Starting phenix.real_space_refine on Mon Aug 25 06:10:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dok_27596/08_2025/8dok_27596.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dok_27596/08_2025/8dok_27596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dok_27596/08_2025/8dok_27596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dok_27596/08_2025/8dok_27596.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dok_27596/08_2025/8dok_27596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dok_27596/08_2025/8dok_27596.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.048 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 135 5.16 5 C 16219 2.51 5 N 4324 2.21 5 O 5166 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25844 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3458 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 23, 'TRANS': 413} Chain breaks: 4 Chain: "B" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 970 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "E" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3442 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 4 Chain: "F" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 939 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "G" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "H" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "I" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3438 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 23, 'TRANS': 410} Chain breaks: 4 Chain: "J" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 966 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "K" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "M" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "N" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "O" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "P" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "Q" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "R" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "S" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "Z" 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: "b" 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: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "j" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" 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: "F" 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: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "J" 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: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.64, per 1000 atoms: 0.18 Number of scatterers: 25844 At special positions: 0 Unit cell: (162.68, 164.34, 149.4, 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 135 16.00 O 5166 8.00 N 4324 7.00 C 16219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 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=2.01 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.00 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.51 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 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 ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN S 8 " - " MAN S 9 " " MAN Y 4 " - " MAN Y 5 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN Z 4 " - " MAN Z 5 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " " MAN i 8 " - " MAN i 9 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 7 " - " MAN Y 10 " " BMA Z 3 " - " MAN Z 4 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " ALPHA1-6 " BMA S 3 " - " MAN S 7 " " MAN S 7 " - " MAN S 8 " " BMA Y 3 " - " MAN Y 7 " " MAN Y 7 " - " MAN Y 8 " " BMA Z 3 " - " MAN Z 6 " " BMA i 3 " - " MAN i 7 " " MAN i 7 " - " MAN i 8 " " BMA j 3 " - " MAN j 5 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " NAG U 3 " " NAG U 3 " - " NAG U 4 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " NAG b 3 " " NAG b 3 " - " NAG b 4 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " NAG m 3 " " NAG m 3 " - " NAG m 4 " " 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 s 2 " - " BMA s 3 " NAG-ASN " NAG A1001 " - " ASN A 160 " " NAG A1002 " - " ASN A 241 " " NAG A1003 " - " ASN A 295 " " NAG A1004 " - " ASN A 301 " " NAG A1005 " - " ASN A 448 " " NAG A1006 " - " ASN A 156 " " NAG A1007 " - " ASN A 289 " " NAG A1008 " - " ASN A 392 " " NAG A1009 " - " ASN A 197 " " NAG A1010 " - " ASN A 130 " " NAG B 701 " - " ASN B 616 " " NAG B 702 " - " ASN B 625 " " NAG C 301 " - " ASN C 82B" " NAG E 601 " - " ASN E 160 " " NAG E 602 " - " ASN E 241 " " NAG E 603 " - " ASN E 295 " " NAG E 604 " - " ASN E 301 " " NAG E 605 " - " ASN E 355 " " NAG E 606 " - " ASN E 448 " " NAG E 607 " - " ASN E 156 " " NAG E 608 " - " ASN E 289 " " NAG E 609 " - " ASN E 386 " " NAG E 610 " - " ASN E 392 " " NAG E 611 " - " ASN E 197 " " NAG E 612 " - " ASN E 130 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 616 " " NAG F 703 " - " ASN F 625 " " NAG G 301 " - " ASN G 82B" " NAG I 601 " - " ASN I 160 " " NAG I 602 " - " ASN I 241 " " NAG I 603 " - " ASN I 295 " " NAG I 604 " - " ASN I 301 " " NAG I 605 " - " ASN I 355 " " NAG I 606 " - " ASN I 448 " " NAG I 607 " - " ASN I 156 " " NAG I 608 " - " ASN I 386 " " NAG I 609 " - " ASN I 392 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 616 " " NAG J 703 " - " ASN J 625 " " NAG K 301 " - " ASN K 82B" " NAG S 1 " - " ASN A 234 " " NAG T 1 " - " ASN A 276 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 262 " " NAG X 1 " - " ASN B 637 " " NAG Y 1 " - " ASN E 234 " " NAG Z 1 " - " ASN E 276 " " NAG b 1 " - " ASN E 332 " " NAG g 1 " - " ASN E 262 " " NAG h 1 " - " ASN F 637 " " NAG i 1 " - " ASN I 234 " " NAG j 1 " - " ASN I 276 " " NAG l 1 " - " ASN I 289 " " NAG m 1 " - " ASN I 332 " " NAG p 1 " - " ASN I 197 " " NAG q 1 " - " ASN I 130 " " NAG r 1 " - " ASN I 262 " " NAG s 1 " - " ASN J 637 " Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 789.