Starting phenix.real_space_refine on Tue May 20 21:20:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ber_44482/05_2025/9ber_44482.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ber_44482/05_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_44482/05_2025/9ber_44482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ber_44482/05_2025/9ber_44482.map" model { file = "/net/cci-nas-00/data/ceres_data/9ber_44482/05_2025/9ber_44482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ber_44482/05_2025/9ber_44482.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.81, per 1000 atoms: 0.68 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: 6.72 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 3.02 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: 6.98 Time building geometry restraints manager: 7.65 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 505 or resid 601 through 611)) selection = chain 'F' selection = (chain 'G' and (resid 32 through 505 or resid 601 through 611)) } ncs_group { reference = (chain 'B' and (resid 519 through 546 or resid 569 through 661 or resid 701 thro \ ugh 703)) selection = (chain 'C' and (resid 519 through 661 or resid 701 through 703)) selection = (chain 'I' and (resid 519 through 546 or resid 569 through 661 or resid 701 thro \ ugh 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.010 Check model and map are aligned: 0.150 Set scattering table: 0.240 Process input model: 50.710 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.250 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.066 0.001 TRP C 596 HIS 0.004 0.001 HIS A 330 PHE 0.018 0.001 PHE G 317 TYR 0.028 0.001 TYR J 100M ARG 0.013 0.000 ARG L 31 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 62) link_NAG-ASN : angle 3.20165 ( 186) 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_ALPHA1-3 : bond 0.00468 ( 9) link_ALPHA1-3 : angle 1.55297 ( 27) hydrogen bonds : bond 0.30879 ( 477) hydrogen bonds : angle 10.43607 ( 1233) SS BOND : bond 0.00502 ( 39) SS BOND : angle 1.40329 ( 78) covalent geometry : bond 0.00490 (20773) covalent geometry : angle 0.82834 (28237) *********************** 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 : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.8089 (pmm) REVERT: A 434 MET cc_start: 0.9241 (ttt) cc_final: 0.8854 (tmm) REVERT: C 626 MET cc_start: 0.8465 (ttm) cc_final: 0.7974 (tpp) REVERT: C 629 MET cc_start: 0.9266 (mmm) cc_final: 0.8662 (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: 0.8264 (m-10) REVERT: F 167 ASP cc_start: 0.8888 (t0) cc_final: 0.8640 (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: 0.8903 (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: 0.8189 (m-10) outliers start: 5 outliers final: 1 residues processed: 203 average time/residue: 0.4114 time to fit residues: 118.8155 Evaluate side-chains 97 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 chunk 95 optimal weight: 20.0000 chunk 185 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- 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** G 377 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN B 651 ASN A 287 GLN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 ASN I 575 GLN H 5 GLN ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.033176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.026549 restraints weight = 255583.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.027175 restraints weight = 159138.