Starting phenix.real_space_refine on Thu Sep 18 21:53:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ber_44482/09_2025/9ber_44482.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ber_44482/09_2025/9ber_44482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ber_44482/09_2025/9ber_44482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ber_44482/09_2025/9ber_44482.map" model { file = "/net/cci-nas-00/data/ceres_data/9ber_44482/09_2025/9ber_44482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ber_44482/09_2025/9ber_44482.cif" } resolution = 4.1 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= 0.004 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 12766 2.51 5 N 3371 2.21 5 O 4098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20350 Number of models: 1 Model: "" Number of chains: 36 Chain: "G" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3504 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 2 Chain: "B" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "A" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3504 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 2 Chain: "C" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 966 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "F" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3504 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "I" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 985 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "L" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "D" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "J" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain breaks: 1 Chain: "K" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 173 Unusual residues: {'NAG': 12, 'SO4': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.39, per 1000 atoms: 0.26 Number of scatterers: 20350 At special positions: 0 Unit cell: (152.409, 153.482, 152.409, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 4098 8.00 N 3371 7.00 C 12766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 113 " - pdb=" SG CYS G 431B" distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.04 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 431B" distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 431B" distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.05 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.04 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA R 3 " - " MAN R 6 " " MAN R 4 " - " MAN R 5 " " BMA U 3 " - " MAN U 4 " " BMA X 3 " - " MAN X 6 " " MAN X 4 " - " MAN X 5 " " BMA a 3 " - " MAN a 4 " " BMA d 3 " - " MAN d 6 " " MAN d 4 " - " MAN d 5 " ALPHA1-6 " BMA R 3 " - " MAN R 4 " " BMA X 3 " - " MAN X 4 " " BMA d 3 " - " MAN d 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 276 " " NAG A 604 " - " ASN A 295 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 339 " " NAG A 607 " - " ASN A 362 " " NAG A 608 " - " ASN A 392 " " NAG A 609 " - " ASN A 197 " " NAG A 610 " - " ASN A 234 " " NAG A 611 " - " ASN A 355 " " NAG A 612 " - " ASN A 187 " " NAG B 701 " - " ASN B 625 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 611 " " NAG C 701 " - " ASN C 637 " " NAG C 702 " - " ASN C 611 " " NAG C 703 " - " ASN C 625 " " NAG C 704 " - " ASN C 616 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 160 " " NAG F 603 " - " ASN F 276 " " NAG F 604 " - " ASN F 295 " " NAG F 605 " - " ASN F 301 " " NAG F 606 " - " ASN F 339 " " NAG F 607 " - " ASN F 362 " " NAG F 608 " - " ASN F 392 " " NAG F 609 " - " ASN F 197 " " NAG F 610 " - " ASN F 234 " " NAG F 611 " - " ASN F 187 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 160 " " NAG G 603 " - " ASN G 276 " " NAG G 604 " - " ASN G 295 " " NAG G 605 " - " ASN G 301 " " NAG G 606 " - " ASN G 339 " " NAG G 607 " - " ASN G 362 " " NAG G 608 " - " ASN G 392 " " NAG G 609 " - " ASN G 197 " " NAG G 610 " - " ASN G 234 " " NAG G 611 " - " ASN G 355 " " NAG G 612 " - " ASN G 187 " " NAG I 702 " - " ASN I 637 " " NAG I 703 " - " ASN I 611 " " NAG M 1 " - " ASN G 156 " " NAG N 1 " - " ASN G 241 " " NAG O 1 " - " ASN G 262 " " NAG P 1 " - " ASN G 386 " " NAG Q 1 " - " ASN G 448 " " NAG R 1 " - " ASN G 332 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 241 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 448 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN F 156 " " NAG Z 1 " - " ASN F 241 " " NAG a 1 " - " ASN F 262 " " NAG b 1 " - " ASN F 386 " " NAG c 1 " - " ASN F 448 " " NAG d 1 " - " ASN F 332 " Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 865.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4474 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 52 sheets defined 18.5% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'G' and resid 98 through 116 removed outlier: 3.925A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE G 108 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 4.024A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 349 removed outlier: 3.816A pdb=" N LYS G 348 " --> pdb=" O GLN G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.599A pdb=" N VAL G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 391 removed outlier: 3.586A pdb=" N LEU G 390 " --> pdb=" O SER G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 4.383A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 482 through 484 No H-bonds generated for 'chain 'G' and resid 482 through 484' Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 545 removed outlier: 3.790A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 597 removed outlier: 4.149A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 590 " --> pdb=" O TYR B 586 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY B 597 " --> pdb=" O LEU B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.570A pdb=" N ARG B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 634 " --> pdb=" O GLU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 645 removed outlier: 3.612A pdb=" N LEU B 645 " --> pdb=" O GLU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 661 removed outlier: 3.783A pdb=" N LEU B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.557A pdb=" N ILE A 109 " --> pdb=" O GLN A 105 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.966A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 removed outlier: 3.675A pdb=" N LYS A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 4.036A pdb=" N VAL A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 373' Processing helix chain 'A' and resid 388 through 392 removed outlier: 4.080A pdb=" N ASN A 392 " --> pdb=" O GLN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 431A Processing helix chain 'A' and resid 474 through 482 