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5672 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 67 sheets defined 15.8% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.664A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.722A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'B' and resid 529 through 541 removed outlier: 4.127A pdb=" N ILE B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 4.070A pdb=" N ILE B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 60 through 65 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 115 Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.534A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 474 through 480 removed outlier: 3.506A pdb=" N ASN E 478 " --> pdb=" O ILE E 475 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG E 480 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 536 removed outlier: 3.889A pdb=" N ILE F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.550A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 removed outlier: 3.965A pdb=" N ASN F 625 " --> pdb=" O GLU F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.658A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 98 No H-bonds generated for 'chain 'I' and resid 96 through 98' Processing helix chain 'I' and resid 99 through 116 Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.549A pdb=" N CYS I 126 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 197 No H-bonds generated for 'chain 'I' and resid 195 through 197' Processing helix chain 'I' and resid 334 through 353 Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 475 through 479 Processing helix chain 'J' and resid 529 through 537 removed outlier: 3.895A pdb=" N ILE J 535 " --> pdb=" O GLY J 531 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR J 536 " --> pdb=" O ALA J 532 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 596 removed outlier: 3.827A pdb=" N ILE J 573 " --> pdb=" O THR J 569 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS J 574 " --> pdb=" O VAL J 570 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN J 575 " --> pdb=" O TRP J 571 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP J 596 " --> pdb=" O PHE J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 624 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 662 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 99 through 100C removed outlier: 3.636A pdb=" N SER K 100B" --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY K 100C" --> pdb=" O ARG K 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 99 through 100C' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 60 through 64 Processing helix chain 'N' and resid 79 through 84 removed outlier: 3.910A pdb=" N ALA N 84 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 100D through 100H Processing helix chain 'P' and resid 79 through 84 removed outlier: 3.547A pdb=" N ALA P 84 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 64 Processing helix chain 'R' and resid 79 through 84 removed outlier: 4.195A pdb=" N ALA R 84 " --> pdb=" O ALA R 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.497A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.352A pdb=" N LYS A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.473A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N LYS A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.612A pdb=" N ILE A 294 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N LEU A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N VAL A 292 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 9.689A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 357 through 361 Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 7.130A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.689A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N VAL A 292 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N LEU A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.612A pdb=" N ILE A 294 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N LYS A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 457 current: chain 'A' and resid 413 through 418 Processing sheet with id=AA9, first strand: chain 'A' and resid 302 through 312 removed outlier: 6.790A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A 319 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 377 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.549A pdb=" N VAL C 5 " --> pdb=" O LYS C 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.769A pdb=" N GLU C 10 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG C 38 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TYR C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.769A pdb=" N GLU C 10 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 100E through 100F Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.724A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.658A pdb=" N VAL D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR D 49 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AB9, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.193A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC5, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.292A pdb=" N LYS E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.254A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.935A pdb=" N LEU E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.200A pdb=" N PHE E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.928A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.538A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER E 334 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 271 through 273 removed outlier: 11.538A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.928A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.200A pdb=" N PHE E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.935A pdb=" N LEU E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.574A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.651A pdb=" N GLU G 10 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG G 38 " --> pdb=" O TYR G 47 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N TYR G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.651A pdb=" N GLU G 10 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER G 102 " --> pdb=" O THR G 94 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 100E through 100F Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.658A pdb=" N VAL H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.543A pdb=" N VAL H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AD7, first strand: chain 'I' and resid 494 through 499 removed outlier: 5.137A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N TYR I 40 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N CYS J 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AD9, first strand: chain 'I' and resid 53 through 55 removed outlier: 3.535A pdb=" N PHE I 53 " --> pdb=" O CYS I 218 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 66 through 67 removed outlier: 6.328A pdb=" N HIS I 66 " --> pdb=" O SER I 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AE3, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=AE4, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.648A pdb=" N LYS I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.239A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY I 451 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 10.510A pdb=" N GLU I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 11.873A pdb=" N LEU I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 12.450A pdb=" N PHE I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 10.746A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 11.465A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 