE 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: 5.9990 chunk 234 optimal weight: 1.9990 chunk 206 optimal weight: 40.0000 chunk 59 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 233 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 176 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 607 ASN B 611 ASN B 620 ASN D 67 ASN F 590 GLN F 611 ASN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 ASN K 58 HIS K 64 GLN G 590 GLN G 607 ASN G 620 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.130737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.103116 restraints weight = 52903.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.106950 restraints weight = 28383.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.109636 restraints weight = 18618.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.111472 restraints weight = 13827.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.112807 restraints weight = 11195.785| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 21399 Z= 0.194 Angle : 0.709 8.993 29187 Z= 0.362 Chirality : 0.047 0.236 3447 Planarity : 0.005 0.043 3606 Dihedral : 5.133 28.455 2697 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.90 % Favored : 95.98 % Rotamer: Outliers : 4.46 % Allowed : 14.32 % Favored : 81.22 % 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: -0.16 (0.16), residues: 2487 helix: 1.92 (0.25), residues: 408 sheet: 0.44 (0.20), residues: 705 loop : -1.07 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 18 TYR 0.030 0.002 TYR M 100E PHE 0.020 0.002 PHE E 376 TRP 0.023 0.002 TRP D 395 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (21288) covalent geometry : angle 0.69591 / 0.36 (28893) SS BOND : bond 0.00368 / 0.22 ( 39) SS BOND : angle 1.36774 / 0.98 ( 78) hydrogen bonds : bond 0.04606 / 3.06 ( 825) hydrogen bonds : angle 5.58233 / 4.00 ( 2079) link_ALPHA1-2 : bond 0.00124 / 0.04 ( 3) link_ALPHA1-2 : angle 2.07812 / 1.26 ( 9) link_ALPHA1-3 : bond 0.00817 / 0.31 ( 3) link_ALPHA1-3 : angle 1.32880 / 0.80 ( 9) link_BETA1-4 : bond 0.00270 / 0.12 ( 30) link_BETA1-4 : angle 1.43254 / 0.96 ( 90) link_NAG-ASN : bond 0.00385 / 0.23 ( 36) link_NAG-ASN : angle 1.70102 / 1.18 ( 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 526 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 428 time to evaluate : 0.824 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: A 33 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8093 (mmmm) REVERT: A 209 SER cc_start: 0.7347 (t) cc_final: 0.7044 (p) REVERT: A 358 ILE cc_start: 0.8438 (mm) cc_final: 0.8193 (mm) REVERT: L 38 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7951 (tm-30) REVERT: B 530 MET cc_start: 0.8591 (mmm) cc_final: 0.8115 (mmt) REVERT: B 540 GLN cc_start: 0.8920 (mm110) cc_final: 0.8183 (tt0) REVERT: B 584 GLU cc_start: 0.8103 (pt0) cc_final: 0.7394 (tm-30) REVERT: B 592 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7847 (mm) REVERT: B 629 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7255 (mtt) REVERT: B 632 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8046 (tm-30) REVERT: C 67 PHE cc_start: 0.8728 (m-80) cc_final: 0.8200 (m-80) REVERT: C 80 ASP cc_start: 0.8140 (t70) cc_final: 0.7885 (t70) REVERT: H 3 GLN cc_start: 0.8500 (mp10) cc_final: 0.8054 (mp10) REVERT: H 25 SER cc_start: 0.8290 (t) cc_final: 0.7870 (p) REVERT: H 30 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8082 (tt) REVERT: H 72 ASP cc_start: 0.7153 (t0) cc_final: 0.6684 (t0) REVERT: H 83 ARG cc_start: 0.8267 (ptp-170) cc_final: 0.7943 (ptt-90) REVERT: D 33 LYS cc_start: 0.8305 (mmtt) cc_final: 0.8059 (mmmm) REVERT: D 107 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7528 (t70) REVERT: D 358 ILE cc_start: 0.8267 (mm) cc_final: 0.8056 (mm) REVERT: D 475 MET cc_start: 0.7038 (mmm) cc_final: 0.6764 (mmm) REVERT: N 38 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7952 (tm-30) REVERT: N 42 GLN cc_start: 0.6565 (mm-40) cc_final: 0.6247 (mp10) REVERT: N 48 ILE cc_start: 0.9243 (mm) cc_final: 0.9009 (mm) REVERT: F 530 MET cc_start: 0.8107 (mtm) cc_final: 0.7760 (mtt) REVERT: F 611 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8411 (t0) REVERT: F 629 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7456 (mtm) REVERT: I 73 ASN cc_start: 0.7789 (t0) cc_final: 0.7492 (p0) REVERT: I 76 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9071 (pt) REVERT: I 81 THR cc_start: 0.8986 (m) cc_final: 0.8781 (t) REVERT: K 23 LYS cc_start: 0.8459 (tmmt) cc_final: 0.8112 (tmmt) REVERT: K 25 SER cc_start: 0.8165 (t) cc_final: 0.7838 (m) REVERT: E 33 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8199 (mmmm) REVERT: E 209 SER cc_start: 0.7355 (t) cc_final: 0.7027 (p) REVERT: E 217 TYR cc_start: 0.7015 (OUTLIER) cc_final: 0.5558 (m-80) REVERT: E 475 MET cc_start: 0.6389 (mmm) cc_final: 0.4725 (mmm) REVERT: E 479 TRP cc_start: 0.6292 (m-90) cc_final: 0.5893 (m-90) REVERT: O 33 LEU cc_start: 0.7723 (mm) cc_final: 0.7188 (mt) REVERT: O 38 GLN cc_start: 0.8261 (tm-30) cc_final: 0.8048 (tm-30) REVERT: O 49 TYR cc_start: 0.8041 (t80) cc_final: 0.7839 (t80) REVERT: O 58 VAL cc_start: 0.7245 (t) cc_final: 0.6939 (t) REVERT: O 70 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8280 (mm-30) REVERT: G 530 MET cc_start: 0.8152 (mmm) cc_final: 0.7776 (mmt) REVERT: G 540 GLN cc_start: 0.8958 (mm110) cc_final: 0.8377 (tt0) REVERT: G 629 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7463 (mtt) REVERT: J 33 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7574 (pp30) REVERT: J 73 ASN cc_start: 0.8140 (t0) cc_final: 0.7867 (p0) REVERT: M 3 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8323 (mp10) REVERT: M 5 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8129 (mp) REVERT: M 12 LYS cc_start: 0.9031 (mttp) cc_final: 0.8648 (mtpp) REVERT: M 23 LYS cc_start: 0.8359 (tmmt) cc_final: 0.7838 (tmmt) REVERT: M 25 SER cc_start: 0.8205 (t) cc_final: 0.7793 (m) REVERT: M 100 PHE cc_start: 0.7368 (m-80) cc_final: 0.6674 (m-80) outliers start: 98 outliers final: 66 residues processed: 487 average time/residue: 0.1513 time to fit residues: 114.6594 Evaluate side-chains 459 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 383 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 251 ILE 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 L residue 13 VAL 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 592 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 647 GLU 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 30 ILE Chi-restraints excluded: chain H residue 82 ASN 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 108 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 209 SER 