removed outlier: 3.650A pdb=" N ASN A 478 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP A 479 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A 481 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 482 " --> pdb=" O TRP A 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 535 removed outlier: 3.933A pdb=" N SER C 534 " --> pdb=" O GLY C 531 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N MET C 535 " --> pdb=" O ALA C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 570 through 586 Processing helix chain 'C' and resid 589 through 594 Processing helix chain 'C' and resid 618 through 624 removed outlier: 3.692A pdb=" N ASN C 624 " --> pdb=" O ASP C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.549A pdb=" N GLU C 634 " --> pdb=" O GLU C 630 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 635 " --> pdb=" O TRP C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 648 removed outlier: 3.999A pdb=" N THR C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 661 removed outlier: 3.902A pdb=" N ASN C 656 " --> pdb=" O GLN C 652 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU C 657 " --> pdb=" O GLN C 653 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN C 658 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 116 removed outlier: 3.558A pdb=" N GLN F 103 " --> pdb=" O ASN F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 removed outlier: 3.846A pdb=" N CYS F 126 " --> pdb=" O THR F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 350 removed outlier: 4.311A pdb=" N LYS F 348 " --> pdb=" O GLN F 344 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG F 350 " --> pdb=" O VAL F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.673A pdb=" N VAL F 372 " --> pdb=" O ASP F 368 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET F 373 " --> pdb=" O PRO F 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 368 through 373' Processing helix chain 'F' and resid 427 through 431A Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 537 through 541 Processing helix chain 'I' and resid 570 through 589 removed outlier: 3.839A pdb=" N LEU I 581 " --> pdb=" O GLN I 577 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA I 582 " --> pdb=" O ALA I 578 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP I 589 " --> pdb=" O ARG I 585 " (cutoff:3.500A) Processing helix chain 'I' and resid 589 through 596 removed outlier: 3.784A pdb=" N LEU I 593 " --> pdb=" O ASP I 589 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP I 596 " --> pdb=" O LEU I 592 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 623 Processing helix chain 'I' and resid 627 through 633 removed outlier: 3.623A pdb=" N ARG I 633 " --> pdb=" O MET I 629 " (cutoff:3.500A) Processing helix chain 'I' and resid 634 through 637 removed outlier: 6.079A pdb=" N ASN I 637 " --> pdb=" O GLU I 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 634 through 637' Processing helix chain 'I' and resid 638 through 647 removed outlier: 3.670A pdb=" N THR I 644 " --> pdb=" O SER I 640 " (cutoff:3.500A) Processing helix chain 'I' and resid 650 through 661 removed outlier: 4.081A pdb=" N ASN I 656 " --> pdb=" O GLN I 652 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU I 661 " --> pdb=" O GLU I 657 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.521A pdb=" N ASP H 31 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.744A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.651A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.542A pdb=" N ASP D 31 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN D 32 " --> pdb=" O VAL D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.806A pdb=" N GLU E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.785A pdb=" N LYS J 64 " --> pdb=" O PRO J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.533A pdb=" N SER J 87 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.744A pdb=" N GLU K 83 " --> pdb=" O ALA K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 494 through 499 removed outlier: 3.950A pdb=" N CYS B 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 84 through 85 removed outlier: 4.179A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 91 through 93 removed outlier: 3.897A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS G 239 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 129 through 130 Processing sheet with id=AA5, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AA6, first strand: chain 'G' and resid 158 through 162 removed outlier: 3.639A pdb=" N PHE G 159 " --> pdb=" O GLU G 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU G 172 " --> pdb=" O PHE G 159 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN G 170 " --> pdb=" O ILE G 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.969A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 259 through 261 removed outlier: 3.692A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLU G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N SER G 334 " --> pdb=" O GLU G 293 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASN G 295 " --> pdb=" O ASN G 332 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN G 332 " --> pdb=" O ASN G 295 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR G 297 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.717A pdb=" N VAL G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU G 452 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE G 467 " --> pdb=" O ASP G 457 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 305 through 308 Processing sheet with id=AB2, first strand: chain 'A' and resid 494 through 499 removed outlier: 3.555A pdb=" N GLY A 495 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 37 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS C 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.032A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 91 through 93 removed outlier: 4.051A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AB6, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AB7, first strand: chain 'A' and resid 158 through 160 Processing sheet with id=AB8, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.789A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 259 through 261 removed outlier: 7.400A pdb=" N VAL A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP A 395 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.559A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG A 298 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.763A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.976A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.029A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN A 332 " --> pdb=" O ASN A 295 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AC3, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.183A pdb=" N ARG A 419 " --> pdb=" O TYR A 384 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 496 through 499 removed outlier: 3.632A pdb=" N THR F 499 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL F 36 " --> pdb=" O THR I 606 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AC6, first strand: chain 'F' and resid 92 through 93 Processing sheet with id=AC7, first strand: chain 'F' and resid 129 through 130 Processing sheet with id=AC8, first strand: chain 'F' and resid 154 through 155 removed outlier: 3.654A pdb=" N PHE F 176 " --> pdb=" O LYS F 155 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 158 through 161 removed outlier: 3.542A pdb=" N GLU F 172 " --> pdb=" O PHE F 159 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 215 through 216 Processing sheet with id=AD2, first strand: chain 'F' and resid 223 through 227 Processing sheet with id=AD3, first strand: chain 'F' and resid 259 through 261 removed outlier: 3.574A pdb=" N GLY F 451 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS F 296 " --> pdb=" O CYS F 445 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER F 447 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 271 through 273 removed outlier: 3.525A pdb=" N VAL F 286 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU F 452 " --> pdb=" O VAL F 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 304 through 308 Processing sheet with id=AD6, first strand: chain 'F' and resid 329 through 334 removed outlier: 3.509A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 360 through 361 removed outlier: 3.621A pdb=" N PHE F 361 " --> pdb=" O SER F 393 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER F 393 " --> pdb=" O PHE F 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AD9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.695A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.562A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR H 33 " --> pdb=" O THR H 95 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR H 50 " --> pdb=" O ASN H 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.562A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG H 100 " --> pdb=" O PHE H 100K" (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE H 100K" --> pdb=" O ARG H 100 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 6 through 13 removed outlier: 6.418A pdb=" N VAL L 11 " --> pdb=" O ILE L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'L' and resid 19 through 22 Processing sheet with id=AE5, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.279A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.898A pdb=" N VAL D 78 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER D 70 " --> pdb=" O SER D 79 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AE8, first strand: chain 'D' and resid 58 through 59 removed outlier: 3.524A pdb=" N TYR D 50 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR D 50 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR D 33 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER D 35 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA D 93 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 37 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL D 102 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LYS D 96 " --> pdb=" O MET D 100P" (cutoff:3.500A) removed outlier: 5.802A pdb=" N MET D 100P" --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLY D 98 " --> pdb=" O PHE D 100N" (cutoff:3.500A) removed outlier: 5.388A pdb=" N PHE D 100N" --> pdb=" O GLY D 98 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 58 through 59 removed outlier: 3.524A pdb=" N TYR D 50 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR D 50 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR D 33 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER D 35 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA D 93 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 37 " --> pdb=" O TYR D 91 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 6 through 13 removed outlier: 3.531A pdb=" N THR E 102 " --> pdb=" O TYR E 86 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR E 86 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP E 85 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TRP E 35 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE E 47 " --> pdb=" O TRP E 35 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 19 through 26 removed outlier: 3.845A pdb=" N ALA E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AF4, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=AF5, first strand: chain 'J' and resid 58 through 59 removed outlier: 7.058A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR J 33 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER J 35 " --> pdb=" O ALA J 93 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA J 93 " --> pdb=" O SER J 35 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 6 through 13 removed outlier: 6.409A pdb=" N VAL K 11 " --> pdb=" O ILE K 105 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 19 through 21 489 hydrogen bonds defined for protein. 1233 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: 3.93 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3503 1.33 - 1.46: 6547 1.46 - 1.59: 10573 1.59 - 1.72: 0 1.72 - 1.85: 150 Bond restraints: 20773 Sorted by residual: bond pdb=" N ILE A 161 " pdb=" CA ILE A 161 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.11e-02 8.12e+03 9.36e+00 bond pdb=" C PRO A 470 " pdb=" O PRO A 470 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.30e-02 5.92e+03 9.18e+00 bond pdb=" N ILE A 165 " pdb=" CA ILE A 165 " ideal model delta sigma weight residual 1.460 1.491 -0.032 1.10e-02 8.26e+03 8.23e+00 bond pdb=" N ASP A 474 " pdb=" CA ASP A 474 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.80e+00 bond pdb=" N VAL A 169 " pdb=" CA VAL A 169 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.86e+00 ... (remaining 20768 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 27833 2.92 - 5.83: 346 5.83 - 8.75: 53 8.75 - 11.67: 4 11.67 - 14.58: 1 Bond angle restraints: 28237 Sorted by residual: angle pdb=" N MET A 475 " pdb=" CA MET A 475 " pdb=" C MET A 475 " ideal model delta sigma weight residual 112.87 105.25 7.62 1.20e+00 6.94e-01 4.04e+01 angle pdb=" C ASP A 167 " pdb=" CA ASP A 167 " pdb=" CB ASP A 167 " ideal model delta sigma weight residual 110.35 119.02 -8.67 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C PRO A 470 " pdb=" CA PRO A 470 " pdb=" CB PRO A 470 " ideal model delta sigma weight