11.995A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 284 through 298 current: chain 'I' and resid 357 through 360 Processing sheet with id=AE6, first strand: chain 'I' and resid 271 through 274 removed outlier: 11.995A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 11.465A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.746A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.450A pdb=" N PHE I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 11.873A pdb=" N LEU I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.510A pdb=" N GLU I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY I 451 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 443 through 457 current: chain 'I' and resid 414 through 418 Processing sheet with id=AE7, first strand: chain 'I' and resid 302 through 312 removed outlier: 4.926A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 374 through 377 Processing sheet with id=AE9, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.472A pdb=" N GLU K 10 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N TYR K 33 " --> pdb=" O TRP K 52 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N TRP K 52 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL K 35 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN K 50 " --> pdb=" O VAL K 35 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.472A pdb=" N GLU K 10 " --> pdb=" O SER K 110 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 100E through 100F Processing sheet with id=AF4, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.531A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.625A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AF7, first strand: chain 'M' and resid 5 through 7 removed outlier: 3.565A pdb=" N THR M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS M 22 " --> pdb=" O LEU M 78 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN M 77 " --> pdb=" O ASP M 72 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER M 79 " --> pdb=" O SER M 70 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AF9, first strand: chain 'M' and resid 47 through 51 removed outlier: 4.823A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TRP M 36 " --> pdb=" O GLY M 49 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL M 89 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 20 through 22 Processing sheet with id=AG2, first strand: chain 'N' and resid 45 through 49 removed outlier: 6.695A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 11 through 12 Processing sheet with id=AG4, first strand: chain 'O' and resid 18 through 23 removed outlier: 3.882A pdb=" N LYS O 81 " --> pdb=" O VAL O 68 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 57 through 59 removed outlier: 4.815A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL O 89 " --> pdb=" O GLN O 39 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 57 through 59 removed outlier: 4.815A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR O 94 " --> pdb=" O ASP O 101 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 45 through 48 removed outlier: 3.754A pdb=" N ILE P 45 " --> pdb=" O GLN P 37 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN P 37 " --> pdb=" O ILE P 45 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 4 through 6 removed outlier: 3.577A pdb=" N SER Q 79 " --> pdb=" O SER Q 70 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER Q 70 " --> pdb=" O SER Q 79 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS Q 81 " --> pdb=" O VAL Q 68 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 11 through 12 Processing sheet with id=AH1, first strand: chain 'Q' and resid 57 through 58 removed outlier: 4.873A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL Q 89 " --> pdb=" O GLN Q 39 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N THR Q 94 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP Q 101 " --> pdb=" O THR Q 94 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.937A pdb=" N LEU R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'R' and resid 19 through 22 Processing sheet with id=AH4, first strand: chain 'R' and resid 45 through 48 removed outlier: 4.885A pdb=" N LEU R 46 " --> pdb=" O GLN R 37 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLN R 37 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE R 48 " --> pdb=" O TRP R 35 " (cutoff:3.500A) 841 hydrogen bonds defined for protein. 2175 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: 4.91 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4013 1.30 - 1.43: 7222 1.43 - 1.56: 14985 1.56 - 1.69: 5 1.69 - 1.82: 180 Bond restraints: 26405 Sorted by residual: bond pdb=" C CYS I 331 " pdb=" N ASN I 332 " ideal model delta sigma weight residual 1.330 1.201 0.128 1.39e-02 5.18e+03 8.50e+01 bond pdb=" CA ALA E 70 " pdb=" C ALA E 70 " ideal model delta sigma weight residual 1.526 1.435 0.091 1.29e-02 6.01e+03 4.96e+01 bond pdb=" C ASN I 156 " pdb=" N CYS I 157 " ideal model delta sigma weight residual 1.329 1.231 0.098 1.44e-02 4.82e+03 4.62e+01 bond pdb=" C ASN I 130 " pdb=" N CYS I 131 " ideal model delta sigma weight residual 1.329 1.414 -0.084 1.36e-02 5.41e+03 3.85e+01 bond pdb=" C LEU I 129 " pdb=" O LEU I 129 " ideal model delta sigma weight residual 1.236 1.174 0.062 1.21e-02 6.83e+03 2.63e+01 ... (remaining 26400 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 35107 2.79 - 5.58: 628 5.58 - 8.37: 110 8.37 - 11.16: 10 11.16 - 13.96: 4 Bond angle restraints: 35859 Sorted by residual: angle pdb=" N HIS A 72 " pdb=" CA HIS A 72 " pdb=" C HIS A 72 " ideal model delta sigma weight residual 113.97 100.01 13.96 1.28e+00 6.10e-01 1.19e+02 angle pdb=" N SER H 7 " pdb=" CA SER H 7 " pdb=" C SER H 7 " ideal model delta sigma weight residual 112.55 124.13 -11.58 1.35e+00 5.49e-01 7.36e+01 angle pdb=" N GLN E 432 " pdb=" CA GLN E 432 " pdb=" C GLN E 432 " ideal model delta sigma weight residual 109.96 122.68 -12.72 1.49e+00 4.50e-01 7.28e+01 angle pdb=" CA GLY I 263 " pdb=" C GLY I 263 " pdb=" O GLY I 263 " ideal model delta sigma weight residual 122.28 114.28 8.00 1.00e+00 1.00e+00 6.41e+01 angle pdb=" CA GLY A 263 " pdb=" C GLY A 263 " pdb=" O GLY A 263 " ideal model delta sigma weight residual 122.47 114.96 7.51 1.08e+00 8.57e-01 4.83e+01 ... (remaining 35854 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.75: 15998 23.75 - 47.50: 840 47.50 - 71.26: 184 71.26 - 95.01: 101 95.01 - 118.76: 83 Dihedral angle restraints: 17206 sinusoidal: 8356 harmonic: 8850 Sorted by residual: dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 92 " pdb=" CB CYS M 92 " ideal model delta sinusoidal sigma weight residual 93.00 30.57 62.43 1 1.00e+01 1.00e-02 5.16e+01 dihedral pdb=" CB CYS I 126 " pdb=" SG CYS I 126 " pdb=" SG CYS I 196 " pdb=" CB CYS I 196 " ideal model delta sinusoidal sigma weight residual -86.00 -143.88 57.88 1 1.00e+01 1.00e-02 