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 N residue 13 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 611 ASN 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 30 ILE Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 105 GLN 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 217 TYR 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 O residue 21 LEU Chi-restraints excluded: chain O residue 74 THR 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 5 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 30 ILE Chi-restraints excluded: chain M residue 82 ASN 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: 8.9990 chunk 100 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 187 optimal weight: 0.5980 chunk 227 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 590 GLN B 607 ASN B 611 ASN B 620 ASN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 607 ASN G 611 ASN G 620 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.125336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.097434 restraints weight = 53172.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.101037 restraints weight = 29022.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.103554 restraints weight = 19392.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.105276 restraints weight = 14662.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.106481 restraints weight = 12056.869| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 21399 Z= 0.247 Angle : 0.755 12.235 29187 Z= 0.384 Chirality : 0.048 0.245 3447 Planarity : 0.005 0.051 3606 Dihedral : 5.247 28.667 2697 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.71 % Favored : 94.17 % Rotamer: Outliers : 4.87 % Allowed : 15.78 % Favored : 79.35 % 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: -0.65 (0.16), residues: 2487 helix: 1.58 (0.25), residues: 420 sheet: 0.07 (0.20), residues: 696 loop : -1.39 (0.15), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 66 TYR 0.032 0.002 TYR K 100E PHE 0.022 0.003 PHE E 376 TRP 0.019 0.002 TRP J 28 HIS 0.010 0.002 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.25 (21288) covalent geometry : angle 0.74005 / 0.38 (28893) SS BOND : bond 0.00461 / 0.27 ( 39) SS BOND : angle 1.71886 / 1.26 ( 78) hydrogen bonds : bond 0.04854 / 3.24 ( 825) hydrogen bonds : angle 5.66673 / 4.06 ( 2079) link_ALPHA1-2 : bond 0.00428 / 0.19 ( 3) link_ALPHA1-2 : angle 2.16276 / 1.33 ( 9) link_ALPHA1-3 : bond 0.00538 / 0.25 ( 3) link_ALPHA1-3 : angle 1.43232 / 0.89 ( 9) link_BETA1-4 : bond 0.00298 / 0.13 ( 30) link_BETA1-4 : angle 1.46390 / 1.00 ( 90) link_NAG-ASN : bond 0.00476 / 0.29 ( 36) link_NAG-ASN : angle 1.78403 / 1.23 ( 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 492 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 385 time to evaluate : 0.870 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: A 33 LYS cc_start: 0.8364 (mmtt) cc_final: 0.8137 (mmmm) REVERT: A 107 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7663 (t70) REVERT: A 209 SER cc_start: 0.7534 (t) cc_final: 0.7268 (p) REVERT: A 258 GLN cc_start: 0.8111 (mt0) cc_final: 0.7645 (mt0) REVERT: A 271 VAL cc_start: 0.8275 (t) cc_final: 0.8055 (m) REVERT: A 475 MET cc_start: 0.7036 (mmt) cc_final: 0.6220 (mmm) REVERT: A 478 ASN cc_start: 0.8372 (m-40) cc_final: 0.8110 (m110) REVERT: L 38 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7905 (tm-30) REVERT: B 540 GLN cc_start: 0.8938 (mm110) cc_final: 0.8208 (tt0) REVERT: B 584 GLU cc_start: 0.8130 (pt0) cc_final: 0.7272 (tm-30) REVERT: B 629 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.6727 (mtm) REVERT: B 632 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8020 (tm-30) REVERT: B 633 LYS cc_start: 0.8960 (mmtm) cc_final: 0.8752 (mmtm) REVERT: C 66 ASN cc_start: 0.8502 (t0) cc_final: 0.8033 (m-40) REVERT: H 3 GLN cc_start: 0.8511 (mp10) cc_final: 0.8249 (mp10) REVERT: H 30 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8115 (tt) REVERT: H 72 ASP cc_start: 0.7108 (t0) cc_final: 0.6627 (t0) REVERT: H 83 ARG cc_start: 0.8265 (ptp-170) cc_final: 0.7926 (ptt-90) REVERT: H 100 PHE cc_start: 0.7405 (m-80) cc_final: 0.6890 (m-80) REVERT: D 107 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7552 (t70) REVERT: D 258 GLN cc_start: 0.8334 (mt0) cc_final: 0.7881 (mt0) REVERT: D 358 ILE cc_start: 0.8182 (mm) cc_final: 0.7947 (mm) REVERT: D 475 MET cc_start: 0.7212 (mmm) cc_final: 0.5976 (mmm) REVERT: D 478 ASN cc_start: 0.8756 (m-40) cc_final: 0.8371 (m110) REVERT: N 38 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7845 (tm-30) REVERT: N 42 GLN cc_start: 0.6742 (mm-40) cc_final: 0.6437 (mp10) REVERT: N 48 ILE cc_start: 0.9216 (mm) cc_final: 0.8924 (mm) REVERT: F 543 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9036 (mm) REVERT: F 629 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7544 (mtm) REVERT: F 655 LYS cc_start: 0.9518 (tttt) cc_final: 0.9156 (ttmt) REVERT: I 66 ASN cc_start: 0.8423 (t0) cc_final: 0.8206 (m-40) REVERT: I 76 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9061 (pt) REVERT: I 85 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7616 (tm-30) REVERT: K 23 LYS cc_start: 0.8607 (tmmt) cc_final: 0.8301 (tmmt) REVERT: E 33 LYS cc_start: 0.8552 (mmtt) cc_final: 0.8262 (mmmm) REVERT: E 209 SER cc_start: 0.7497 (t) cc_final: 0.7203 (p) REVERT: E 217 TYR cc_start: 0.6959 (OUTLIER) cc_final: 0.5450 (m-80) REVERT: E 258 GLN cc_start: 0.8058 (mt0) cc_final: 0.7284 (mt0) REVERT: E 271 VAL cc_start: 0.8074 (t) cc_final: 0.7832 (m) REVERT: E 475 MET cc_start: 0.6544 (mmm) cc_final: 0.4795 (mmm) REVERT: E 479 TRP cc_start: 0.6418 (m-10) cc_final: 0.6060 (m-90) REVERT: O 38 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7809 (tm-30) REVERT: O 58 VAL cc_start: 0.7306 (t) cc_final: 0.7012 (t) REVERT: G 540 GLN cc_start: 0.8957 (mm110) cc_final: 0.8388 (tt0) REVERT: J 56 ASP cc_start: 0.8264 (t70) cc_final: 0.8038 (t0) REVERT: M 3 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8324 (mp10) REVERT: M 5 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8241 (mp) REVERT: M 12 LYS cc_start: 0.9068 (mttp) cc_final: 0.8839 (mttt) REVERT: M 23 LYS cc_start: 0.8455 (tmmt) cc_final: 0.7930 (tmmt) REVERT: M 25 SER cc_start: 0.8220 (t) cc_final: 0.7886 (m) REVERT: M 81 GLU cc_start: 0.8756 (tt0) cc_final: 0.8133 (tm-30) REVERT: M 84 SER cc_start: 0.9387 (OUTLIER) cc_final: 0.9125 (p) outliers start: 107 outliers final: 69 residues processed: 457 average time/residue: 0.1532 time to fit residues: 109.0082 Evaluate side-chains 435 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 356 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 