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.027599 restraints weight = 115658.232| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 20910 Z= 0.210 Angle : 0.740 9.955 28609 Z= 0.364 Chirality : 0.050 0.459 3458 Planarity : 0.005 0.099 3453 Dihedral : 11.871 81.441 4628 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.24 % Allowed : 4.02 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.17), residues: 2370 helix: -1.42 (0.25), residues: 358 sheet: -0.47 (0.20), residues: 707 loop : -1.57 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 596 HIS 0.012 0.001 HIS D 68 PHE 0.019 0.002 PHE F 382 TYR 0.014 0.002 TYR F 486 ARG 0.011 0.001 ARG J 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 62) link_NAG-ASN : angle 2.53561 ( 186) link_ALPHA1-6 : bond 0.00316 ( 3) link_ALPHA1-6 : angle 1.77257 ( 9) link_BETA1-4 : bond 0.00460 ( 24) link_BETA1-4 : angle 2.24454 ( 72) link_ALPHA1-3 : bond 0.00854 ( 9) link_ALPHA1-3 : angle 2.27715 ( 27) hydrogen bonds : bond 0.04941 ( 477) hydrogen bonds : angle 7.12432 ( 1233) SS BOND : bond 0.00331 ( 39) SS BOND : angle 1.20273 ( 78) covalent geometry : bond 0.00459 (20773) covalent geometry : angle 0.69980 (28237) *********************** 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: 5 poor density : 114 time to evaluate : 2.488 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: G 95 MET cc_start: 0.9303 (ptm) cc_final: 0.7871 (ppp) REVERT: G 373 MET cc_start: 0.8511 (mmt) cc_final: 0.8130 (tpp) REVERT: B 577 GLN cc_start: 0.9511 (OUTLIER) cc_final: 0.9269 (pt0) REVERT: A 373 MET cc_start: 0.8663 (mtm) cc_final: 0.7972 (mtt) REVERT: A 434 MET cc_start: 0.9328 (ttt) cc_final: 0.9013 (tmm) REVERT: A 475 MET cc_start: 0.8493 (tpp) cc_final: 0.8278 (tpp) REVERT: C 626 MET cc_start: 0.8738 (ttm) cc_final: 0.8239 (tpp) REVERT: C 630 GLU cc_start: 0.9289 (tp30) cc_final: 0.8639 (tp30) REVERT: F 61 TYR cc_start: 0.8640 (m-80) cc_final: 0.8396 (m-10) REVERT: F 104 MET cc_start: 0.9071 (tpp) cc_final: 0.8870 (tpp) REVERT: F 373 MET cc_start: 0.8320 (ptp) cc_final: 0.8094 (mtt) REVERT: I 577 GLN cc_start: 0.9242 (pt0) cc_final: 0.8312 (tm-30) REVERT: I 643 TYR cc_start: 0.9530 (m-80) cc_final: 0.9188 (m-80) REVERT: H 90 TYR cc_start: 0.8851 (m-80) cc_final: 0.8535 (m-10) REVERT: L 95 ASN cc_start: 0.9394 (m110) cc_final: 0.9045 (t0) REVERT: E 90 ILE cc_start: 0.9360 (mm) cc_final: 0.9146 (pt) REVERT: J 90 TYR cc_start: 0.8284 (m-80) cc_final: 0.7748 (m-80) outliers start: 5 outliers final: 0 residues processed: 118 average time/residue: 0.4101 time to fit residues: 71.1582 Evaluate side-chains 76 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 125 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 180 optimal weight: 20.0000 chunk 224 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 226 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 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** H 3 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.030543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.024152 restraints weight = 263977.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.024751 restraints weight = 162763.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.025147 restraints weight = 117664.073| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 20910 Z= 0.309 Angle : 0.856 12.443 28609 Z= 0.416 Chirality : 0.051 0.485 3458 Planarity : 0.005 0.066 3453 Dihedral : 10.050 71.084 4628 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.05 % Allowed : 5.90 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.17), residues: 2370 helix: -1.29 (0.26), residues: 362 sheet: -0.62 (0.20), residues: 704 loop : -1.61 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP G 45 HIS 0.007 0.002 HIS D 52 PHE 0.029 0.002 PHE K 67 TYR 0.030 0.002 TYR H 90 ARG 0.015 0.001 ARG J 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00629 ( 62) link_NAG-ASN : angle 2.78782 ( 186) link_ALPHA1-6 : bond 