residual 111.56 104.54 7.02 1.65e+00 3.67e-01 1.81e+01 angle pdb=" N SER A 164 " pdb=" CA SER A 164 " pdb=" C SER A 164 " ideal model delta sigma weight residual 111.28 106.70 4.58 1.09e+00 8.42e-01 1.77e+01 angle pdb=" CA LEU B 645 " pdb=" CB LEU B 645 " pdb=" CG LEU B 645 " ideal model delta sigma weight residual 116.30 130.88 -14.58 3.50e+00 8.16e-02 1.74e+01 ... (remaining 28232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.05: 12513 22.05 - 44.10: 914 44.10 - 66.15: 130 66.15 - 88.20: 62 88.20 - 110.25: 40 Dihedral angle restraints: 13659 sinusoidal: 6711 harmonic: 6948 Sorted by residual: dihedral pdb=" CA VAL J 100D" pdb=" C VAL J 100D" pdb=" N VAL J 100E" pdb=" CA VAL J 100E" ideal model delta harmonic sigma weight residual 180.00 121.28 58.72 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " pdb=" SG CYS A 431B" pdb=" CB CYS A 431B" ideal model delta sinusoidal sigma weight residual -86.00 -168.66 82.66 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -164.22 78.22 1 1.00e+01 1.00e-02 7.64e+01 ... (remaining 13656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 3351 0.122 - 0.243: 92 0.243 - 0.365: 9 0.365 - 0.486: 3 0.486 - 0.608: 3 Chirality restraints: 3458 Sorted by residual: chirality pdb=" C1 NAG d 1 " pdb=" ND2 ASN F 332 " pdb=" C2 NAG d 1 " pdb=" O5 NAG d 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.24e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN G 332 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.18e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN A 332 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.90e+00 ... (remaining 3455 not shown) Planarity restraints: 3515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 386 " 0.007 2.00e-02 2.50e+03 4.13e-02 2.13e+01 pdb=" CG ASN F 386 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN F 386 " 0.049 2.00e-02 2.50e+03 pdb=" ND2 ASN F 386 " -0.041 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 596 " -0.024 2.00e-02 2.50e+03 2.45e-02 1.50e+01 pdb=" CG TRP C 596 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP C 596 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP C 596 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 596 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 596 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 596 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 596 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 596 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 596 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 197 " 0.034 2.00e-02 2.50e+03 3.11e-02 1.21e+01 pdb=" CG ASN G 197 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN G 197 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN G 197 " -0.032 2.00e-02 2.50e+03 pdb=" C1 NAG G 609 " 0.033 2.00e-02 2.50e+03 ... (remaining 3512 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 86 2.50 - 3.10: 13605 3.10 - 3.70: 28459 3.70 - 4.30: 39181 4.30 - 4.90: 64590 Nonbonded interactions: 145921 Sorted by model distance: nonbonded pdb=" NH1 ARG D 100 " pdb=" OD1 ASN E 50 " model vdw 1.899 3.120 nonbonded pdb=" OD1 ASN A 67 " pdb=" OG SER A 209 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR F 297 " pdb=" O ILE F 443 " model vdw 2.278 3.040 nonbonded pdb=" O ALA I 526 " pdb=" OG1 THR I 627 " model vdw 2.307 3.040 nonbonded pdb=" OD2 ASP G 107 " pdb=" OH TYR G 217 " model vdw 2.315 3.040 ... (remaining 145916 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 32 through 611) selection = chain 'F' selection = (chain 'G' and resid 32 through 611) } ncs_group { reference = (chain 'B' and (resid 519 through 546 or resid 569 through 703)) selection = (chain 'C' and resid 519 through 703) selection = (chain 'I' and (resid 519 through 546 or resid 569 through 703)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'O' selection = chain 'U' selection = chain 'a' } ncs_group { reference = chain 'R' selection = chain 'X' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.870 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20910 Z= 0.247 Angle : 0.880 15.063 28609 Z= 0.419 Chirality : 0.057 0.608 3458 Planarity : 0.005 0.070 3453 Dihedral : 16.150 110.248 9068 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.38 % Favored : 92.53 % Rotamer: Outliers : 0.24 % Allowed : 0.38 % Favored : 99.39 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.16), residues: 2370 helix: -2.73 (0.23), residues: 315 sheet: -0.19 (0.21), residues: 666 loop : -1.66 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 31 TYR 0.028 0.001 TYR J 100M PHE 0.018 0.001 PHE G 317 TRP 0.066 0.001 TRP C 596 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00490 (20773) covalent geometry : angle 0.82834 (28237) SS BOND : bond 0.00502 ( 39) SS BOND : angle 1.40329 ( 78) hydrogen bonds : bond 0.30879 ( 477) hydrogen bonds : angle 10.43607 ( 1233) link_ALPHA1-3 : bond 0.00468 ( 9) link_ALPHA1-3 : angle 1.55297 ( 27) link_ALPHA1-6 : bond 0.00345 ( 3) link_ALPHA1-6 : angle 1.75409 ( 9) link_BETA1-4 : bond 0.00611 ( 24) link_BETA1-4 : angle 2.89663 ( 72) link_NAG-ASN : bond 0.00634 ( 62) link_NAG-ASN : angle 3.20165 ( 186) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 198 time to evaluate : 0.819 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: G 95 MET cc_start: 0.9319 (ptm) cc_final: 0.8654 (ppp) REVERT: G 373 MET cc_start: 0.8561 (mmt) cc_final: 0.8043 (tpp) REVERT: B 626 MET cc_start: 0.8283 (ttt) cc_final: 0.7148 (tmm) REVERT: B 629 MET cc_start: 0.9071 (mmm) cc_final: 0.8844 (mmt) REVERT: B 630 GLU cc_start: 0.9115 (tp30) cc_final: 0.8904 (tm-30) REVERT: B 633 ARG cc_start: 0.9466 (mtt180) cc_final: 0.9251 (ptp-110) REVERT: A 163 THR cc_start: 0.6291 (OUTLIER) cc_final: 0.5983 (p) REVERT: A 373 MET cc_start: 0.8826 (mtm) cc_final: 0.8091 (pmm) REVERT: A 434 MET cc_start: 0.9241 (ttt) cc_final: 0.8853 (tmm) REVERT: C 626 MET cc_start: 0.8465 (ttm) cc_final: 0.7975 (tpp) REVERT: C 629 MET cc_start: 0.9266 (mmm) cc_final: 0.8663 (tpt) REVERT: C 630 GLU cc_start: 0.9531 (tp30) cc_final: 0.9034 (tp30) REVERT: C 647 GLU cc_start: 0.9200 (tt0) cc_final: 0.8985 (tp30) REVERT: F 61 TYR cc_start: 0.8515 (m-80) cc_final: 0.8263 (m-10) REVERT: F 167 ASP cc_start: 0.8888 (t0) cc_final: 0.8641 (t70) REVERT: I 577 GLN cc_start: 0.9060 (pt0) cc_final: 0.8227 (tm-30) REVERT: I 584 GLU cc_start: 0.9204 (pp20) cc_final: 0.8904 (pp20) REVERT: H 90 TYR cc_start: 0.8864 (m-80) cc_final: 0.8595 (m-10) REVERT: L 95 ASN cc_start: 0.9202 (m110) cc_final: 0.8951 (t0) REVERT: L 100 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8659 (pm20) REVERT: D 30 ARG cc_start: 0.9143 (ttp-170) cc_final: 0.8926 (ttp80) REVERT: D 101 ASP cc_start: 0.8966 (t0) cc_final: 0.8726 (m-30) REVERT: E 90 ILE cc_start: 0.9147 (mm) cc_final: 0.8880 (pt) REVERT: J 48 ILE cc_start: 0.8381 (mt) cc_final: 0.8077 (mm) REVERT: J 90 TYR cc_start: 0.8679 (m-80) cc_final: 0.8190 (m-10) outliers start: 5 outliers final: 1 residues processed: 203 average time/residue: 0.2114 time to fit residues: 60.8300 Evaluate side-chains 94 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 overall best weight: 2.