4.50e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 35.40 57.60 1 1.00e+01 1.00e-02 4.46e+01 ... (remaining 17203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 4230 0.164 - 0.328: 80 0.328 - 0.492: 13 0.492 - 0.657: 7 0.657 - 0.821: 2 Chirality restraints: 4332 Sorted by residual: chirality pdb=" C1 NAG A1007 " pdb=" ND2 ASN A 289 " pdb=" C2 NAG A1007 " pdb=" O5 NAG A1007 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.68e+01 chirality pdb=" C1 NAG E 602 " pdb=" ND2 ASN E 241 " pdb=" C2 NAG E 602 " pdb=" O5 NAG E 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" CA TRP E 69 " pdb=" N TRP E 69 " pdb=" C TRP E 69 " pdb=" CB TRP E 69 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 4329 not shown) Planarity restraints: 4444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1007 " -0.352 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG A1007 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG A1007 " -0.159 2.00e-02 2.50e+03 pdb=" N2 NAG A1007 " 0.532 2.00e-02 2.50e+03 pdb=" O7 NAG A1007 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 1 " 0.238 2.00e-02 2.50e+03 2.02e-01 5.12e+02 pdb=" C7 NAG V 1 " -0.061 2.00e-02 2.50e+03 pdb=" C8 NAG V 1 " 0.160 2.00e-02 2.50e+03 pdb=" N2 NAG V 1 " -0.345 2.00e-02 2.50e+03 pdb=" O7 NAG V 1 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 1 " -0.238 2.00e-02 2.50e+03 1.97e-01 4.87e+02 pdb=" C7 NAG T 1 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG T 1 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG T 1 " 0.324 2.00e-02 2.50e+03 pdb=" O7 NAG T 1 " 0.017 2.00e-02 2.50e+03 ... (remaining 4441 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 735 2.69 - 3.24: 24020 3.24 - 3.79: 39448 3.79 - 4.35: 54433 4.35 - 4.90: 91257 Nonbonded interactions: 209893 Sorted by model distance: nonbonded pdb=" OD1 ASP A 57 " pdb=" N ALA A 58 " model vdw 2.136 3.120 nonbonded pdb=" O SER A 264 " pdb=" NE2 HIS A 287 " model vdw 2.201 3.120 nonbonded pdb=" NZ LYS I 444 " pdb=" O7 NAG m 1 " model vdw 2.206 3.120 nonbonded pdb=" O CYS A 74 " pdb=" O PRO A 76 " model vdw 2.214 3.040 nonbonded pdb=" OD2 ASP C 73 " pdb=" O3 NAG S 1 " model vdw 2.215 3.040 ... (remaining 209888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 132 or resid 152 through 396 or resid 408 throu \ gh 1009)) selection = (chain 'E' and (resid 33 through 458 or resid 464 through 609)) selection = chain 'I' } ncs_group { reference = (chain 'B' and (resid 522 through 542 or resid 568 through 702)) selection = (chain 'F' and resid 522 through 702) selection = (chain 'J' and (resid 522 through 542 or resid 568 through 702)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 1 through 106) selection = (chain 'L' and resid 1 through 106) } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } ncs_group { reference = (chain 'S' and (resid 1 or resid 4 through 9)) selection = (chain 'Y' and (resid 2 or resid 5 through 10)) selection = (chain 'i' and (resid 1 or resid 4 through 9)) } ncs_group { reference = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'g' selection = chain 'h' selection = chain 'r' selection = chain 's' } ncs_group { reference = chain 'U' selection = chain 'b' selection = chain 'm' } ncs_group { reference = chain 'V' selection = chain 'l' selection = chain 'p' selection = chain 'q' } 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 individual isotropic 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: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 20.730 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.484 26571 Z= 0.403 Angle : 1.020 23.389 36313 Z= 0.545 Chirality : 0.067 0.821 4332 Planarity : 0.009 0.300 4383 Dihedral : 17.804 118.760 11402 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.77 % Favored : 96.07 % Rotamer: Outliers : 0.71 % Allowed : 1.05 % Favored : 98.24 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.15), residues: 3025 helix: 0.78 (0.28), residues: 384 sheet: -0.25 (0.17), residues: 923 loop : -0.69 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 504 TYR 0.016 0.001 TYR Q 100B PHE 0.024 0.002 PHE I 233 TRP 0.044 0.002 TRP I 112 HIS 0.011 0.001 HIS E 61 Details of bonding type rmsd covalent geometry : bond 0.00617 (26405) covalent geometry : angle 0.91610 (35859) SS BOND : bond 0.07321 ( 44) SS BOND : angle 5.83588 ( 88) hydrogen bonds : bond 0.22557 ( 798) hydrogen bonds : angle 8.85188 ( 2175) link_ALPHA1-2 : bond 0.00316 ( 10) link_ALPHA1-2 : angle 1.74262 ( 30) link_ALPHA1-3 : bond 0.00590 ( 6) link_ALPHA1-3 : angle 1.65974 ( 18) link_ALPHA1-6 : bond 0.00197 ( 8) link_ALPHA1-6 : angle 2.15268 ( 24) link_BETA1-4 : bond 0.00611 ( 37) link_BETA1-4 : angle 1.98769 ( 111) link_NAG-ASN : bond 0.00754 ( 61) link_NAG-ASN : angle 4.69341 ( 183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 300 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 SER cc_start: 0.7932 (t) cc_final: 0.7723 (m) REVERT: A 439 ILE cc_start: 0.8903 (mm) cc_final: 0.8513 (mm) REVERT: D 31 ASN cc_start: 0.8201 (m-40) cc_final: 0.7986 (m-40) REVERT: E 155 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7753 (mmt90) REVERT: E 439 ILE cc_start: 0.8944 (mm) cc_final: 0.8607 (mm) REVERT: F 626 MET cc_start: 0.7765 (ttm) cc_final: 0.7517 (ttm) REVERT: I 190 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7654 (mt-10) REVERT: I 502 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8342 (tttp) REVERT: M 29 MET cc_start: 0.2029 (mtp) cc_final: 0.1790 (ttm) REVERT: M 100 MET cc_start: 0.3357 (mmt) cc_final: 0.3119 (mmt) REVERT: N 90 MET cc_start: 0.4396 (tpp) cc_final: 0.4077 (ttp) REVERT: O 100 PHE cc_start: 0.6912 (p90) cc_final: 0.6700 (p90) REVERT: R 31 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6372 (pmt-80) outliers start: 19 outliers final: 9 residues processed: 319 average time/residue: 0.1268 time to fit residues: 66.8801 Evaluate side-chains 271 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 259 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 155 ARG Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 502 LYS Chi-restraints excluded: chain I residue 503 ARG Chi-restraints excluded: chain R residue 31 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 20.