0.00395 ( 3) link_ALPHA1-6 : angle 1.87165 ( 9) link_BETA1-4 : bond 0.00448 ( 24) link_BETA1-4 : angle 2.23434 ( 72) link_ALPHA1-3 : bond 0.00924 ( 9) link_ALPHA1-3 : angle 2.01509 ( 27) hydrogen bonds : bond 0.04742 ( 477) hydrogen bonds : angle 6.62556 ( 1233) SS BOND : bond 0.00399 ( 39) SS BOND : angle 1.63465 ( 78) covalent geometry : bond 0.00665 (20773) covalent geometry : angle 0.81631 (28237) *********************** 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 88 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9522 (ptm) cc_final: 0.7994 (ppp) REVERT: G 373 MET cc_start: 0.8633 (mmt) cc_final: 0.8326 (tpp) REVERT: G 475 MET cc_start: 0.9133 (tpt) cc_final: 0.8845 (tpp) REVERT: B 626 MET cc_start: 0.8207 (ttt) cc_final: 0.7536 (tmm) REVERT: B 629 MET cc_start: 0.8960 (mmt) cc_final: 0.8554 (mmt) REVERT: B 630 GLU cc_start: 0.9374 (mt-10) cc_final: 0.9080 (mt-10) REVERT: A 373 MET cc_start: 0.8387 (mtm) cc_final: 0.7825 (ttm) REVERT: A 475 MET cc_start: 0.8585 (tpp) cc_final: 0.8347 (tpp) REVERT: C 626 MET cc_start: 0.8828 (ttm) cc_final: 0.8328 (tpp) REVERT: F 61 TYR cc_start: 0.8466 (m-80) cc_final: 0.8185 (m-80) REVERT: I 577 GLN cc_start: 0.9225 (pt0) cc_final: 0.8118 (tm-30) REVERT: I 643 TYR cc_start: 0.9480 (m-80) cc_final: 0.9092 (m-80) REVERT: J 90 TYR cc_start: 0.8407 (m-80) cc_final: 0.8021 (m-80) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.3783 time to fit residues: 51.4105 Evaluate side-chains 61 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 234 optimal weight: 4.9990 chunk 207 optimal weight: 30.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 287 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** ** K 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.029423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.023209 restraints weight = 274937.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.023784 restraints weight = 168214.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.024181 restraints weight = 121534.125| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 20910 Z= 0.363 Angle : 0.894 12.161 28609 Z= 0.434 Chirality : 0.053 0.492 3458 Planarity : 0.006 0.066 3453 Dihedral : 9.597 59.946 4628 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.16), residues: 2370 helix: -1.55 (0.25), residues: 392 sheet: -0.90 (0.20), residues: 683 loop : -1.79 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP I 596 HIS 0.008 0.002 HIS G 374 PHE 0.019 0.002 PHE L 67 TYR 0.023 0.002 TYR C 586 ARG 0.013 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00703 ( 62) link_NAG-ASN : angle 2.97916 ( 186) link_ALPHA1-6 : bond 0.00412 ( 3) link_ALPHA1-6 : angle 2.00478 ( 9) link_BETA1-4 : bond 0.00430 ( 24) link_BETA1-4 : angle 2.40711 ( 72) link_ALPHA1-3 : bond 0.00933 ( 9) link_ALPHA1-3 : angle 2.37936 ( 27) hydrogen bonds : bond 0.04255 ( 477) hydrogen bonds : angle 6.73731 ( 1233) SS BOND : bond 0.00680 ( 39) SS BOND : angle 1.67041 ( 78) covalent geometry : bond 0.00773 (20773) covalent geometry : angle 0.84949 (28237) *********************** 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 69 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9617 (ptm) cc_final: 0.8801 (ppp) REVERT: G 373 MET cc_start: 0.8413 (mmt) cc_final: 0.8027 (tpp) REVERT: B 626 MET cc_start: 0.8352 (ttt) cc_final: 0.7963 (ttt) REVERT: A 373 MET cc_start: 0.8614 (mtm) cc_final: 0.7973 (mtm) REVERT: A 475 MET cc_start: 0.8180 (tpp) cc_final: 0.7908 (tpp) REVERT: C 626 MET cc_start: 0.8931 (ttm) cc_final: 0.8317 (tpp) REVERT: F 61 TYR cc_start: 0.8455 (m-80) cc_final: 0.8144 (m-10) REVERT: F 373 MET cc_start: 0.8539 (mtm) cc_final: 0.8315 (mtm) REVERT: F 434 MET cc_start: 0.9034 (tmm) cc_final: 