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 377 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 HIS F 478 ASN I 575 GLN H 5 GLN E 17 GLN K 17 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.033763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.027130 restraints weight = 254221.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.027755 restraints weight = 159438.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.028181 restraints weight = 116454.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.028472 restraints weight = 93617.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.028681 restraints weight = 80452.636| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 20910 Z= 0.174 Angle : 0.702 10.458 28609 Z= 0.344 Chirality : 0.049 0.419 3458 Planarity : 0.005 0.082 3453 Dihedral : 11.876 80.846 4628 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.28 % Allowed : 3.73 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.17), residues: 2370 helix: -1.42 (0.25), residues: 358 sheet: -0.47 (0.20), residues: 713 loop : -1.51 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 38 TYR 0.014 0.001 TYR F 486 PHE 0.017 0.001 PHE F 382 TRP 0.020 0.001 TRP C 596 HIS 0.019 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00383 (20773) covalent geometry : angle 0.66048 (28237) SS BOND : bond 0.00327 ( 39) SS BOND : angle 1.12251 ( 78) hydrogen bonds : bond 0.05012 ( 477) hydrogen bonds : angle 7.14056 ( 1233) link_ALPHA1-3 : bond 0.00810 ( 9) link_ALPHA1-3 : angle 2.24978 ( 27) link_ALPHA1-6 : bond 0.00334 ( 3) link_ALPHA1-6 : angle 1.67807 ( 9) link_BETA1-4 : bond 0.00405 ( 24) link_BETA1-4 : angle 2.23946 ( 72) link_NAG-ASN : bond 0.00416 ( 62) link_NAG-ASN : angle 2.48870 ( 186) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.796 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: G 95 MET cc_start: 0.9255 (ptm) cc_final: 0.8239 (ppp) REVERT: G 373 MET cc_start: 0.8484 (mmt) cc_final: 0.8036 (tpp) REVERT: B 577 GLN cc_start: 0.9531 (OUTLIER) cc_final: 0.9207 (pt0) REVERT: A 373 MET cc_start: 0.8666 (mtm) cc_final: 0.7933 (mtt) REVERT: A 434 MET cc_start: 0.9393 (ttt) cc_final: 0.9009 (tmm) REVERT: C 581 LEU cc_start: 0.9584 (tp) cc_final: 0.9381 (tp) REVERT: C 626 MET cc_start: 0.8716 (ttm) cc_final: 0.8169 (tpp) REVERT: C 630 GLU cc_start: 0.9257 (tp30) cc_final: 0.8635 (tp30) REVERT: F 61 TYR cc_start: 0.8564 (m-80) cc_final: 0.8326 (m-10) REVERT: I 577 GLN cc_start: 0.9209 (pt0) cc_final: 0.8296 (tm-30) REVERT: I 626 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7904 (tmm) REVERT: I 643 TYR cc_start: 0.9520 (m-80) cc_final: 0.9222 (m-80) REVERT: H 90 TYR cc_start: 0.8831 (m-80) cc_final: 0.8534 (m-10) REVERT: L 95 ASN cc_start: 0.9368 (m110) cc_final: 0.9028 (t0) REVERT: D 105 LYS cc_start: 0.9022 (mtpp) cc_final: 0.8802 (mtmm) REVERT: J 90 TYR cc_start: 0.8228 (m-80) cc_final: 0.7667 (m-80) outliers start: 6 outliers final: 0 residues processed: 118 average time/residue: 0.1926 time to fit residues: 33.5246 Evaluate side-chains 81 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 193 optimal weight: 30.0000 chunk 143 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 9 optimal weight: 0.3980 chunk 78 optimal weight: 20.0000 chunk 213 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN B 651 ASN C 590 GLN C 658 GLN F 72 HIS ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.032616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.026021 restraints weight = 258171.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.026649 restraints weight = 159416.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.027077 restraints weight = 115291.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.027376 restraints weight = 92183.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.027580 restraints weight = 78814.834| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20910 Z= 0.175 Angle : 0.666 12.822 28609 Z= 0.323 Chirality : 0.047 0.407 3458 Planarity : 0.004 0.071 3453 Dihedral : 9.604 67.644 4628 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.05 % Allowed : 3.87 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.17), residues: 2370 helix: -0.99 (0.27), residues: 359 sheet: -0.42 (0.20), residues: 710 loop : -1.42 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 81 TYR 0.030 0.001 TYR H 90 PHE 0.012 0.001 PHE G 317 TRP 0.015 0.002 TRP A 112 HIS 0.003 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00378 (20773) covalent geometry : angle 0.62520 (28237) SS BOND : bond 0.00345 ( 39) SS BOND : angle 1.20897 ( 78) hydrogen bonds : bond 0.04083 ( 477) hydrogen bonds : angle 6.38979 ( 1233) link_ALPHA1-3 : bond 0.00848 ( 9) link_ALPHA1-3 : angle 1.77581 ( 27) link_ALPHA1-6 : bond 0.00404 ( 3) link_ALPHA1-6 : angle 1.60310 ( 9) link_BETA1-4 : bond 0.00449 ( 24) link_BETA1-4 : angle 2.10571 ( 72) link_NAG-ASN : bond 0.00431 ( 62) link_NAG-ASN : angle 2.43716 ( 186) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.813 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: G 95 MET cc_start: 0.9334 (ptm) cc_final: 0.8436 (ppp) REVERT: G 373 MET cc_start: 0.8525 (mmt) cc_final: 0.8232 (tpp) REVERT: B 629 MET cc_start: 0.8659 (mmt) cc_final: 0.7622 (mmt) REVERT: A 373 MET cc_start: 0.8493 (mtm) cc_final: 0.7994 (mtt) REVERT: A 434 MET cc_start: 0.9368 (ttt) cc_final: 0.9029 (tmm) REVERT: C 589 ASP cc_start: 0.9120 (p0) cc_final: 0.8905 (p0) REVERT: C 626 MET cc_start: 0.8727 (ttm) cc_final: 0.8313 (tpp) REVERT: F 61 TYR cc_start: 0.8478 (m-80) cc_final: 0.8274 (m-10) REVERT: I 577 GLN cc_start: 0.9139 (pt0) cc_final: 0.8150 (tm-30) REVERT: I 643 TYR cc_start: 0.9508 (m-80) cc_final: 0.9154 (m-80) REVERT: H 90 TYR cc_start: 0.8622 (m-10) cc_final: 0.7681 (m-10) REVERT: L 95 ASN cc_start: 0.9449 (m110) cc_final: 0.8979 (t0) REVERT: J 90 TYR cc_start: 0.8137 (m-80) cc_final: 0.7642 (m-80) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.1810 time to fit residues: 27.2470 Evaluate side-chains 68 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 161 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 190 optimal weight: 40.0000 chunk 83 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 229 ASN G 374 HIS ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN C 658 GLN ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN K 17 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.031431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.024985 restraints weight = 264111.