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 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 569 THR 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 30 ILE Chi-restraints excluded: chain H residue 82 ASN 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 100 MET 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 209 SER 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 423 ILE Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 569 THR 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 60 SER Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 217 TYR 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 488 VAL Chi-restraints excluded: chain O residue 74 THR 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 611 ASN Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain J residue 5 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 31 optimal weight: 0.0470 chunk 97 optimal weight: 6.9990 chunk 206 optimal weight: 30.0000 chunk 89 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 212 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 607 ASN ** D 308 HIS ** 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 67 ASN E 478 ASN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4441 r_free = 0.4441 target = 0.126763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.098952 restraints weight = 52857.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.102615 restraints weight = 28828.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.105180 restraints weight = 19138.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.106945 restraints weight = 14418.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.107918 restraints weight = 11802.779| |-----------------------------------------------------------------------------| r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21399 Z= 0.181 Angle : 0.706 12.440 29187 Z= 0.358 Chirality : 0.047 0.232 3447 Planarity : 0.005 0.053 3606 Dihedral : 5.086 25.815 2697 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.47 % Favored : 94.41 % Rotamer: Outliers : 4.59 % Allowed : 17.37 % Favored : 78.04 % 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: -0.69 (0.16), residues: 2487 helix: 1.70 (0.25), residues: 420 sheet: 0.02 (0.20), residues: 684 loop : -1.44 (0.15), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O 18 TYR 0.031 0.002 TYR M 100E PHE 0.021 0.002 PHE D 376 TRP 0.016 0.002 TRP J 28 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (21288) covalent geometry : angle 0.69206 / 0.35 (28893) SS BOND : bond 0.00361 / 0.21 ( 39) SS BOND : angle 1.70445 / 1.25 ( 78) hydrogen bonds : bond 0.04361 / 2.89 ( 825) hydrogen bonds : angle 5.47888 / 3.91 ( 2079) link_ALPHA1-2 : bond 0.00258 / 0.11 ( 3) link_ALPHA1-2 : angle 2.00170 / 1.21 ( 9) link_ALPHA1-3 : bond 0.00584 / 0.27 ( 3) link_ALPHA1-3 : angle 1.25752 / 0.76 ( 9) link_BETA1-4 : bond 0.00262 / 0.11 ( 30) link_BETA1-4 : angle 1.31180 / 0.90 ( 90) link_NAG-ASN : bond 0.00355 / 0.22 ( 36) link_NAG-ASN : angle 1.58593 / 1.10 ( 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 487 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 386 time to evaluate : 0.758 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: 0.8460 (mmtt) cc_final: 0.8137 (mmmm) REVERT: A 107 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7631 (t70) REVERT: A 209 SER cc_start: 0.7424 (t) cc_final: 0.7172 (p) REVERT: A 258 GLN cc_start: 0.8019 (mt0) cc_final: 0.7522 (mt0) REVERT: A 475 MET cc_start: 0.6823 (mmt) cc_final: 0.5908 (mmm) REVERT: B 540 GLN cc_start: 0.8913 (mm110) cc_final: 0.8228 (tt0) REVERT: B 584 GLU cc_start: 0.8203 (pt0) cc_final: 0.7345 (tm-30) REVERT: B 592 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7698 (mm) REVERT: B 629 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7187 (mtm) REVERT: B 632 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8108 (tm-30) REVERT: C 66 ASN cc_start: 0.8413 (t0) cc_final: 0.8033 (m-40) REVERT: C 85 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7682 (tm-30) REVERT: H 3 GLN cc_start: 0.8472 (mp10) cc_final: 0.8250 (mp10) REVERT: H 12 LYS cc_start: 0.8701 (mttt) cc_final: 0.8480 (mttt) REVERT: H 23 LYS cc_start: 0.8107 (tmmt) cc_final: 0.7673 (mmtm) REVERT: H 30 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8030 (tt) REVERT: H 72 ASP cc_start: 0.7153 (t0) cc_final: 0.6731 (t0) REVERT: H 83 ARG cc_start: 0.8275 (ptp-170) cc_final: 0.7874 (ptt-90) REVERT: D 107 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7576 (t70) REVERT: D 358 ILE cc_start: 0.8155 (mm) cc_final: 0.7893 (mm) REVERT: D 475 MET cc_start: 0.7068 (mmm) cc_final: 0.6638 (mmm) REVERT: D 478 ASN cc_start: 0.8721 (m-40) cc_final: 0.8461 (m110) REVERT: N 38 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7894 (tm-30) REVERT: N 42 GLN cc_start: 0.6774 (mm-40) cc_final: 0.6514 (mp-120) REVERT: N 48 ILE cc_start: 0.9167 (mm) cc_final: 0.8870 (mm) REVERT: N 49 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7590 (t80) REVERT: F 543 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9017 (mm) REVERT: F 629 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7373 (mtm) REVERT: I 66 ASN cc_start: 0.8321 (t0) cc_final: 0.8118 (m-40) REVERT: I 76 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9153 (pt) REVERT: I 85 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7567 (tm-30) REVERT: K 3 GLN cc_start: 0.8318 (mp10) cc_final: 0.8019 (mp10) REVERT: K 12 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8518 (mttt) REVERT: K 23 LYS cc_start: 0.8616 (tmmt) cc_final: 0.8220 (mmtm) REVERT: E 33 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8299 (mmmm) REVERT: E 111 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8276 (tp) REVERT: E 209 SER cc_start: 0.7392 (t) cc_final: 0.7126 (p) REVERT: E 217 TYR cc_start: 0.6998 (OUTLIER) cc_final: 0.5490 (m-80) REVERT: O 27 GLU cc_start: 0.9188 (tp30) cc_final: 0.8869 (tp30) REVERT: O 33 LEU cc_start: 0.7823 (mm) cc_final: 0.7593 (mm) REVERT: O 38 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7884 (tm-30) REVERT: O 49 TYR cc_start: 0.8421 (t80) cc_final: 0.8149 (t80) REVERT: O 58 VAL cc_start: 0.7379 (t) cc_final: 0.7064 (t) REVERT: O 70 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8252 (mm-30) REVERT: G 540 GLN cc_start: 0.8907 (mm110) cc_final: 0.8370 (tt0) REVERT: G 629 MET cc_start: 0.7734 (mtt) cc_final: 0.7470 (mtt) REVERT: G 657 GLU cc_start: 0.9084 (tp30) cc_final: 0.8782 (tp30) REVERT: J 85 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7610 (tm-30) REVERT: M 12 LYS cc_start: 0.9118 (mttp) cc_final: 0.8911 (mttt) REVERT: M 13 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8574 (mmmt) REVERT: M 23 LYS cc_start: 0.8434 (tmmt) cc_final: 0.8106 (tmmt) REVERT: M 25 SER cc_start: 0.8149 (t) cc_final: 0.7834 (m) REVERT: M 81 GLU cc_start: 0.8733 (tt0) cc_final: 0.8059 (tm-30) REVERT: M 84 SER cc_start: 0.9433 (OUTLIER) cc_final: 0.9205 (p) REVERT: M 100 PHE cc_start: 0.7458 (m-80) cc_final: 0.6884 (m-80) outliers start: 101 outliers final: 76 residues processed: 442 average time/residue: 0.1497 time to fit residues: 102.7832 Evaluate side-chains 450 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 362 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 ILE 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 L residue 49 TYR 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 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 30 ILE 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 200 VAL Chi-restraints excluded: chain D residue 209 SER 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 13 VAL Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain F residue 543 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 F residue 661 LEU Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 217 TYR 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 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 93 ASN 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 626 MET Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain M residue 11 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 Chi-restraints excluded: chain M residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 151 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 ASN B 607 ASN B 620 ASN B 658 GLN F 620 ASN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN G 607 ASN G 611 ASN G 620 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 = 0.4412 r_free = 0.4412 target = 0.124465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.096649 restraints weight = 53750.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.100236 restraints weight = 29566.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.102695 restraints weight = 19743.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.104398 restraints weight = 14946.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.105483 restraints weight = 12283.291| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 21399 Z= 0.226 Angle : 0.740 11.722 29187 Z= 0.377 Chirality : 0.048 0.256 3447 Planarity : 0.005 0.055 3606 Dihedral : 5.168 25.445 2697 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.76 % Favored : 93.12 % Rotamer: Outliers : 5.00 % Allowed : 18.10 % Favored : 76.90 % 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: -0.87 (0.16), residues: 2487 helix: 1.40 (0.24), residues: 438 sheet: -0.04 (0.20), residues: 666 loop : -1.57 (0.15), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 18 TYR 0.030 0.002 TYR K 100E PHE 0.043 0.003 PHE L 83 TRP 0.022 0.002 TRP J 28 HIS 0.007 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.23 (21288) covalent geometry : angle 0.72515 / 0.37 (28893) SS BOND : bond 0.00457 / 0.27 ( 39) SS BOND : angle 1.83975 / 1.35 ( 78) hydrogen bonds : bond 0.04632 / 3.07 ( 825) hydrogen bonds : angle 5.57701 / 3.96 ( 2079) link_ALPHA1-2 : bond 0.00460 / 0.20 ( 3) link_ALPHA1-2 : angle 2.05688 / 1.25 ( 9) link_ALPHA1-3 : bond 0.00940 / 0.36 ( 3) link_ALPHA1-3 : angle 1.58444 / 0.97 ( 9) link_BETA1-4 : bond 0.00311 / 0.13 ( 30) link_BETA1-4 : angle 1.38267 / 0.96 ( 90) link_NAG-ASN : bond 0.00438 / 0.27 ( 36) link_NAG-ASN : angle 1.70210 / 1.18 ( 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 471 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 361 time to evaluate : 0.789 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: A 33 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8183 (mmmm) REVERT: A 107 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7639 (t70) REVERT: A 111 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8306 (tp) REVERT: A 209 SER cc_start: 0.7499 (t) cc_final: 0.7275 (p) REVERT: A 231 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8774 (mmtm) REVERT: A 258 GLN cc_start: 0.8175 (mt0) cc_final: 0.7355 (mt0) REVERT: L 21 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8641 (mp) REVERT: B 540 GLN cc_start: 0.8908 (mm110) cc_final: 0.8250 (tt0) REVERT: B 629 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7511 (mtm) REVERT: B 632 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8029 (tm-30) REVERT: C 80 ASP cc_start: 0.8467 (t0) cc_final: 0.8147 (t0) REVERT: C 85 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7610 (tm-30) REVERT: H 3 GLN cc_start: 0.8489 (mp10) cc_final: 0.8263 (mp10) REVERT: H 23 LYS cc_start: 0.8190 (tmmt) cc_final: 0.7738 (mmtm) REVERT: H 30 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8090 (tt) REVERT: H 72 ASP cc_start: 0.7059 (t0) cc_final: 0.6624 (t0) REVERT: H 83 ARG cc_start: 0.8194 (ptp-170) cc_final: 0.7830 (ptt-90) REVERT: D 107 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7775 (t70) REVERT: D 202 THR cc_start: 0.9496 (m) cc_final: 0.9251 (p) REVERT: D 217 TYR cc_start: 0.6316 (OUTLIER) cc_final: 0.5167 (m-80) REVERT: D 258 GLN cc_start: 0.8332 (mt0) cc_final: 0.7533 (mt0) REVERT: D 358 ILE cc_start: 0.8168 (mm) cc_final: 0.7869 (mm) REVERT: D 453 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8791 (mt) REVERT: D 475 MET cc_start: 0.7235 (mmm) cc_final: 0.5903 (mmm) REVERT: D 478 ASN cc_start: 0.8603 (m-40) cc_final: 0.8336 (m110) REVERT: N 38 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7837 (tm-30) REVERT: N 42 GLN cc_start: 0.6835 (mm-40) cc_final: 0.6613 (mp10) REVERT: N 46 LEU cc_start: 0.8454 (tp) cc_final: 0.8182 (tp) REVERT: F 543 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9031 (mm) REVERT: F 629 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7543 (mtm) REVERT: I 60 SER cc_start: 0.9235 (OUTLIER) cc_final: 0.9019 (p) REVERT: I 76 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9117 (pt) REVERT: I 80 ASP cc_start: 0.8433 (t0) cc_final: 0.8117 (t0) REVERT: I 85 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7521 (tm-30) REVERT: I 94 GLN cc_start: 0.7302 (tp40) cc_final: 0.6859 (tp40) REVERT: K 3 GLN cc_start: 0.8433 (mp10) cc_final: 0.8123 (mp10) REVERT: K 12 LYS cc_start: 0.8792 (mtmm) cc_final: 0.8302 (mtmm) REVERT: K 23 LYS cc_start: 0.8637 (tmmt) cc_final: 0.8206 (mmtm) REVERT: E 33 LYS cc_start: 0.8541 (mmtt) cc_final: 0.8310 (mmmm) REVERT: E 111 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8268 (tp) REVERT: E 209 SER cc_start: 0.7476 (t) cc_final: 0.7212 (p) REVERT: E 217 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.5372 (m-80) REVERT: E 258 GLN cc_start: 0.8057 (mt0) cc_final: 0.7626 (mt0) REVERT: O 27 GLU cc_start: 0.9200 (tp30) cc_final: 0.8936 (tp30) REVERT: O 49 TYR cc_start: 0.8495 (t80) cc_final: 0.8191 (t80) REVERT: O 58 VAL cc_start: 0.7443 (t) cc_final: 0.7147 (t) REVERT: G 540 GLN cc_start: 0.8976 (mm110) cc_final: 0.8416 (tt0) REVERT: G 629 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7621 (mtt) REVERT: G 657 GLU cc_start: 0.9142 (tp30) cc_final: 0.8857 (tp30) REVERT: J 73 ASN cc_start: 0.8111 (t0) cc_final: 0.7845 (p0) REVERT: J 76 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9110 (pt) REVERT: J 80 ASP cc_start: 0.8070 (t70) cc_final: 0.7804 (t0) REVERT: J 85 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7478 (tm-30) REVERT: J 94 GLN cc_start: 0.7239 (tp40) cc_final: 0.6764 (tp40) REVERT: M 13 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8608 (mmmt) REVERT: M 23 LYS cc_start: 0.8421 (tmmt) cc_final: 0.8136 (tmmt) REVERT: M 81 GLU cc_start: 0.8736 (tt0) cc_final: 0.8495 (tm-30) REVERT: M 83 ARG cc_start: 0.8080 (ptp-170) cc_final: 0.7715 (ptt-90) REVERT: M 100 PHE cc_start: 0.7551 (m-80) cc_final: 0.6980 (m-10) outliers start: 110 outliers final: 77 residues processed: 424 average time/residue: 0.1444 time to fit residues: 96.0828 Evaluate side-chains 444 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 350 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 107 ASP 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 231 LYS Chi-restraints excluded: chain A residue 251 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 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 603 ILE 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 30 ILE Chi-restraints excluded: chain H residue 85 ASP 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 37 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 100 MET 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 209 SER Chi-restraints excluded: chain D residue 217 TYR 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 423 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain F residue 543 LEU 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 629 MET Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 60 SER 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 K residue 110 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 217 TYR 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 402 ASP 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 626 MET Chi-restraints excluded: chain G residue 629 MET Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain G residue 661 LEU Chi-restraints excluded: chain J residue 5 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 82 ASN Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 91 PHE Chi-restraints excluded: chain M residue 110 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 607 ASN B 620 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 E 67 ASN G 620 ASN 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 = 0.125338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.097763 restraints weight = 53281.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.101344 restraints weight = 29091.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.103856 restraints weight = 19335.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.105594 restraints weight = 14551.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.106694 restraints weight = 11902.837| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 21399 Z= 0.190 Angle : 0.719 11.895 29187 Z= 0.366 Chirality : 0.047 0.258 3447 Planarity : 0.005 0.056 3606 Dihedral : 5.069 23.079 2697 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.19 % Favored : 93.69 % Rotamer: Outliers : 4.77 % Allowed : 18.46 % Favored : 76.76 % 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: -0.77 (0.16), residues: 2487 helix: 1.47 (0.24), residues: 438 sheet: 0.06 (0.21), residues: 645 loop : -1.50 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 66 TYR 0.031 0.002 TYR M 100E PHE 0.044 0.002 PHE L 83 TRP 0.046 0.002 TRP E 479 HIS 0.006 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (21288) covalent geometry : angle 0.70455 / 0.36 (28893) SS BOND : bond 0.00368 / 0.21 ( 39) SS BOND : angle 1.86603 / 1.38 ( 78) hydrogen bonds : bond 0.04391 / 2.92 ( 825) hydrogen bonds : angle 5.46295 / 3.88 ( 2079) link_ALPHA1-2 : bond 0.00292 / 0.13 ( 3) link_ALPHA1-2 : angle 2.01715 / 1.22 ( 9) link_ALPHA1-3 : bond 0.00548 / 0.24 ( 3) link_ALPHA1-3 : angle 1.36783 / 0.83 ( 9) link_BETA1-4 : bond 0.00293 / 0.12 ( 30) link_BETA1-4 : angle 1.30271 / 0.90 ( 90) link_NAG-ASN : bond 0.00357 / 0.22 ( 36) link_NAG-ASN : angle 1.57406 / 1.09 ( 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 470 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 365 time to evaluate : 0.861 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: A 33 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8208 (mmmm) REVERT: A 107 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7707 (t70) REVERT: A 209 SER cc_start: 0.7449 (t) cc_final: 0.7230 (p) REVERT: A 217 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.5349 (m-80) REVERT: A 258 GLN cc_start: 0.8139 (mt0) cc_final: 0.7352 (mt0) REVERT: L 21 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8645 (mp) REVERT: B 540 GLN cc_start: 0.8908 (mm110) cc_final: 0.8304 (tt0) REVERT: B 629 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7437 (mtm) REVERT: B 632 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8050 (tm-30) REVERT: C 76 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9123 (pt) REVERT: C 80 ASP cc_start: 0.8440 (t0) cc_final: 0.7952 (t0) REVERT: C 85 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7593 (tm-30) REVERT: C 94 GLN cc_start: 0.7318 (tp40) cc_final: 0.6979 (tp40) REVERT: H 3 GLN cc_start: 0.8489 (mp10) cc_final: 0.8260 (mp10) REVERT: H 23 LYS cc_start: 0.8298 (tmmt) cc_final: 0.7828 (mmtm) REVERT: H 30 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8045 (tt) REVERT: H 72 ASP cc_start: 0.7035 (t0) cc_final: 0.6588 (t0) REVERT: H 83 ARG cc_start: 0.8152 (ptp-170) cc_final: 0.7801 (ptt-90) REVERT: D 107 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7815 (t70) REVERT: D 202 THR cc_start: 0.9464 (m) cc_final: 0.9215 (p) REVERT: D 217 TYR cc_start: 0.6268 (OUTLIER) cc_final: 0.5187 (m-80) REVERT: D 258 GLN cc_start: 0.8333 (mt0) cc_final: 0.7498 (mt0) REVERT: D 358 ILE cc_start: 0.8147 (mm) cc_final: 0.7856 (mm) REVERT: D 453 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8714 (mt) REVERT: D 475 MET cc_start: 0.7130 (mmm) cc_final: 0.6647 (mmm) REVERT: F 543 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9002 (mm) REVERT: F 629 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7562 (mtm) REVERT: F 654 GLU cc_start: 0.8955 (tp30) cc_final: 0.8722 (tp30) REVERT: I 60 SER cc_start: 0.9247 (OUTLIER) cc_final: 0.9028 (p) REVERT: I 66 ASN cc_start: 0.8485 (t0) cc_final: 0.8077 (m-40) REVERT: I 76 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9132 (pt) REVERT: I 85 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7521 (tm-30) REVERT: K 3 GLN cc_start: 0.8452 (mp10) cc_final: 0.8138 (mp10) REVERT: K 23 LYS cc_start: 0.8655 (tmmt) cc_final: 0.8213 (mmtm) REVERT: E 33 LYS cc_start: 0.8466 (mmtt) cc_final: 0.8220 (mmmm) REVERT: E 111 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8335 (tp) REVERT: E 209 SER cc_start: 0.7423 (t) cc_final: 0.7196 (p) REVERT: E 217 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.5466 (m-80) REVERT: E 231 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8971 (mptt) REVERT: E 475 MET cc_start: 0.6429 (mmm) cc_final: 0.5415 (mmm) REVERT: E 479 TRP cc_start: 0.6313 (m-90) cc_final: 0.5946 (m-90) REVERT: O 27 GLU cc_start: 0.9219 (tp30) cc_final: 0.8917 (tp30) REVERT: O 49 TYR cc_start: 0.8431 (t80) cc_final: 0.8132 (t80) REVERT: O 58 VAL cc_start: 0.7471 (t) cc_final: 0.7156 (t) REVERT: O 70 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8235 (mm-30) REVERT: G 540 GLN cc_start: 0.8917 (mm110) cc_final: 0.8405 (tt0) REVERT: G 657 GLU cc_start: 0.9140 (tp30) cc_final: 0.8851 (tp30) REVERT: J 85 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7440 (tm-30) REVERT: M 12 LYS cc_start: 0.9106 (mttp) cc_final: 0.8838 (mtpp) REVERT: M 13 LYS cc_start: 0.8881 (mmtt) cc_final: 0.8617 (mmmt) REVERT: M 23 LYS cc_start: 0.8537 (tmmt) cc_final: 0.7965 (mmtm) REVERT: M 30 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8156 (tt) REVERT: M 81 GLU cc_start: 0.8717 (tt0) cc_final: 0.8478 (tm-30) REVERT: M 83 ARG cc_start: 0.8024 (ptp-170) cc_final: 0.7414 (ptt-90) REVERT: M 100 PHE cc_start: 0.7634 (m-80) cc_final: 0.6995 (m-10) outliers start: 105 outliers final: 80 residues processed: 424 average time/residue: 0.1502 time to fit residues: 99.7938 Evaluate side-chains 444 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 347 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 251 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 488 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 49 TYR 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 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 30 ILE Chi-restraints excluded: chain H residue 85 ASP 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 37 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 100 MET 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 209 SER Chi-restraints excluded: chain D residue 217 TYR 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 453 LEU Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain F residue 543 LEU 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 661 LEU Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 217 TYR 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 402 ASP Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 423 ILE 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 626 MET Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain G residue 661 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain M residue 30 ILE 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: 0.8980 chunk 219 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 205 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 226 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN B 607 ASN B 620 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN F 620 ASN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN E 478 ASN G 620 ASN ** M 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.129636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.102115 restraints weight = 53393.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.105852 restraints weight = 29065.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.108479 restraints weight = 19186.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.110179 restraints weight = 14313.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.111537 restraints weight = 11719.741| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.6001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21399 Z= 0.138 Angle : 0.711 13.026 29187 Z= 0.357 Chirality : 0.046 0.221 3447 Planarity : 0.005 0.055 3606 Dihedral : 4.893 19.950 2697 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.67 % Favored : 94.21 % Rotamer: Outliers : 4.05 % Allowed : 19.24 % Favored : 76.72 % 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: -0.72 (0.16), residues: 2487 helix: 1.66 (0.25), residues: 438 sheet: -0.08 (0.20), residues: 696 loop : -1.47 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 18 TYR 0.029 0.002 TYR K 100E PHE 0.042 0.002 PHE L 83 TRP 0.041 0.001 TRP E 479 HIS 0.005 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (21288) covalent geometry : angle 0.69792 / 0.35 (28893) SS BOND : bond 0.00270 / 0.16 ( 39) SS BOND : angle 1.85428 / 1.37 ( 78) hydrogen bonds : bond 0.03945 / 2.60 ( 825) hydrogen bonds : angle 5.28299 / 3.76 ( 2079) link_ALPHA1-2 : bond 0.00115 / 0.05 ( 3) link_ALPHA1-2 : angle 1.83037 / 1.09 ( 9) link_ALPHA1-3 : bond 0.00573 / 0.25 ( 3) link_ALPHA1-3 : angle 1.26545 / 0.74 ( 9) link_BETA1-4 : bond 0.00300 / 0.15 ( 30) link_BETA1-4 : angle 1.20450 / 0.82 ( 90) link_NAG-ASN : bond 0.00302 / 0.18 ( 36) link_NAG-ASN : angle 1.43284 / 0.99 ( 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 464 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 375 time to evaluate : 0.815 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: A 33 LYS cc_start: 0.8483 (mmtt) cc_final: 0.8209 (mmmm) REVERT: A 107 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7688 (t70) REVERT: A 209 SER cc_start: 0.7397 (t) cc_final: 0.7168 (p) REVERT: A 217 TYR cc_start: 0.6851 (OUTLIER) cc_final: 0.5347 (m-80) REVERT: A 258 GLN cc_start: 0.8238 (mt0) cc_final: 0.7656 (mt0) REVERT: B 540 GLN cc_start: 0.8874 (mm110) cc_final: 0.8297 (tt0) REVERT: B 584 GLU cc_start: 0.8229 (pt0) cc_final: 0.7307 (tm-30) REVERT: B 629 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7261 (mtm) REVERT: B 632 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7970 (tm-30) REVERT: C 76 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9141 (pt) REVERT: C 80 ASP cc_start: 0.8422 (t0) cc_final: 0.8017 (t0) REVERT: H 3 GLN cc_start: 0.8451 (mp10) cc_final: 0.8212 (mp10) REVERT: H 23 LYS cc_start: 0.8345 (tmmt) cc_final: 0.7874 (mmtm) REVERT: H 72 ASP cc_start: 