0.8765 (tmm) REVERT: J 90 TYR cc_start: 0.8567 (m-80) cc_final: 0.8233 (m-80) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.3594 time to fit residues: 39.4110 Evaluate side-chains 52 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 80 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 188 optimal weight: 20.0000 chunk 232 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** A 258 GLN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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 = 0.3037 r_free = 0.3037 target = 0.030053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.023773 restraints weight = 268658.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.024377 restraints weight = 163651.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.024789 restraints weight = 117560.854| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.5081 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= 0.191 Angle : 0.714 12.692 28609 Z= 0.345 Chirality : 0.049 0.481 3458 Planarity : 0.004 0.065 3453 Dihedral : 8.630 59.406 4628 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.17), residues: 2370 helix: -1.32 (0.25), residues: 399 sheet: -0.84 (0.19), residues: 689 loop : -1.72 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 596 HIS 0.005 0.001 HIS D 52 PHE 0.016 0.002 PHE E 62 TYR 0.016 0.001 TYR H 90 ARG 0.009 0.001 ARG G 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 62) link_NAG-ASN : angle 2.69278 ( 186) link_ALPHA1-6 : bond 0.00459 ( 3) link_ALPHA1-6 : angle 2.04529 ( 9) link_BETA1-4 : bond 0.00338 ( 24) link_BETA1-4 : angle 2.35238 ( 72) link_ALPHA1-3 : bond 0.00846 ( 9) link_ALPHA1-3 : angle 1.92597 ( 27) hydrogen bonds : bond 0.03497 ( 477) hydrogen bonds : angle 6.23482 ( 1233) SS BOND : bond 0.00418 ( 39) SS BOND : angle 1.52440 ( 78) covalent geometry : bond 0.00421 (20773) covalent geometry : angle 0.66543 (28237) *********************** 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 72 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9564 (ptm) cc_final: 0.8803 (ppp) REVERT: G 373 MET cc_start: 0.8371 (mmt) cc_final: 0.8064 (tpp) REVERT: B 629 MET cc_start: 0.8977 (mmt) cc_final: 0.8159 (mmt) REVERT: A 373 MET cc_start: 0.8389 (mtm) cc_final: 0.7889 (ttm) REVERT: C 589 ASP cc_start: 0.9074 (p0) cc_final: 0.8824 (p0) REVERT: C 626 MET cc_start: 0.8959 (ttm) cc_final: 0.8444 (tpp) REVERT: F 61 TYR cc_start: 0.8482 (m-80) cc_final: 0.8260 (m-10) REVERT: I 577 GLN cc_start: 0.9194 (pt0) cc_final: 0.8088 (tm-30) REVERT: I 629 MET cc_start: 0.8483 (mmm) cc_final: 0.8263 (tpp) REVERT: E 6 PHE cc_start: 0.9511 (m-80) cc_final: 0.9286 (m-80) REVERT: J 90 TYR cc_start: 0.8557 (m-80) cc_final: 0.8208 (m-80) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.3428 time to fit residues: 39.8399 Evaluate side-chains 52 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 103 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 221 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** ** L 17 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 = 0.3036 r_free = 0.3036 target = 0.029957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.023738 restraints weight = 267868.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.024332 restraints weight = 164558.