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.025599 restraints weight = 161507.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.026020 restraints weight = 116427.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.026305 restraints weight = 92929.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.026504 restraints weight = 79510.064| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20910 Z= 0.211 Angle : 0.709 11.529 28609 Z= 0.343 Chirality : 0.048 0.450 3458 Planarity : 0.004 0.066 3453 Dihedral : 8.404 57.531 4628 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.09 % Allowed : 3.64 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.17), residues: 2370 helix: -1.02 (0.27), residues: 361 sheet: -0.46 (0.20), residues: 665 loop : -1.48 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 38 TYR 0.017 0.002 TYR H 90 PHE 0.023 0.002 PHE K 67 TRP 0.020 0.002 TRP G 45 HIS 0.011 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00457 (20773) covalent geometry : angle 0.66765 (28237) SS BOND : bond 0.00546 ( 39) SS BOND : angle 1.48284 ( 78) hydrogen bonds : bond 0.03479 ( 477) hydrogen bonds : angle 6.07823 ( 1233) link_ALPHA1-3 : bond 0.00857 ( 9) link_ALPHA1-3 : angle 2.17092 ( 27) link_ALPHA1-6 : bond 0.00354 ( 3) link_ALPHA1-6 : angle 1.83332 ( 9) link_BETA1-4 : bond 0.00357 ( 24) link_BETA1-4 : angle 2.09183 ( 72) link_NAG-ASN : bond 0.00439 ( 62) link_NAG-ASN : angle 2.46969 ( 186) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9487 (ptm) cc_final: 0.9090 (ppp) REVERT: G 373 MET cc_start: 0.8439 (mmt) cc_final: 0.8142 (tpp) REVERT: A 373 MET cc_start: 0.8510 (mtm) cc_final: 0.8061 (mtt) REVERT: A 434 MET cc_start: 0.9201 (ttt) cc_final: 0.8954 (tmm) REVERT: A 475 MET cc_start: 0.8014 (tpp) cc_final: 0.7699 (tpp) REVERT: C 626 MET cc_start: 0.8824 (ttm) cc_final: 0.8375 (tpp) REVERT: F 61 TYR cc_start: 0.8479 (m-80) cc_final: 0.8171 (m-80) REVERT: I 577 GLN cc_start: 0.9152 (pt0) cc_final: 0.8153 (tm-30) REVERT: I 643 TYR cc_start: 0.9510 (m-80) cc_final: 0.9142 (m-80) REVERT: L 95 ASN cc_start: 0.9063 (m110) cc_final: 0.8830 (t0) REVERT: J 90 TYR cc_start: 0.8307 (m-80) cc_final: 0.7782 (m-80) outliers start: 2 outliers final: 0 residues processed: 87 average time/residue: 0.1948 time to fit residues: 25.1802 Evaluate side-chains 58 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 127 optimal weight: 8.9990 chunk 179 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 66 optimal weight: 0.0980 chunk 67 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.031032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.024619 restraints weight = 264240.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.025228 restraints weight = 161634.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.025644 restraints weight = 116675.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.025925 restraints weight = 93318.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.026126 restraints weight = 79970.842| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20910 Z= 0.196 Angle : 0.684 12.726 28609 Z= 0.332 Chirality : 0.048 0.419 3458 Planarity : 0.004 0.063 3453 Dihedral : 7.935 56.819 4628 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.17), residues: 2370 helix: -1.03 (0.27), residues: 372 sheet: -0.49 (0.20), residues: 704 loop : -1.41 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 38 TYR 0.012 0.001 TYR C 586 PHE 0.010 0.001 PHE A 159 TRP 0.033 0.002 TRP I 596 HIS 0.007 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00426 (20773) covalent geometry : angle 0.64059 (28237) SS BOND : bond 0.00375 ( 39) SS BOND : angle 1.38629 ( 78) hydrogen bonds : bond 0.03278 ( 477) hydrogen bonds : angle 5.93607 ( 1233) link_ALPHA1-3 : bond 0.00841 ( 9) link_ALPHA1-3 : angle 1.96652 ( 27) link_ALPHA1-6 : bond 0.00462 ( 3) link_ALPHA1-6 : angle 1.74261 ( 9) link_BETA1-4 : bond 0.00331 ( 24) link_BETA1-4 : angle 2.11806 ( 72) link_NAG-ASN : bond 0.00453 ( 62) link_NAG-ASN : angle 2.51501 ( 186) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9524 (ptm) cc_final: 0.7872 (ppp) REVERT: G 373 MET cc_start: 0.8421 (mmt) cc_final: 0.8129 (tpp) REVERT: A 373 MET cc_start: 0.8431 (mtm) cc_final: 0.8090 (mtt) REVERT: A 434 MET cc_start: 0.9254 (ttt) cc_final: 0.8998 (tmm) REVERT: A 475 MET cc_start: 0.7983 (tpp) cc_final: 0.7579 (tpp) REVERT: C 626 MET cc_start: 0.8811 (ttm) cc_final: 0.8377 (tpp) REVERT: F 61 TYR cc_start: 0.8346 (m-80) cc_final: 0.8104 (m-80) REVERT: F 95 MET cc_start: 0.9499 (ppp) cc_final: 0.9265 (ppp) REVERT: F 373 MET cc_start: 0.7997 (ttt) cc_final: 0.7712 (ptm) REVERT: I 577 GLN cc_start: 0.9101 (pt0) cc_final: 0.8133 (tm-30) REVERT: L 95 ASN cc_start: 0.9079 (m110) cc_final: 0.8856 (t0) REVERT: J 90 TYR cc_start: 0.8320 (m-80) cc_final: 0.7804 (m-80) REVERT: J 100 MET cc_start: 0.7410 (pmm) cc_final: 0.7179 (pmm) REVERT: K 95 ASN cc_start: 0.8685 (t0) cc_final: 0.8476 (t0) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1710 time to fit residues: 20.4999 Evaluate side-chains 58 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 85 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 178 optimal weight: 0.2980 chunk 117 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.030544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.024243 restraints weight = 264991.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.024840 restraints weight = 161643.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.025253 restraints weight = 116572.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.025541 restraints weight = 93173.