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN I 67 ASN J 590 GLN M 77 GLN P 37 GLN ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 ASN ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.205668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.153295 restraints weight = 29633.068| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 4.53 r_work: 0.3293 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26571 Z= 0.173 Angle : 0.725 20.082 36313 Z= 0.341 Chirality : 0.050 0.625 4332 Planarity : 0.005 0.058 4383 Dihedral : 15.217 100.732 5847 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.67 % Favored : 96.30 % Rotamer: Outliers : 1.65 % Allowed : 6.45 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.15), residues: 3025 helix: 0.72 (0.28), residues: 399 sheet: -0.24 (0.17), residues: 909 loop : -0.54 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 504 TYR 0.016 0.001 TYR L 91 PHE 0.029 0.002 PHE M 100K TRP 0.028 0.001 TRP E 427 HIS 0.013 0.001 HIS E 61 Details of bonding type rmsd covalent geometry : bond 0.00407 (26405) covalent geometry : angle 0.65338 (35859) SS BOND : bond 0.00359 ( 44) SS BOND : angle 1.25781 ( 88) hydrogen bonds : bond 0.04734 ( 798) hydrogen bonds : angle 6.44231 ( 2175) link_ALPHA1-2 : bond 0.00762 ( 10) link_ALPHA1-2 : angle 1.67611 ( 30) link_ALPHA1-3 : bond 0.00975 ( 6) link_ALPHA1-3 : angle 1.93343 ( 18) link_ALPHA1-6 : bond 0.00269 ( 8) link_ALPHA1-6 : angle 1.73091 ( 24) link_BETA1-4 : bond 0.00558 ( 37) link_BETA1-4 : angle 2.11276 ( 111) link_NAG-ASN : bond 0.00580 ( 61) link_NAG-ASN : angle 3.99075 ( 183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 275 time to evaluate : 0.612 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: A 57 ASP cc_start: 0.7687 (t0) cc_final: 0.7300 (t0) REVERT: A 439 ILE cc_start: 0.9017 (mm) cc_final: 0.8638 (mm) REVERT: E 64 GLU cc_start: 0.2397 (OUTLIER) cc_final: 0.1300 (tt0) REVERT: E 439 ILE cc_start: 0.9061 (mm) cc_final: 0.8717 (mm) REVERT: I 33 ASN cc_start: 0.6725 (p0) cc_final: 0.6429 (p0) REVERT: J 523 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8675 (pp) REVERT: M 29 MET cc_start: 0.2083 (mtp) cc_final: 0.1817 (ttm) REVERT: M 100 MET cc_start: 0.3488 (mmt) cc_final: 0.3197 (mmt) REVERT: N 90 MET cc_start: 0.4809 (tpp) cc_final: 0.4355 (ttp) outliers start: 44 outliers final: 26 residues processed: 293 average time/residue: 0.1416 time to fit residues: 67.9003 Evaluate side-chains 282 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 254 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 410 ASP Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain P residue 37 GLN Chi-restraints excluded: chain P residue 93 SER Chi-restraints excluded: chain R residue 31 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 57 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 226 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 222 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 295 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 247 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN E 425 ASN I 67 ASN J 590 GLN K 50 GLN M 77 GLN N 50 ASN ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** 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 = 0.4250 r_free = 0.4250 target = 0.204323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149473 restraints weight = 29770.423| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 4.36 r_work: 0.3053 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26571 Z= 0.198 Angle : 0.712 20.105 36313 Z= 0.334 Chirality : 0.050 0.651 4332 Planarity : 0.005 0.057 4383 Dihedral : 12.726 100.162 5830 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.87 % Allowed : 9.60 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.15), residues: 3025 helix: 0.71 (0.27), residues: 407 sheet: -0.30 (0.16), residues: 919 loop : -0.53 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 379 TYR 0.017 0.001 TYR D 91 PHE 0.023 0.002 PHE M 100K TRP 0.022 0.002 TRP E 427 HIS 0.014 0.001 HIS E 61 Details of bonding type rmsd covalent geometry : bond 0.00477 (26405) covalent geometry : angle 0.64378 (35859) SS BOND : bond 0.00401 ( 44) SS BOND : angle 1.25973 ( 88) hydrogen bonds : bond 0.04303 ( 798) hydrogen bonds : angle 5.95658 ( 2175) link_ALPHA1-2 : bond 0.00649 ( 10) link_ALPHA1-2 : angle 1.76416 ( 30) link_ALPHA1-3 : bond 0.01129 ( 6) link_ALPHA1-3 : angle 2.03685 ( 18) link_ALPHA1-6 : bond 0.00399 ( 8) link_ALPHA1-6 : angle 1.72662 ( 24) link_BETA1-4 : bond 0.00492 ( 37) link_BETA1-4 : angle 2.12889 ( 111) link_NAG-ASN : bond 0.00544 ( 61) link_NAG-ASN : angle 3.79830 ( 183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 261 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.9074 (m-80) cc_final: 0.8529 (m-80) REVERT: A 439 ILE cc_start: 0.9069 (mm) cc_final: 0.8680 (mm) REVERT: E 64 GLU cc_start: 0.2256 (OUTLIER) cc_final: 0.1317 (tt0) REVERT: E 439 ILE cc_start: 0.9050 (mm) cc_final: 0.8699 (mm) REVERT: I 33 ASN cc_start: 0.6745 (p0) cc_final: 0.6466 (p0) REVERT: I 217 TYR cc_start: 0.9067 (m-80) cc_final: 0.8757 (m-80) REVERT: M 100 MET cc_start: 0.3478 (mmt) cc_final: 0.3166 (mmt) REVERT: N 90 MET cc_start: 0.4923 (tpp) cc_final: 0.4503 (ttp) REVERT: O 100 PHE cc_start: 0.7030 (p90) cc_final: 0.6762 (p90) outliers start: 50 outliers final: 32 residues processed: 286 average time/residue: 0.1416 time to fit residues: 66.2587 Evaluate side-chains 278 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 410 ASP Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 93 SER Chi-restraints excluded: chain R residue 31 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 212 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 239 optimal weight: 50.0000 chunk 213 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 214 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 242 optimal weight: 50.0000 chunk 272 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100FHIS D 31 ASN I 67 ASN J 543 GLN J 590 GLN O 1 GLN ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.201125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.148384 restraints weight = 29513.190| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 4.57 r_work: 0.3316 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 26571 Z= 0.299 Angle : 0.802 21.755 36313 Z= 0.378 Chirality : 0.053 0.660 4332 Planarity : 0.005 0.057 4383 Dihedral : 11.513 104.724 5827 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.04 % Allowed : 12.04 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.15), residues: 3025 helix: 0.79 (0.28), residues: 381 sheet: -0.45 (0.17), residues: 913 loop : -0.72 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 585 TYR 0.022 0.002 TYR I 217 PHE 0.029 0.002 PHE M 100K TRP 0.019 0.002 TRP E 69 HIS 0.011 0.002 HIS E 61 Details of bonding type rmsd covalent geometry : bond 0.00730 (26405) covalent geometry : angle 0.73091 (35859) SS BOND : bond 0.00519 ( 44) SS BOND : angle 1.50660 ( 88) hydrogen bonds : bond 0.04639 ( 798) hydrogen bonds : angle 5.97649 ( 2175) link_ALPHA1-2 : bond 0.00725 ( 10) link_ALPHA1-2 : angle 2.01339 ( 30) link_ALPHA1-3 : bond 0.01122 ( 6) link_ALPHA1-3 : angle 2.23500 ( 18) link_ALPHA1-6 : bond 0.00401 ( 8) link_ALPHA1-6 : angle 1.85511 ( 24) link_BETA1-4 : bond 0.00555 ( 37) link_BETA1-4 : angle 2.37685 ( 111) link_NAG-ASN : bond 0.00754 ( 61) link_NAG-ASN : angle 4.11082 ( 183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 254 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.9006 (m-80) cc_final: 0.8349 (m-80) REVERT: A 439 ILE cc_start: 0.9232 (mm) cc_final: 0.8865 (mm) REVERT: E 64 GLU cc_start: 0.2640 (OUTLIER) cc_final: 0.1506 (tt0) REVERT: E 189 SER cc_start: 0.8982 (t) cc_final: 0.8762 (m) REVERT: I 33 ASN cc_start: 0.6873 (p0) cc_final: 0.6611 (p0) REVERT: I 217 TYR cc_start: 0.9057 (m-80) cc_final: 0.8706 (m-80) REVERT: M 100 MET cc_start: 0.3445 (mmt) cc_final: 0.3139 (mmt) REVERT: N 90 MET cc_start: 0.4895 (tpp) cc_final: 0.4468 (ttp) outliers start: 81 outliers final: 49 residues processed: 305 average time/residue: 0.1288 time to fit residues: 64.9821 Evaluate side-chains 290 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 240 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain P residue 93 SER Chi-restraints excluded: chain R residue 31 ARG Chi-restraints excluded: chain R residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 24 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 297 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 247 optimal weight: 30.0000 chunk 174 optimal weight: 0.3980 chunk 175 optimal weight: 0.0970 chunk 53 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS D 31 ASN E 425 ASN H 27 GLN I 33 ASN I 490 GLN J 590 GLN ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.206463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.155028 restraints weight = 29572.476| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 4.64 r_work: 0.3410 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26571 Z= 0.119 Angle : 0.645 20.779 36313 Z= 0.300 Chirality : 0.047 0.575 4332 Planarity : 0.004 0.056 4383 Dihedral : 10.199 101.238 5827 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.17 % Allowed : 13.84 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.15), residues: 3025 helix: 1.14 (0.28), residues: 381 sheet: -0.47 (0.16), residues: 943 loop : -0.52 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 480 TYR 0.027 0.001 TYR O 32 PHE 0.027 0.001 PHE M 100K TRP 0.018 0.001 TRP E 69 HIS 0.011 0.001 HIS E 61 Details of bonding type rmsd covalent geometry : bond 0.00271 (26405) covalent geometry : angle 0.57828 (35859) SS BOND : bond 0.00231 ( 44) SS BOND : angle 0.92528 ( 88) hydrogen bonds : bond 0.03540 ( 798) hydrogen bonds : angle 5.51084 ( 2175) link_ALPHA1-2 : bond 0.00764 ( 10) link_ALPHA1-2 : angle 1.70272 ( 30) link_ALPHA1-3 : bond 0.01221 ( 6) link_ALPHA1-3 : angle 2.12565 ( 18) link_ALPHA1-6 : bond 0.00501 ( 8) link_ALPHA1-6 : angle 1.75328 ( 24) link_BETA1-4 : bond 0.00444 ( 37) link_BETA1-4 : angle 1.82449 ( 111) link_NAG-ASN : bond 0.00571 ( 61) link_NAG-ASN : angle 3.63384 ( 183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 270 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.8878 (m-80) cc_final: 0.8338 (m-80) REVERT: A 432 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.6940 (mt0) REVERT: A 439 ILE cc_start: 0.9153 (mm) cc_final: 0.8718 (mm) REVERT: E 64 GLU cc_start: 0.2579 (OUTLIER) cc_final: 0.1540 (tt0) REVERT: E 189 SER cc_start: 0.9033 (OUTLIER) cc_final: 0.8829 (m) REVERT: E 439 ILE cc_start: 0.9122 (mm) cc_final: 0.8754 (mm) REVERT: F 591 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7810 (tptt) REVERT: I 217 TYR cc_start: 0.8909 (m-80) cc_final: 0.8660 (m-80) REVERT: M 100 MET cc_start: 0.3448 (mmt) cc_final: 0.3062 (mmt) REVERT: N 90 MET cc_start: 0.4963 (tpp) cc_final: 0.4591 (ttp) outliers start: 58 outliers final: 39 residues processed: 304 average time/residue: 0.1365 time to fit residues: 67.2640 Evaluate side-chains 295 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 253 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 31 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 134 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 254 optimal weight: 9.9990 chunk 294 optimal weight: 30.0000 chunk 51 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 196 optimal weight: 0.8980 chunk 258 optimal weight: 50.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN H 6 GLN H 27 GLN I 67 ASN I 490 GLN J 590 GLN ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.194202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.143984 restraints weight = 29817.440| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 4.86 r_work: 0.3070 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 26571 Z= 0.208 Angle : 0.698 21.361 36313 Z= 0.326 Chirality : 0.049 0.561 4332 Planarity : 0.004 0.055 4383 Dihedral : 9.897 101.485 5827 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.59 % Allowed : 14.40 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.15), residues: 3025 helix: 1.11 (0.29), residues: 381 sheet: -0.45 (0.16), residues: 962 loop : -0.60 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 585 TYR 0.017 0.001 TYR D 91 PHE 0.026 0.002 PHE E 53 TRP 0.015 0.001 TRP E 69 HIS 0.011 0.001 HIS E 61 Details of bonding type rmsd covalent geometry : bond 0.00507 (26405) covalent geometry : angle 0.63128 (35859) SS BOND : bond 0.00363 ( 44) SS BOND : angle 1.17520 ( 88) hydrogen bonds : bond 0.03931 ( 798) hydrogen bonds : angle 5.55474 ( 2175) link_ALPHA1-2 : bond 0.00756 ( 10) link_ALPHA1-2 : angle 1.85039 ( 30) link_ALPHA1-3 : bond 0.01202 ( 6) link_ALPHA1-3 : angle 2.23854 ( 18) link_ALPHA1-6 : bond 0.00433 ( 8) link_ALPHA1-6 : angle 1.80754 ( 24) link_BETA1-4 : bond 0.00463 ( 37) link_BETA1-4 : angle 2.02117 ( 111) link_NAG-ASN : bond 0.00538 ( 61) link_NAG-ASN : angle 3.73274 ( 183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 251 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.8971 (m-80) cc_final: 0.8351 (m-80) REVERT: A 432 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7012 (mt0) REVERT: A 439 ILE cc_start: 0.9192 (mm) cc_final: 0.8776 (mm) REVERT: E 64 GLU cc_start: 0.2418 (OUTLIER) cc_final: 0.1415 (tt0) REVERT: E 189 SER cc_start: 0.9031 (t) cc_final: 0.8796 (m) REVERT: E 439 ILE cc_start: 0.9126 (mm) cc_final: 0.8757 (mm) REVERT: I 50 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8474 (t) REVERT: I 217 TYR cc_start: 0.9012 (m-80) cc_final: 0.8751 (m-80) REVERT: M 100 MET cc_start: 0.3423 (mmt) cc_final: 0.3079 (mmt) REVERT: N 90 MET cc_start: 0.4983 (tpp) cc_final: 0.4540 (ttp) REVERT: Q 100 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.6287 (mm-30) REVERT: R 31 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6440 (ptt90) outliers start: 69 outliers final: 49 residues processed: 296 average time/residue: 0.1356 time to fit residues: 65.6231 Evaluate side-chains 298 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 244 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 93 SER Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 31 ARG Chi-restraints excluded: chain R residue 93 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 246 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 213 optimal weight: 4.9990 chunk 239 optimal weight: 30.0000 chunk 166 optimal weight: 0.8980 chunk 294 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 chunk 295 optimal weight: 20.