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.024746 restraints weight = 118634.947| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.5209 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= 0.176 Angle : 0.699 13.389 28609 Z= 0.335 Chirality : 0.049 0.462 3458 Planarity : 0.004 0.062 3453 Dihedral : 8.132 59.344 4628 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.17), residues: 2370 helix: -1.14 (0.26), residues: 399 sheet: -0.87 (0.19), residues: 719 loop : -1.63 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 45 HIS 0.004 0.001 HIS D 52 PHE 0.011 0.001 PHE F 391 TYR 0.016 0.001 TYR C 586 ARG 0.009 0.000 ARG K 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 62) link_NAG-ASN : angle 2.70226 ( 186) link_ALPHA1-6 : bond 0.00428 ( 3) link_ALPHA1-6 : angle 2.01916 ( 9) link_BETA1-4 : bond 0.00347 ( 24) link_BETA1-4 : angle 2.33904 ( 72) link_ALPHA1-3 : bond 0.00787 ( 9) link_ALPHA1-3 : angle 1.93299 ( 27) hydrogen bonds : bond 0.03248 ( 477) hydrogen bonds : angle 6.08432 ( 1233) SS BOND : bond 0.00433 ( 39) SS BOND : angle 1.34680 ( 78) covalent geometry : bond 0.00389 (20773) covalent geometry : angle 0.65084 (28237) *********************** 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 68 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9508 (ptm) cc_final: 0.8394 (ppp) REVERT: G 373 MET cc_start: 0.8376 (mmt) cc_final: 0.8052 (tpp) REVERT: B 535 MET cc_start: 0.9069 (pmm) cc_final: 0.8844 (pmm) REVERT: A 373 MET cc_start: 0.8361 (mtm) cc_final: 0.7917 (ttm) REVERT: A 475 MET cc_start: 0.8124 (tpp) cc_final: 0.7849 (tpp) REVERT: C 589 ASP cc_start: 0.9064 (p0) cc_final: 0.8760 (p0) REVERT: C 626 MET cc_start: 0.8919 (ttm) cc_final: 0.8446 (tpp) REVERT: F 61 TYR cc_start: 0.8492 (m-80) cc_final: 0.8242 (m-10) REVERT: I 577 GLN cc_start: 0.9167 (pt0) cc_final: 0.8131 (tm-30) REVERT: I 629 MET cc_start: 0.8555 (mmm) cc_final: 0.8258 (tpp) REVERT: E 6 PHE cc_start: 0.9511 (m-80) cc_final: 0.9278 (m-80) REVERT: J 90 TYR cc_start: 0.8711 (m-80) cc_final: 0.8402 (m-80) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.3416 time to fit residues: 37.5094 Evaluate side-chains 55 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 149 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 208 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 230 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 233 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- 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 577 GLN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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 = 0.3029 r_free = 0.3029 target = 0.029776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.023593 restraints weight = 268866.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.024192 restraints weight = 165407.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.024599 restraints weight = 118835.439| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20910 Z= 0.183 Angle : 0.694 13.246 28609 Z= 0.334 Chirality : 0.048 0.458 3458 Planarity : 0.004 0.062 3453 Dihedral : 7.807 58.958 4628 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.17), residues: 2370 helix: -1.07 (0.26), residues: 393 sheet: -0.85 (0.19), residues: 719 loop : -1.61 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 45 HIS 0.004 0.001 HIS D 52 PHE 0.011 0.001 PHE F 391 TYR 0.014 0.001 TYR C 586 ARG 0.014 0.001 ARG G 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 62) link_NAG-ASN : angle 2.66259 ( 186) link_ALPHA1-6 : bond 0.00420 ( 3) link_ALPHA1-6 : angle 1.99296 ( 9) link_BETA1-4 : bond 0.00334 ( 24) link_BETA1-4 : angle 2.37055 ( 72) link_ALPHA1-3 : bond 0.00779 ( 9) link_ALPHA1-3 : angle 1.86327 ( 27) hydrogen bonds : bond 0.03157 ( 477) hydrogen bonds : angle 5.98163 ( 1233) SS BOND : bond 0.00398 ( 39) SS BOND : angle 1.46515 ( 78) covalent geometry : bond 0.00404 (20773) covalent geometry : angle 0.64533 (28237) *********************** 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 67 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9502 (ptm) cc_final: 0.9022 (ppp) REVERT: G 373 MET cc_start: 0.8359 (mmt) cc_final: 