0.6943 (t0) cc_final: 0.6508 (t0) REVERT: H 83 ARG cc_start: 0.8160 (ptp-170) cc_final: 0.7807 (ptt-90) REVERT: D 202 THR cc_start: 0.9449 (m) cc_final: 0.9198 (p) REVERT: D 217 TYR cc_start: 0.6385 (OUTLIER) cc_final: 0.5064 (m-80) REVERT: D 258 GLN cc_start: 0.8186 (mt0) cc_final: 0.7369 (mt0) REVERT: D 358 ILE cc_start: 0.8132 (mm) cc_final: 0.7845 (mm) REVERT: N 48 ILE cc_start: 0.9041 (mm) cc_final: 0.8798 (mm) REVERT: N 58 VAL cc_start: 0.7840 (t) cc_final: 0.7396 (t) REVERT: F 629 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7443 (mtm) REVERT: I 66 ASN cc_start: 0.8373 (t0) cc_final: 0.8040 (m-40) REVERT: I 85 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7446 (tm-30) REVERT: K 3 GLN cc_start: 0.8422 (mp10) cc_final: 0.8081 (mp10) REVERT: K 23 LYS cc_start: 0.8615 (tmmt) cc_final: 0.8206 (mmtm) REVERT: K 85 ASP cc_start: 0.8459 (m-30) cc_final: 0.8091 (t0) REVERT: E 33 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8204 (mmmm) REVERT: E 67 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8240 (t0) REVERT: E 202 THR cc_start: 0.9362 (m) cc_final: 0.9007 (p) REVERT: E 209 SER cc_start: 0.7277 (t) cc_final: 0.7011 (p) REVERT: E 217 TYR cc_start: 0.6861 (OUTLIER) cc_final: 0.5319 (m-80) REVERT: E 231 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8984 (mptt) REVERT: E 479 TRP cc_start: 0.6250 (m-90) cc_final: 0.5881 (m-90) REVERT: O 18 ARG cc_start: 0.8906 (ttm170) cc_final: 0.8593 (tpp80) REVERT: O 27 GLU cc_start: 0.9165 (tp30) cc_final: 0.8905 (tp30) REVERT: O 46 LEU cc_start: 0.8558 (tp) cc_final: 0.8107 (tp) REVERT: O 58 VAL cc_start: 0.7485 (t) cc_final: 0.7192 (t) REVERT: O 70 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8064 (mm-30) REVERT: G 540 GLN cc_start: 0.8916 (mm110) cc_final: 0.8402 (tt0) REVERT: G 657 GLU cc_start: 0.9154 (tp30) cc_final: 0.8866 (tp30) REVERT: M 12 LYS cc_start: 0.9038 (mttp) cc_final: 0.8798 (mtpp) REVERT: M 13 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8574 (mmmt) REVERT: M 23 LYS cc_start: 0.8616 (tmmt) cc_final: 0.8027 (mmtm) REVERT: M 30 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.7984 (tt) REVERT: M 81 GLU cc_start: 0.8691 (tt0) cc_final: 0.8446 (tm-30) REVERT: M 83 ARG cc_start: 0.8007 (ptp-170) cc_final: 0.7638 (ptt-90) REVERT: M 100 PHE cc_start: 0.7583 (m-80) cc_final: 0.7296 (m-80) outliers start: 89 outliers final: 67 residues processed: 423 average time/residue: 0.1536 time to fit residues: 101.6152 Evaluate side-chains 427 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 350 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain L residue 49 TYR 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 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 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 200 VAL Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 217 TYR 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 373 THR Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 21 LEU 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 661 LEU Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 60 SER 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 67 ASN Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 217 TYR 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 368 ASP Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 423 ILE 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 592 LEU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 626 MET Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain G residue 661 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 82 ASN 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: 0.0000 chunk 66 optimal weight: 6.9990 chunk 239 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 91 optimal weight: 0.4980 chunk 242 optimal weight: 10.0000 chunk 55 optimal weight: 0.0670 chunk 81 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 189 optimal weight: 7.9990 overall best weight: 0.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 ASN B 607 ASN B 620 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 HIS F 620 ASN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN E 67 ASN G 620 ASN G 658 GLN ** M 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.134678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.105471 restraints weight = 55388.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.109359 restraints weight = 30323.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.112114 restraints weight = 20015.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.114100 restraints weight = 14874.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.115335 restraints weight = 11950.773| |-----------------------------------------------------------------------------| r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.6184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21399 Z= 0.129 Angle : 0.712 14.169 29187 Z= 0.358 Chirality : 0.046 0.211 3447 Planarity : 0.005 0.066 3606 Dihedral : 4.738 18.061 2697 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.43 % Favored : 94.45 % Rotamer: Outliers : 2.77 % Allowed : 20.78 % 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: -0.41 (0.16), residues: 2487 helix: 2.11 (0.25), residues: 414 sheet: 0.36 (0.20), residues: 684 loop : -1.42 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 542 TYR 0.028 0.002 TYR K 100E PHE 0.039 0.002 PHE L 83 TRP 0.042 0.001 TRP E 479 HIS 0.011 0.001 HIS E 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (21288) covalent geometry : angle 0.69957 / 0.35 (28893) SS BOND : bond 0.00253 / 0.14 ( 39) SS BOND : angle 1.92950 / 1.42 ( 78) hydrogen bonds : bond 0.03606 / 2.36 ( 825) hydrogen bonds : angle 5.11641 / 3.63 ( 2079) link_ALPHA1-2 : bond 0.00088 / 0.04 ( 3) link_ALPHA1-2 : angle 1.66293 / 0.98 ( 9) link_ALPHA1-3 : bond 0.00579 / 0.26 ( 3) link_ALPHA1-3 : angle 1.29453 / 0.75 ( 9) link_BETA1-4 : bond 0.00362 / 0.19 ( 30) link_BETA1-4 : angle 1.18140 / 0.80 ( 90) link_NAG-ASN : bond 0.00308 / 0.18 ( 36) link_NAG-ASN : angle 1.39442 / 0.95 ( 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 464 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 403 time to evaluate : 0.862 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: A 33 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8199 (mmmm) REVERT: A 209 SER cc_start: 0.7330 (t) cc_final: 0.7064 (p) REVERT: A 217 TYR cc_start: 0.6777 (OUTLIER) cc_final: 0.5333 (m-80) REVERT: A 377 ASN cc_start: 0.7758 (p0) cc_final: 0.7477 (p0) REVERT: B 540 GLN cc_start: 0.8873 (mm110) cc_final: 0.8300 (tt0) REVERT: B 584 GLU cc_start: 0.8134 (pt0) cc_final: 0.7414 (tm-30) REVERT: B 629 