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.025741 restraints weight = 79642.181| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20910 Z= 0.207 Angle : 0.705 12.492 28609 Z= 0.341 Chirality : 0.048 0.441 3458 Planarity : 0.004 0.060 3453 Dihedral : 7.695 59.201 4628 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.17), residues: 2370 helix: -1.06 (0.26), residues: 386 sheet: -0.56 (0.20), residues: 695 loop : -1.44 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 38 TYR 0.014 0.001 TYR C 586 PHE 0.016 0.002 PHE F 277 TRP 0.032 0.002 TRP B 571 HIS 0.005 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00451 (20773) covalent geometry : angle 0.66255 (28237) SS BOND : bond 0.00441 ( 39) SS BOND : angle 1.34850 ( 78) hydrogen bonds : bond 0.03207 ( 477) hydrogen bonds : angle 5.89829 ( 1233) link_ALPHA1-3 : bond 0.00821 ( 9) link_ALPHA1-3 : angle 2.07945 ( 27) link_ALPHA1-6 : bond 0.00348 ( 3) link_ALPHA1-6 : angle 1.81600 ( 9) link_BETA1-4 : bond 0.00331 ( 24) link_BETA1-4 : angle 2.17765 ( 72) link_NAG-ASN : bond 0.00448 ( 62) link_NAG-ASN : angle 2.52123 ( 186) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9533 (ptm) cc_final: 0.8032 (ppp) REVERT: G 373 MET cc_start: 0.8332 (mmt) cc_final: 0.7991 (tpp) REVERT: A 373 MET cc_start: 0.8312 (mtm) cc_final: 0.7910 (ttm) REVERT: A 434 MET cc_start: 0.9274 (ttt) cc_final: 0.9061 (tmm) REVERT: A 475 MET cc_start: 0.8138 (tpp) cc_final: 0.7757 (tpp) REVERT: C 626 MET cc_start: 0.8826 (ttm) cc_final: 0.8352 (tpp) REVERT: F 61 TYR cc_start: 0.8360 (m-80) cc_final: 0.8119 (m-80) REVERT: F 95 MET cc_start: 0.9539 (ppp) cc_final: 0.9321 (ppp) REVERT: F 373 MET cc_start: 0.8131 (ttt) cc_final: 0.7843 (ttt) REVERT: I 577 GLN cc_start: 0.9099 (pt0) cc_final: 0.8102 (tm-30) REVERT: J 90 TYR cc_start: 0.8338 (m-80) cc_final: 0.7922 (m-80) REVERT: K 95 ASN cc_start: 0.8692 (t0) cc_final: 0.8439 (t0) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1701 time to fit residues: 19.0409 Evaluate side-chains 54 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 153 optimal weight: 0.9990 chunk 190 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 208 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 220 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.030561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.024282 restraints weight = 266427.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.024892 restraints weight = 161879.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.025311 restraints weight = 116221.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.025596 restraints weight = 92629.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.025794 restraints weight = 79118.881| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20910 Z= 0.179 Angle : 0.676 13.365 28609 Z= 0.326 Chirality : 0.048 0.427 3458 Planarity : 0.004 0.059 3453 Dihedral : 7.436 59.229 4628 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.17), residues: 2370 helix: -0.83 (0.27), residues: 379 sheet: -0.50 (0.20), residues: 689 loop : -1.42 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 38 TYR 0.014 0.001 TYR F 217 PHE 0.011 0.001 PHE F 277 TRP 0.027 0.002 TRP B 571 HIS 0.004 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00393 (20773) covalent geometry : angle 0.62985 (28237) SS BOND : bond 0.00371 ( 39) SS BOND : angle 1.56604 ( 78) hydrogen bonds : bond 0.03044 ( 477) hydrogen bonds : angle 5.82314 ( 1233) link_ALPHA1-3 : bond 0.00836 ( 9) link_ALPHA1-3 : angle 1.92955 ( 27) link_ALPHA1-6 : bond 0.00256 ( 3) link_ALPHA1-6 : angle 1.87008 ( 9) link_BETA1-4 : bond 0.00316 ( 24) link_BETA1-4 : angle 2.23552 ( 72) link_NAG-ASN : bond 0.00424 ( 62) link_NAG-ASN : angle 2.52365 ( 186) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9511 (ptm) cc_final: 0.9113 (ppp) REVERT: G 373 MET cc_start: 0.8313 (mmt) cc_final: 0.7981 (tpp) REVERT: A 373 MET cc_start: 0.8324 (mtm) cc_final: 0.7881 (ttm) REVERT: A 434 MET cc_start: 0.9278 (ttt) cc_final: 0.9067 (tmm) REVERT: A 475 MET cc_start: 0.8148 (tpp) cc_final: 0.7815 (tpp) REVERT: C 626 MET cc_start: 0.8784 (ttm) cc_final: 0.8354 (tpp) REVERT: F 61 TYR cc_start: 0.8236 (m-80) cc_final: 0.7994 (m-80) REVERT: I 577 GLN cc_start: 0.9069 (pt0) cc_final: 0.8087 (tm-30) REVERT: I 643 TYR cc_start: 0.9392 (m-80) cc_final: 0.9129 (m-80) REVERT: J 90 TYR cc_start: 0.8415 (m-80) cc_final: 0.7985 (m-80) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1497 time to fit residues: 17.1203 Evaluate side-chains 54 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.0470 chunk 114 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 121 optimal weight: 0.0980 chunk 112 optimal weight: 0.8980 chunk 199 optimal weight: 7.9990 chunk 209 optimal weight: 20.0000 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.030982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.024612 restraints weight = 252973.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.025221 restraints weight = 156557.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.025635 restraints weight = 113822.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.025924 restraints weight = 91470.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.026115 restraints weight = 78486.867| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20910 Z= 0.108 Angle : 0.638 12.719 28609 Z= 0.306 Chirality : 0.047 0.409 3458 Planarity : 0.004 0.060 3453 Dihedral : 6.935 59.553 4628 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.09 % Allowed : 1.09 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.17), residues: 2370 helix: -0.41 (0.29), residues: 356 sheet: -0.48 (0.19), residues: 707 loop : -1.37 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 192 TYR 0.011 0.001 TYR H 100B PHE 0.010 0.001 PHE F 391 TRP 0.044 0.001 TRP B 571 HIS 0.003 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00247 (20773) covalent geometry : angle 0.59213 (28237) SS BOND : bond 0.00424 ( 39) SS BOND : angle 1.38550 ( 78) hydrogen bonds : bond 0.02701 ( 477) hydrogen bonds : angle 5.55222 ( 1233) link_ALPHA1-3 : bond 0.00800 ( 9) link_ALPHA1-3 : angle 1.71578 ( 27) link_ALPHA1-6 : bond 0.00391 ( 3) link_ALPHA1-6 : angle 1.90500 ( 9) link_BETA1-4 : bond 0.00428 ( 24) link_BETA1-4 : angle 2.25132 ( 72) link_NAG-ASN : bond 0.00479 ( 62) link_NAG-ASN : angle 2.44191 ( 186) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9548 (ptm) cc_final: 0.9120 (ppp) REVERT: G 373 MET cc_start: 0.8275 (mmt) cc_final: 0.7929 (tpp) REVERT: B 626 MET cc_start: 0.6556 (tpt) cc_final: 0.6206 (tpt) REVERT: B 629 MET cc_start: 0.7955 (tpp) cc_final: 0.7738 (tpp) REVERT: A 373 MET cc_start: 0.8279 (mtm) cc_final: 0.7976 (mtt) REVERT: A 434 MET cc_start: 0.9326 (ttt) cc_final: 0.9069 (tmm) REVERT: A 475 MET cc_start: 0.8123 (tpp) cc_final: 0.7803 (tpp) REVERT: C 626 MET cc_start: 0.8810 (ttm) cc_final: 0.8268 (tpp) REVERT: F 61 TYR cc_start: 0.8280 (m-80) cc_final: 0.8027 (m-80) REVERT: I 577 GLN cc_start: 0.9026 (pt0) cc_final: 0.8507 (tm-30) REVERT: I 626 MET cc_start: 0.7704 (tmm) cc_final: 0.6966 (tmm) REVERT: I 643 TYR cc_start: 0.9444 (m-80) cc_final: 0.9182 (m-80) REVERT: D 100 MET cc_start: 0.8758 (mmm) cc_final: 0.8490 (mmm) REVERT: J 90 TYR cc_start: 0.8391 (m-80) cc_final: 0.7974 (m-80) outliers start: 2 outliers final: 0 residues processed: 82 average time/residue: 0.1618 time to fit residues: 20.7723 Evaluate side-chains 58 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 50 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 209 optimal weight: 0.7980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.030748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.024505 restraints weight = 263206.