0.8025 (tpp) REVERT: A 373 MET cc_start: 0.8383 (mtm) cc_final: 0.7942 (mtm) REVERT: C 626 MET cc_start: 0.8896 (ttm) cc_final: 0.8463 (tpp) REVERT: F 61 TYR cc_start: 0.8585 (m-80) cc_final: 0.8366 (m-10) REVERT: I 577 GLN cc_start: 0.9143 (pt0) cc_final: 0.8496 (tm-30) REVERT: E 6 PHE cc_start: 0.9493 (m-80) cc_final: 0.9252 (m-80) REVERT: J 90 TYR cc_start: 0.8775 (m-80) cc_final: 0.8283 (m-80) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.3488 time to fit residues: 37.3386 Evaluate side-chains 53 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 6 optimal weight: 9.9990 chunk 113 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 0.0070 chunk 123 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 overall best weight: 3.1204 ------------------------------------------------------------------------------- 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** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 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 = 0.3035 r_free = 0.3035 target = 0.029868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.023709 restraints weight = 267884.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.024308 restraints weight = 163081.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.024716 restraints weight = 117132.984| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.5507 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= 0.162 Angle : 0.680 12.726 28609 Z= 0.326 Chirality : 0.048 0.452 3458 Planarity : 0.004 0.062 3453 Dihedral : 7.597 59.089 4628 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.17), residues: 2370 helix: -1.00 (0.26), residues: 399 sheet: -0.81 (0.19), residues: 719 loop : -1.59 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 571 HIS 0.005 0.001 HIS F 374 PHE 0.010 0.001 PHE F 391 TYR 0.013 0.001 TYR C 586 ARG 0.005 0.000 ARG J 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 62) link_NAG-ASN : angle 2.71695 ( 186) link_ALPHA1-6 : bond 0.00344 ( 3) link_ALPHA1-6 : angle 2.00157 ( 9) link_BETA1-4 : bond 0.00338 ( 24) link_BETA1-4 : angle 2.38996 ( 72) link_ALPHA1-3 : bond 0.00718 ( 9) link_ALPHA1-3 : angle 1.81433 ( 27) hydrogen bonds : bond 0.02985 ( 477) hydrogen bonds : angle 5.92508 ( 1233) SS BOND : bond 0.00411 ( 39) SS BOND : angle 1.39272 ( 78) covalent geometry : bond 0.00359 (20773) covalent geometry : angle 0.62873 (28237) *********************** 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 69 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9486 (ptm) cc_final: 0.9046 (ppp) REVERT: G 373 MET cc_start: 0.8377 (mmt) cc_final: 0.8030 (tpp) REVERT: G 475 MET cc_start: 0.9029 (mmm) cc_final: 0.8738 (mmm) REVERT: B 535 MET cc_start: 0.9031 (pmm) cc_final: 0.8744 (pmm) REVERT: A 373 MET cc_start: 0.8373 (mtm) cc_final: 0.7864 (mtm) REVERT: C 530 MET cc_start: 0.8116 (tmm) cc_final: 0.7042 (tmm) REVERT: C 626 MET cc_start: 0.8861 (ttm) cc_final: 0.8448 (tpp) REVERT: F 61 TYR cc_start: 0.8617 (m-80) cc_final: 0.8328 (m-10) REVERT: I 577 GLN cc_start: 0.9124 (pt0) cc_final: 0.8501 (tm-30) REVERT: I 629 MET cc_start: 0.8269 (mmm) cc_final: 0.8024 (mmp) REVERT: I 643 TYR cc_start: 0.9444 (m-10) cc_final: 0.9160 (m-80) REVERT: E 6 PHE cc_start: 0.9503 (m-80) cc_final: 0.9257 (m-80) REVERT: J 90 TYR cc_start: 0.8806 (m-80) cc_final: 0.8346 (m-80) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.3544 time to fit residues: 38.8223 Evaluate side-chains 55 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 167 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 221 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 chunk 199 optimal weight: 30.0000 chunk 203 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 211 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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** ** L 17 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 = 0.3032 r_free = 0.3032 target = 0.029763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.023638 restraints weight = 268826.