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7110 (mtm) REVERT: B 632 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7948 (tm-30) REVERT: C 76 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9152 (pt) REVERT: C 80 ASP cc_start: 0.8420 (t0) cc_final: 0.8045 (t0) REVERT: H 12 LYS cc_start: 0.9202 (ptpp) cc_final: 0.8830 (pttp) REVERT: H 23 LYS cc_start: 0.8306 (tmmt) cc_final: 0.7864 (mmtm) REVERT: H 72 ASP cc_start: 0.7036 (t0) cc_final: 0.6618 (t0) REVERT: H 83 ARG cc_start: 0.8164 (ptp-170) cc_final: 0.7835 (ptt-90) REVERT: D 114 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8275 (mt0) REVERT: D 202 THR cc_start: 0.9390 (m) cc_final: 0.9152 (p) REVERT: D 258 GLN cc_start: 0.7567 (mt0) cc_final: 0.7175 (mt0) REVERT: D 358 ILE cc_start: 0.8104 (mm) cc_final: 0.7820 (mm) REVERT: N 18 ARG cc_start: 0.8656 (tpp80) cc_final: 0.8386 (tpp80) REVERT: N 27 GLU cc_start: 0.8996 (tp30) cc_final: 0.8495 (tp30) REVERT: N 48 ILE cc_start: 0.8996 (mm) cc_final: 0.8796 (mm) REVERT: N 58 VAL cc_start: 0.7866 (t) cc_final: 0.7425 (t) REVERT: F 530 MET cc_start: 0.8126 (mmm) cc_final: 0.7713 (mmt) REVERT: F 542 ARG cc_start: 0.8813 (tpp80) cc_final: 0.8473 (tpp80) REVERT: F 584 GLU cc_start: 0.8093 (pt0) cc_final: 0.7493 (tm-30) REVERT: F 629 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7344 (mtm) REVERT: I 85 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7441 (tm-30) REVERT: K 3 GLN cc_start: 0.8423 (mp10) cc_final: 0.8076 (mp10) REVERT: K 23 LYS cc_start: 0.8634 (tmmt) cc_final: 0.8212 (mmtm) REVERT: E 33 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8281 (mmmm) REVERT: E 114 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8006 (mt0) REVERT: E 209 SER cc_start: 0.7225 (t) cc_final: 0.6958 (p) REVERT: E 231 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.9026 (mptt) REVERT: E 475 MET cc_start: 0.6189 (mmm) cc_final: 0.5636 (mmm) REVERT: E 479 TRP cc_start: 0.6285 (m-90) cc_final: 0.5777 (m-90) REVERT: O 27 GLU cc_start: 0.9128 (tp30) cc_final: 0.8821 (tp30) REVERT: O 33 LEU cc_start: 0.7394 (mm) cc_final: 0.7171 (mm) REVERT: O 36 TYR cc_start: 0.6378 (m-80) cc_final: 0.6051 (m-80) REVERT: O 46 LEU cc_start: 0.8350 (tp) cc_final: 0.8086 (tp) REVERT: O 49 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.8025 (t80) REVERT: O 58 VAL cc_start: 0.7686 (t) cc_final: 0.7378 (t) REVERT: O 70 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8073 (mm-30) REVERT: G 540 GLN cc_start: 0.8981 (mm110) cc_final: 0.8347 (tt0) REVERT: G 581 LEU cc_start: 0.7266 (tp) cc_final: 0.6466 (tp) REVERT: G 584 GLU cc_start: 0.8205 (pt0) cc_final: 0.7516 (tm-30) REVERT: G 657 GLU cc_start: 0.9145 (tp30) cc_final: 0.8870 (tp30) REVERT: J 33 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7460 (tp40) REVERT: J 66 ASN cc_start: 0.8301 (t0) cc_final: 0.8050 (m-40) REVERT: M 12 LYS cc_start: 0.9006 (mttp) cc_final: 0.8777 (mtpp) REVERT: M 13 LYS cc_start: 0.8820 (mmtt) cc_final: 0.8490 (mmmt) REVERT: M 23 LYS cc_start: 0.8552 (tmmt) cc_final: 0.7928 (mmtm) REVERT: M 30 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8008 (tt) REVERT: M 81 GLU cc_start: 0.8669 (tt0) cc_final: 0.8425 (tm-30) REVERT: M 83 ARG cc_start: 0.8193 (ptp-170) cc_final: 0.7940 (ptt-90) REVERT: M 100 PHE cc_start: 0.7282 (m-80) cc_final: 0.7042 (m-80) outliers start: 61 outliers final: 49 residues processed: 433 average time/residue: 0.1518 time to fit residues: 102.1478 Evaluate side-chains 425 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 369 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain L residue 49 TYR 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 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 91 PHE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 110 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 333 ILE Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain N residue 21 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 661 LEU Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 60 SER 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 67 ASN 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 408 THR Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 49 TYR 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 G residue 661 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 97 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: 2.9990 chunk 202 optimal weight: 0.5980 chunk 42 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 168 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 236 optimal weight: 0.3980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN B 620 ASN C 66 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 ASN ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 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 = 0.4462 r_free = 0.4462 target = 0.128132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.100140 restraints weight = 53243.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.103795 restraints weight = 29172.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.106396 restraints weight = 19452.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.108032 restraints weight = 14650.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.109402 restraints weight = 12089.521| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.6259 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= 0.168 Angle : 0.727 14.697 29187 Z= 0.367 Chirality : 0.046 0.227 3447 Planarity : 0.005 0.058 3606 Dihedral : 4.791 18.179 2697 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.51 % Favored : 93.41 % Rotamer: Outliers : 2.91 % Allowed : 21.42 % Favored : 75.67 % 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: -0.83 (0.16), residues: 2487 helix: 1.37 (0.24), residues: 474 sheet: 0.37 (0.21), residues: 618 loop : -1.77 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 542 TYR 0.034 0.002 TYR D 404 PHE 0.041 0.002 PHE L 83 TRP 0.045 0.002 TRP E 96 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (21288) covalent geometry : angle 0.71389 / 0.36 (28893) SS BOND : bond 0.00327 / 0.20 ( 39) SS BOND : angle 1.91163 / 1.40 ( 78) hydrogen bonds : bond 0.03870 / 2.54 ( 825) hydrogen bonds : angle 5.19390 / 3.67 ( 2079) link_ALPHA1-2 : bond 0.00204 / 0.09 ( 3) link_ALPHA1-2 : angle 1.84218 / 1.10 ( 9) link_ALPHA1-3 : bond 0.00465 / 0.21 ( 3) link_ALPHA1-3 : angle 1.31682 / 0.79 ( 9) link_BETA1-4 : bond 0.00260 / 0.13 ( 30) link_BETA1-4 : angle 1.27825 / 0.88 ( 90) link_NAG-ASN : bond 0.00265 / 0.16 ( 36) link_NAG-ASN : angle 1.47411 / 1.01 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4213.49 seconds wall clock time: 74 minutes 14.85 seconds (4454.85 seconds total)