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.025117 restraints weight = 161647.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.025536 restraints weight = 116579.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.025825 restraints weight = 92963.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.026022 restraints weight = 79380.232| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20910 Z= 0.152 Angle : 0.658 12.969 28609 Z= 0.316 Chirality : 0.047 0.408 3458 Planarity : 0.004 0.058 3453 Dihedral : 6.936 59.962 4628 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.17), residues: 2370 helix: -0.74 (0.27), residues: 383 sheet: -0.38 (0.20), residues: 689 loop : -1.35 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 38 TYR 0.018 0.001 TYR G 217 PHE 0.009 0.001 PHE F 391 TRP 0.036 0.002 TRP G 45 HIS 0.004 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00345 (20773) covalent geometry : angle 0.61419 (28237) SS BOND : bond 0.00381 ( 39) SS BOND : angle 1.41283 ( 78) hydrogen bonds : bond 0.02834 ( 477) hydrogen bonds : angle 5.58149 ( 1233) link_ALPHA1-3 : bond 0.00742 ( 9) link_ALPHA1-3 : angle 1.77771 ( 27) link_ALPHA1-6 : bond 0.00328 ( 3) link_ALPHA1-6 : angle 1.84398 ( 9) link_BETA1-4 : bond 0.00330 ( 24) link_BETA1-4 : angle 2.24083 ( 72) link_NAG-ASN : bond 0.00412 ( 62) link_NAG-ASN : angle 2.43787 ( 186) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9494 (ptm) cc_final: 0.9069 (ppp) REVERT: G 373 MET cc_start: 0.8309 (mmt) cc_final: 0.7960 (tpp) REVERT: A 373 MET cc_start: 0.8285 (mtm) cc_final: 0.7797 (ttm) REVERT: A 434 MET cc_start: 0.9281 (ttt) cc_final: 0.9069 (tmm) REVERT: A 475 MET cc_start: 0.8285 (tpp) cc_final: 0.7966 (tpp) REVERT: C 626 MET cc_start: 0.8715 (ttm) cc_final: 0.8301 (tpp) REVERT: F 61 TYR cc_start: 0.8348 (m-80) cc_final: 0.8037 (m-80) REVERT: I 577 GLN cc_start: 0.9020 (pt0) cc_final: 0.8510 (tm-30) REVERT: I 626 MET cc_start: 0.7655 (tmm) cc_final: 0.6968 (tmm) REVERT: I 629 MET cc_start: 0.8556 (mmm) cc_final: 0.8309 (mmp) REVERT: I 643 TYR cc_start: 0.9425 (m-80) cc_final: 0.9180 (m-80) REVERT: J 90 TYR cc_start: 0.8470 (m-80) cc_final: 0.8041 (m-80) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1593 time to fit residues: 18.7349 Evaluate side-chains 58 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 93 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 4 optimal weight: 0.0770 chunk 122 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 157 optimal weight: 7.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.030153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.023948 restraints weight = 268302.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.024562 restraints weight = 164727.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.024980 restraints weight = 117961.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.025264 restraints weight = 93981.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.025460 restraints weight = 80291.404| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20910 Z= 0.187 Angle : 0.689 12.306 28609 Z= 0.333 Chirality : 0.048 0.427 3458 Planarity : 0.004 0.058 3453 Dihedral : 7.135 56.800 4628 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.17), residues: 2370 helix: -0.81 (0.27), residues: 391 sheet: -0.48 (0.20), residues: 689 loop : -1.40 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 38 TYR 0.014 0.001 TYR C 586 PHE 0.012 0.001 PHE L 67 TRP 0.043 0.002 TRP G 45 HIS 0.005 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00413 (20773) covalent geometry : angle 0.64567 (28237) SS BOND : bond 0.00401 ( 39) SS BOND : angle 1.42950 ( 78) hydrogen bonds : bond 0.03001 ( 477) hydrogen bonds : angle 5.74638 ( 1233) link_ALPHA1-3 : bond 0.00668 ( 9) link_ALPHA1-3 : angle 1.81621 ( 27) link_ALPHA1-6 : bond 0.00292 ( 3) link_ALPHA1-6 : angle 1.82753 ( 9) link_BETA1-4 : bond 0.00289 ( 24) link_BETA1-4 : angle 2.31186 ( 72) link_NAG-ASN : bond 0.00434 ( 62) link_NAG-ASN : angle 2.50284 ( 186) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9535 (ptm) cc_final: 0.8763 (ppp) REVERT: G 373 MET cc_start: 0.8337 (mmt) cc_final: 0.7989 (tpp) REVERT: A 373 MET cc_start: 0.8348 (mtm) cc_final: 0.7897 (ttm) REVERT: A 434 MET cc_start: 0.9304 (ttt) cc_final: 0.9074 (tmm) REVERT: A 475 MET cc_start: 0.8267 (tpp) cc_final: 0.7912 (tpp) REVERT: C 626 MET cc_start: 0.8898 (ttm) cc_final: 0.8399 (tpp) REVERT: F 61 TYR cc_start: 0.8413 (m-80) cc_final: 0.8128 (m-10) REVERT: I 577 GLN cc_start: 0.9047 (pt0) cc_final: 0.8470 (tm-30) REVERT: I 629 MET cc_start: 0.8574 (mmm) cc_final: 0.8341 (mmp) REVERT: I 643 TYR cc_start: 0.9465 (m-80) cc_final: 0.9177 (m-80) REVERT: J 90 TYR cc_start: 0.8643 (m-80) cc_final: 0.8224 (m-80) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1538 time to fit residues: 16.8374 Evaluate side-chains 57 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 6 optimal weight: 8.9990 chunk 192 optimal weight: 20.0000 chunk 219 optimal weight: 20.0000 chunk 134 optimal weight: 0.3980 chunk 61 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.029909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.023769 restraints weight = 269994.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.024372 restraints weight = 164586.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.024786 restraints weight = 118193.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.025073 restraints weight = 94032.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.025268 restraints weight = 80086.888| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20910 Z= 0.188 Angle : 0.695 12.865 28609 Z= 0.336 Chirality : 0.048 0.430 3458 Planarity : 0.004 0.058 3453 Dihedral : 7.169 57.606 4628 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.17), residues: 2370 helix: -0.86 (0.27), residues: 391 sheet: -0.62 (0.19), residues: 704 loop : -1.41 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 54 TYR 0.018 0.001 TYR G 217 PHE 0.010 0.001 PHE F 391 TRP 0.030 0.002 TRP A 112 HIS 0.005 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00415 (20773) covalent geometry : angle 0.64973 (28237) SS BOND : bond 0.00384 ( 39) SS BOND : angle 1.39890 ( 78) hydrogen bonds : bond 0.03020 ( 477) hydrogen bonds : angle 5.77415 ( 1233) link_ALPHA1-3 : bond 0.00663 ( 9) link_ALPHA1-3 : angle 1.76584 ( 27) link_ALPHA1-6 : bond 0.00240 ( 3) link_ALPHA1-6 : angle 1.82705 ( 9) link_BETA1-4 : bond 0.00290 ( 24) link_BETA1-4 : angle 2.40890 ( 72) link_NAG-ASN : bond 0.00424 ( 62) link_NAG-ASN : angle 2.54881 ( 186) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3488.71 seconds wall clock time: 61 minutes 33.95 seconds (3693.95 seconds total)