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.024229 restraints weight = 163751.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.024635 restraints weight = 117821.005| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20910 Z= 0.166 Angle : 0.690 12.736 28609 Z= 0.330 Chirality : 0.048 0.448 3458 Planarity : 0.004 0.061 3453 Dihedral : 7.473 59.169 4628 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.17), residues: 2370 helix: -0.93 (0.27), residues: 393 sheet: -0.81 (0.19), residues: 713 loop : -1.56 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 45 HIS 0.004 0.001 HIS D 52 PHE 0.009 0.001 PHE F 391 TYR 0.014 0.001 TYR C 586 ARG 0.005 0.000 ARG J 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 62) link_NAG-ASN : angle 2.69728 ( 186) link_ALPHA1-6 : bond 0.00363 ( 3) link_ALPHA1-6 : angle 1.96046 ( 9) link_BETA1-4 : bond 0.00328 ( 24) link_BETA1-4 : angle 2.41273 ( 72) link_ALPHA1-3 : bond 0.00714 ( 9) link_ALPHA1-3 : angle 1.81867 ( 27) hydrogen bonds : bond 0.02970 ( 477) hydrogen bonds : angle 5.86830 ( 1233) SS BOND : bond 0.00399 ( 39) SS BOND : angle 1.32632 ( 78) covalent geometry : bond 0.00370 (20773) covalent geometry : angle 0.64094 (28237) *********************** 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 68 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9488 (ptm) cc_final: 0.7950 (ppp) REVERT: G 373 MET cc_start: 0.8375 (mmt) cc_final: 0.8024 (tpp) REVERT: G 475 MET cc_start: 0.9099 (mmm) cc_final: 0.8673 (mmm) REVERT: B 535 MET cc_start: 0.9036 (pmm) cc_final: 0.8729 (pmm) REVERT: A 373 MET cc_start: 0.8419 (mtm) cc_final: 0.7913 (mtm) REVERT: C 530 MET cc_start: 0.8185 (tmm) cc_final: 0.7121 (tmm) REVERT: C 626 MET cc_start: 0.8830 (ttm) cc_final: 0.8389 (tpp) REVERT: F 61 TYR cc_start: 0.8637 (m-80) cc_final: 0.8322 (m-10) REVERT: I 577 GLN cc_start: 0.9090 (pt0) cc_final: 0.8499 (tm-30) REVERT: I 626 MET cc_start: 0.7887 (tmm) cc_final: 0.7026 (tmm) REVERT: I 629 MET cc_start: 0.8385 (mmm) cc_final: 0.8145 (mmp) REVERT: I 643 TYR cc_start: 0.9447 (m-10) cc_final: 0.9136 (m-80) REVERT: E 6 PHE cc_start: 0.9512 (m-80) cc_final: 0.9270 (m-80) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.3432 time to fit residues: 37.6549 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 : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 138 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 chunk 229 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 216 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 164 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 66 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** ** L 17 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** ** K 89 HIS ** 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 = 0.2998 r_free = 0.2998 target = 0.029061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.023014 restraints weight = 273423.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.023596 restraints weight = 166437.