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 ASN H 27 GLN J 590 GLN ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.195396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.145254 restraints weight = 29625.223| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 4.34 r_work: 0.3106 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26571 Z= 0.167 Angle : 0.654 19.603 36313 Z= 0.306 Chirality : 0.048 0.569 4332 Planarity : 0.004 0.055 4383 Dihedral : 9.471 101.257 5827 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.36 % Allowed : 15.30 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.15), residues: 3025 helix: 1.08 (0.28), residues: 387 sheet: -0.43 (0.16), residues: 949 loop : -0.55 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 100 TYR 0.015 0.001 TYR D 91 PHE 0.032 0.002 PHE M 100K TRP 0.016 0.001 TRP E 69 HIS 0.011 0.001 HIS E 61 Details of bonding type rmsd covalent geometry : bond 0.00402 (26405) covalent geometry : angle 0.59077 (35859) SS BOND : bond 0.00320 ( 44) SS BOND : angle 1.02690 ( 88) hydrogen bonds : bond 0.03693 ( 798) hydrogen bonds : angle 5.42622 ( 2175) link_ALPHA1-2 : bond 0.00795 ( 10) link_ALPHA1-2 : angle 1.72945 ( 30) link_ALPHA1-3 : bond 0.01217 ( 6) link_ALPHA1-3 : angle 2.16604 ( 18) link_ALPHA1-6 : bond 0.00441 ( 8) link_ALPHA1-6 : angle 1.76444 ( 24) link_BETA1-4 : bond 0.00452 ( 37) link_BETA1-4 : angle 1.87750 ( 111) link_NAG-ASN : bond 0.00517 ( 61) link_NAG-ASN : angle 3.51436 ( 183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 248 time to evaluate : 0.708 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: A 217 TYR cc_start: 0.8958 (m-80) cc_final: 0.8331 (m-80) REVERT: A 432 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.6982 (mt0) REVERT: A 439 ILE cc_start: 0.9161 (mm) cc_final: 0.8735 (mm) REVERT: E 64 GLU cc_start: 0.2392 (OUTLIER) cc_final: 0.1390 (tt0) REVERT: E 189 SER cc_start: 0.9018 (OUTLIER) cc_final: 0.8792 (m) REVERT: E 439 ILE cc_start: 0.9101 (mm) cc_final: 0.8746 (mm) REVERT: F 591 LYS cc_start: 0.8154 (ttmt) cc_final: 0.7632 (tptt) REVERT: I 50 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8451 (t) REVERT: I 217 TYR cc_start: 0.8977 (m-80) cc_final: 0.8706 (m-80) REVERT: M 100 MET cc_start: 0.3478 (mmt) cc_final: 0.3111 (mmt) REVERT: N 90 MET cc_start: 0.5001 (tpp) cc_final: 0.4527 (ttp) REVERT: R 31 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.6446 (ptt90) outliers start: 63 outliers final: 50 residues processed: 284 average time/residue: 0.1307 time to fit residues: 60.6921 Evaluate side-chains 301 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 246 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain J residue 598 CYS Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 93 SER Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 31 ARG Chi-restraints excluded: chain R residue 93 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 44 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 chunk 112 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 264 optimal weight: 5.9990 chunk 250 optimal weight: 0.1980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 ASN I 490 GLN J 590 GLN ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.196027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.146755 restraints weight = 29700.077| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 4.60 r_work: 0.3117 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26571 Z= 0.151 Angle : 0.647 21.133 36313 Z= 0.302 Chirality : 0.047 0.506 4332 Planarity : 0.004 0.055 4383 Dihedral : 9.283 100.872 5827 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.29 % Allowed : 15.75 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.15), residues: 3025 helix: 1.26 (0.29), residues: 380 sheet: -0.42 (0.16), residues: 956 loop : -0.54 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 344 TYR 0.014 0.001 TYR D 91 PHE 0.030 0.001 PHE M 100K TRP 0.016 0.001 TRP E 69 HIS 0.010 0.001 HIS E 61 Details of bonding type rmsd covalent geometry : bond 0.00362 (26405) covalent geometry : angle 0.57946 (35859) SS BOND : bond 0.00323 ( 44) SS BOND : angle 1.00019 ( 88) hydrogen bonds : bond 0.03592 ( 798) hydrogen bonds : angle 5.35653 ( 2175) link_ALPHA1-2 : bond 0.00805 ( 10) link_ALPHA1-2 : angle 1.69258 ( 30) link_ALPHA1-3 : bond 0.01209 ( 6) link_ALPHA1-3 : angle 2.14168 ( 18) link_ALPHA1-6 : bond 0.00444 ( 8) link_ALPHA1-6 : angle 1.73447 ( 24) link_BETA1-4 : bond 0.00451 ( 37) link_BETA1-4 : angle 1.84165 ( 111) link_NAG-ASN : bond 0.00505 ( 61) link_NAG-ASN : angle 3.66380 ( 183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 251 time to evaluate : 0.823 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: A 217 TYR cc_start: 0.8922 (m-80) cc_final: 0.8307 (m-80) REVERT: A 432 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.6973 (mt0) REVERT: A 439 ILE cc_start: 0.9166 (mm) cc_final: 0.8753 (mm) REVERT: E 189 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8684 (m) REVERT: E 439 ILE cc_start: 0.9121 (mm) cc_final: 0.8760 (mm) REVERT: F 591 LYS cc_start: 0.8150 (ttmt) cc_final: 0.7719 (tptt) REVERT: I 50 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8418 (t) REVERT: I 217 TYR cc_start: 0.8943 (m-80) cc_final: 0.8682 (m-80) REVERT: N 90 MET cc_start: 0.5011 (tpp) cc_final: 0.4543 (ttp) REVERT: R 31 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.6407 (ptt90) outliers start: 61 outliers final: 54 residues processed: 289 average time/residue: 0.1399 time to fit residues: 66.0655 Evaluate side-chains 304 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 246 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain J residue 598 CYS Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 93 SER Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 31 ARG Chi-restraints excluded: chain R residue 93 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 265 optimal weight: 30.0000 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 232 optimal weight: 0.2980 chunk 116 optimal weight: 0.9990 chunk 69 optimal weight: 40.0000 chunk 259 optimal weight: 6.9990 chunk 292 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 210 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN E 425 ASN H 31 ASN I 490 GLN J 590 GLN P 37 GLN ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.194883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.143535 restraints weight = 29694.757| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 4.99 r_work: 0.3059 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26571 Z= 0.186 Angle : 0.666 20.628 36313 Z= 0.312 Chirality : 0.048 0.523 4332 Planarity : 0.004 0.055 4383 Dihedral : 9.261 101.257 5827 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.47 % Allowed : 15.75 