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.023994 restraints weight = 119637.325| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20910 Z= 0.267 Angle : 0.790 12.211 28609 Z= 0.381 Chirality : 0.050 0.483 3458 Planarity : 0.005 0.063 3453 Dihedral : 7.979 59.586 4628 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.16), residues: 2370 helix: -1.17 (0.25), residues: 397 sheet: -0.95 (0.20), residues: 668 loop : -1.70 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 571 HIS 0.005 0.001 HIS F 249 PHE 0.013 0.002 PHE F 53 TYR 0.026 0.002 TYR F 217 ARG 0.007 0.001 ARG A 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 62) link_NAG-ASN : angle 2.86244 ( 186) link_ALPHA1-6 : bond 0.00327 ( 3) link_ALPHA1-6 : angle 2.00651 ( 9) link_BETA1-4 : bond 0.00342 ( 24) link_BETA1-4 : angle 2.55964 ( 72) link_ALPHA1-3 : bond 0.00705 ( 9) link_ALPHA1-3 : angle 2.00871 ( 27) hydrogen bonds : bond 0.03487 ( 477) hydrogen bonds : angle 6.25966 ( 1233) SS BOND : bond 0.00434 ( 39) SS BOND : angle 1.54705 ( 78) covalent geometry : bond 0.00579 (20773) covalent geometry : angle 0.74164 (28237) ********************** 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 62 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9539 (ptm) cc_final: 0.8782 (ppp) REVERT: G 373 MET cc_start: 0.8443 (mmt) cc_final: 0.8053 (tpp) REVERT: G 475 MET cc_start: 0.9240 (mmm) cc_final: 0.8729 (mmm) REVERT: A 100 MET cc_start: 0.9065 (mtm) cc_final: 0.8752 (mtm) REVERT: A 373 MET cc_start: 0.8492 (mtm) cc_final: 0.7901 (mtm) REVERT: C 530 MET cc_start: 0.8285 (tmm) cc_final: 0.7144 (tmm) REVERT: C 626 MET cc_start: 0.8910 (ttm) cc_final: 0.8432 (tpp) REVERT: F 373 MET cc_start: 0.8391 (ttt) cc_final: 0.8123 (ttt) REVERT: I 577 GLN cc_start: 0.9182 (pt0) cc_final: 0.8508 (tm-30) REVERT: I 626 MET cc_start: 0.7735 (tmm) cc_final: 0.6904 (tmm) REVERT: I 629 MET cc_start: 0.8480 (mmm) cc_final: 0.8154 (mmp) REVERT: E 6 PHE cc_start: 0.9526 (m-80) cc_final: 0.9276 (m-80) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.3376 time to fit residues: 34.3770 Evaluate side-chains 49 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 37 optimal weight: 0.8980 chunk 191 optimal weight: 10.0000 chunk 211 optimal weight: 0.0870 chunk 215 optimal weight: 9.9990 chunk 138 optimal weight: 0.5980 chunk 229 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 overall best weight: 1.5162 ------------------------------------------------------------------------------- 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** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 HIS ** 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 = 0.3038 r_free = 0.3038 target = 0.029847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.023730 restraints weight = 268498.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.024332 restraints weight = 163327.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.024749 restraints weight = 117008.510| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20910 Z= 0.122 Angle : 0.676 12.742 28609 Z= 0.322 Chirality : 0.048 0.448 3458 Planarity : 0.004 0.065 3453 Dihedral : 7.339 59.973 4628 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.17), residues: 2370 helix: -0.96 (0.26), residues: 404 sheet: -0.83 (0.19), residues: 695 loop : -1.57 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 45 HIS 0.004 0.001 HIS A 216 PHE 0.009 0.001 PHE F 391 TYR 0.011 0.001 TYR F 486 ARG 0.008 0.000 ARG J 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 62) link_NAG-ASN : angle 2.68630 ( 186) link_ALPHA1-6 : bond 0.00307 ( 3) link_ALPHA1-6 : angle 1.94467 ( 9) link_BETA1-4 : bond 0.00401 ( 24) link_BETA1-4 : angle 2.52445 ( 72) link_ALPHA1-3 : bond 0.00716 ( 9) link_ALPHA1-3 : angle 1.67229 ( 27) hydrogen bonds : bond 0.02898 ( 477) hydrogen bonds : angle 5.84914 ( 1233) SS BOND : bond 0.00407 ( 39) SS BOND : angle 1.25356 ( 78) covalent geometry : bond 0.00279 (20773) covalent geometry : angle 0.62509 (28237) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5390.65 seconds wall clock time: 96 minutes 29.52 seconds (5789.52 seconds total)