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.15), residues: 3025 helix: 1.19 (0.29), residues: 380 sheet: -0.41 (0.16), residues: 962 loop : -0.56 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 344 TYR 0.016 0.001 TYR D 91 PHE 0.028 0.002 PHE M 100K TRP 0.016 0.001 TRP E 69 HIS 0.011 0.001 HIS E 61 Details of bonding type rmsd covalent geometry : bond 0.00452 (26405) covalent geometry : angle 0.60039 (35859) SS BOND : bond 0.00357 ( 44) SS BOND : angle 1.09863 ( 88) hydrogen bonds : bond 0.03763 ( 798) hydrogen bonds : angle 5.38132 ( 2175) link_ALPHA1-2 : bond 0.00787 ( 10) link_ALPHA1-2 : angle 1.69942 ( 30) link_ALPHA1-3 : bond 0.01174 ( 6) link_ALPHA1-3 : angle 2.09347 ( 18) link_ALPHA1-6 : bond 0.00417 ( 8) link_ALPHA1-6 : angle 1.74766 ( 24) link_BETA1-4 : bond 0.00460 ( 37) link_BETA1-4 : angle 1.91308 ( 111) link_NAG-ASN : bond 0.00517 ( 61) link_NAG-ASN : angle 3.63289 ( 183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 247 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.9002 (m-80) cc_final: 0.8358 (m-80) REVERT: A 432 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.6974 (mt0) REVERT: A 439 ILE cc_start: 0.9161 (mm) cc_final: 0.8766 (mm) REVERT: E 189 SER cc_start: 0.8966 (OUTLIER) cc_final: 0.8679 (m) REVERT: E 439 ILE cc_start: 0.9106 (mm) cc_final: 0.8754 (mm) REVERT: F 591 LYS cc_start: 0.8176 (ttmt) cc_final: 0.7609 (tptt) REVERT: I 50 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8504 (t) REVERT: I 217 TYR cc_start: 0.9020 (m-80) cc_final: 0.8748 (m-80) REVERT: M 100 MET cc_start: 0.3556 (mmt) cc_final: 0.3195 (mmt) REVERT: N 90 MET cc_start: 0.4941 (tpp) cc_final: 0.4433 (ttp) REVERT: Q 100 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.6422 (mm-30) REVERT: R 31 ARG cc_start: 0.6636 (OUTLIER) cc_final: 0.6323 (ptt90) outliers start: 66 outliers final: 57 residues processed: 288 average time/residue: 0.1401 time to fit residues: 65.4065 Evaluate side-chains 304 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 242 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain J residue 598 CYS Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 37 GLN Chi-restraints excluded: chain P residue 93 SER Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 31 ARG Chi-restraints excluded: chain R residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 92 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 ASN H 31 ASN I 490 GLN J 590 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.196950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.147095 restraints weight = 29565.932| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 4.51 r_work: 0.3122 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26571 Z= 0.129 Angle : 0.623 19.763 36313 Z= 0.291 Chirality : 0.047 0.517 4332 Planarity : 0.004 0.055 4383 Dihedral : 9.013 101.965 5827 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.25 % Allowed : 16.12 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.15), residues: 3025 helix: 1.33 (0.29), residues: 380 sheet: -0.39 (0.16), residues: 956 loop : -0.51 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 39 TYR 0.012 0.001 TYR D 91 PHE 0.033 0.001 PHE M 100K TRP 0.017 0.001 TRP E 69 HIS 0.016 0.001 HIS P 38 Details of bonding type rmsd covalent geometry : bond 0.00305 (26405) covalent geometry : angle 0.56012 (35859) SS BOND : bond 0.00281 ( 44) SS BOND : angle 0.91517 ( 88) hydrogen bonds : bond 0.03453 ( 798) hydrogen bonds : angle 5.26427 ( 2175) link_ALPHA1-2 : bond 0.00782 ( 10) link_ALPHA1-2 : angle 1.59980 ( 30) link_ALPHA1-3 : bond 0.01153 ( 6) link_ALPHA1-3 : angle 2.02302 ( 18) link_ALPHA1-6 : bond 0.00469 ( 8) link_ALPHA1-6 : angle 1.70689 ( 24) link_BETA1-4 : bond 0.00458 ( 37) link_BETA1-4 : angle 1.77815 ( 111) link_NAG-ASN : bond 0.00527 ( 61) link_NAG-ASN : angle 3.45577 ( 183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 250 time to evaluate : 0.765 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: A 217 TYR cc_start: 0.8911 (m-80) cc_final: 0.8305 (m-80) REVERT: A 432 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.6969 (mt0) REVERT: A 439 ILE cc_start: 0.9138 (mm) cc_final: 0.8718 (mm) REVERT: E 64 GLU cc_start: 0.2372 (OUTLIER) cc_final: 0.1284 (tt0) REVERT: E 189 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8658 (m) REVERT: E 439 ILE cc_start: 0.9110 (mm) cc_final: 0.8742 (mm) REVERT: F 591 LYS cc_start: 0.8123 (ttmt) cc_final: 0.7708 (tptt) REVERT: I 50 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8393 (t) REVERT: M 100 MET cc_start: 0.3737 (mmt) cc_final: 0.3334 (mmt) REVERT: N 90 MET cc_start: 0.5042 (tpp) cc_final: 0.4562 (ttp) REVERT: Q 100 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.6513 (mm-30) REVERT: R 31 ARG cc_start: 0.6633 (OUTLIER) cc_final: 0.6375 (ptt90) outliers start: 60 outliers final: 49 residues processed: 290 average time/residue: 0.1289 time to fit residues: 61.4451 Evaluate side-chains 299 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 244 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain J residue 598 CYS Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 31 ARG Chi-restraints excluded: chain R residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 264 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 273 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN I 490 GLN J 590 GLN R 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.194898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.145001 restraints weight = 29484.473| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 4.63 r_work: 0.3112 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26571 Z= 0.162 Angle : 0.642 19.543 36313 Z= 0.301 Chirality : 0.047 0.522 4332 Planarity : 0.004 0.055 4383 Dihedral : 8.982 102.603 5827 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.21 % Allowed : 16.31 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.15), residues: 3025 helix: 1.29 (0.29), residues: 380 sheet: -0.39 (0.16), residues: 954 loop : -0.53 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 504 TYR 0.014 0.001 TYR D 91 PHE 0.030 0.001 PHE M 100K TRP 0.016 0.001 TRP E 69 HIS 0.011 0.001 HIS E 61 Details of bonding type rmsd covalent geometry : bond 0.00391 (26405) covalent geometry : angle 0.57805 (35859) SS BOND : bond 0.00307 ( 44) SS BOND : angle 1.03695 ( 88) hydrogen bonds : bond 0.03586 ( 798) hydrogen bonds : angle 5.27609 ( 2175) link_ALPHA1-2 : bond 0.00744 ( 10) link_ALPHA1-2 : angle 1.62973 ( 30) link_ALPHA1-3 : bond 0.01101 ( 6) link_ALPHA1-3 : angle 1.97232 ( 18) link_ALPHA1-6 : bond 0.00434 ( 8) link_ALPHA1-6 : angle 1.70665 ( 24) link_BETA1-4 : bond 0.00464 ( 37) link_BETA1-4 : angle 1.85007 ( 111) link_NAG-ASN : bond 0.00521 ( 61) link_NAG-ASN : angle 3.53583 ( 183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5388.44 seconds wall clock time: 93 minutes 22.12 seconds (5602.12 seconds total)