Starting phenix.real_space_refine on Sat May 24 18:46:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dok_27596/05_2025/8dok_27596.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dok_27596/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dok_27596/05_2025/8dok_27596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dok_27596/05_2025/8dok_27596.map" model { file = "/net/cci-nas-00/data/ceres_data/8dok_27596/05_2025/8dok_27596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dok_27596/05_2025/8dok_27596.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 15.65, per 1000 atoms: 0.61 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: 7.79 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 3.55 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: 9.64 Time building geometry restraints manager: 8.87 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 504 or resid 1001 through 1009)) selection = (chain 'E' and (resid 33 through 458 or resid 464 through 504 or resid 601 throu \ gh 609)) selection = chain 'I' } ncs_group { reference = (chain 'B' and (resid 522 through 542 or resid 568 through 662 or resid 701 thro \ ugh 702)) selection = (chain 'F' and (resid 522 through 662 or resid 701 through 702)) selection = (chain 'J' and (resid 522 through 542 or resid 568 through 662 or resid 701 thro \ ugh 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 58.010 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.800 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.044 0.002 TRP I 112 HIS 0.011 0.001 HIS E 61 PHE 0.024 0.002 PHE I 233 TYR 0.016 0.001 TYR Q 100B ARG 0.005 0.000 ARG I 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00754 ( 61) link_NAG-ASN : angle 4.69341 ( 183) 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_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) hydrogen bonds : bond 0.22557 ( 798) hydrogen bonds : angle 8.85188 ( 2175) SS BOND : bond 0.07321 ( 44) SS BOND : angle 5.83588 ( 88) covalent geometry : bond 0.00617 (26405) covalent geometry : angle 0.91610 (35859) *********************** 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 : 2.667 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: 0.3518 time to fit residues: 184.5545 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 : 2.637 ------------------------------------------------------------------------------- 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 255 optimal weight: 30.0000 chunk 228 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 236 optimal weight: 30.0000 chunk 91 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 274 optimal weight: 20.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4297 r_free = 0.4297 target = 0.209280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.155977 restraints weight = 29566.392| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 4.42 r_work: 0.3423 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26571 Z= 0.156 Angle : 0.711 20.368 36313 Z= 0.335 Chirality : 0.049 0.585 4332 Planarity : 0.005 0.058 4383 Dihedral : 15.274 100.784 5847 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 1.57 % Allowed : 6.26 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3025 helix: 0.86 (0.28), residues: 392 sheet: -0.23 (0.17), residues: 911 loop : -0.54 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 427 HIS 0.012 0.001 HIS E 61 PHE 0.028 0.001 PHE M 100K TYR 0.015 0.001 TYR L 91 ARG 0.003 0.000 ARG I 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00605 ( 61) link_NAG-ASN : angle 3.96907 ( 183) link_ALPHA1-6 : bond 0.00251 ( 8) link_ALPHA1-6 : angle 1.74427 ( 24) link_BETA1-4 : bond 0.00547 ( 37) link_BETA1-4 : angle 2.06877 ( 111) link_ALPHA1-2 : bond 0.00696 ( 10) link_ALPHA1-2 : angle 1.66767 ( 30) link_ALPHA1-3 : bond 0.00952 ( 6) link_ALPHA1-3 : angle 1.89290 ( 18) hydrogen bonds : bond 0.04736 ( 798) hydrogen bonds : angle 6.44682 ( 2175) SS BOND : bond 0.00433 ( 44) SS BOND : angle 1.20879 ( 88) covalent geometry : bond 0.00358 (26405) covalent geometry : angle 0.63910 (35859) *********************** 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 316 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 2.665 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 57 ASP cc_start: 0.7653 (t0) cc_final: 0.7284 (t0) REVERT: A 439 ILE cc_start: 0.9029 (mm) cc_final: 0.8642 (mm) REVERT: E 64 GLU cc_start: 0.2453 (OUTLIER) cc_final: 0.1348 (tt0) REVERT: E 166 ARG cc_start: 0.8238 (ttp80) cc_final: 0.7914 (ttp80) REVERT: E 439 ILE cc_start: 0.9063 (mm) cc_final: 0.8713 (mm) REVERT: I 33 ASN cc_start: 0.6743 (p0) cc_final: 0.6447 (p0) REVERT: J 523 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8653 (pp) REVERT: M 29 MET cc_start: 0.2061 (mtp) cc_final: 0.1787 (ttm) REVERT: M 100 MET cc_start: 0.3481 (mmt) cc_final: 0.3184 (mmt) REVERT: N 90 MET cc_start: 0.4803 (tpp) cc_final: 0.4371 (ttp) outliers start: 42 outliers final: 25 residues processed: 290 average time/residue: 0.3487 time to fit residues: 164.2030 Evaluate side-chains 278 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 251 time to evaluate : 2.564 ------------------------------------------------------------------------------- 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 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 133 optimal weight: 0.9990 chunk 259 optimal weight: 50.0000 chunk 75 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 chunk 242 optimal weight: 50.0000 chunk 261 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 297 optimal weight: 0.0470 chunk 209 optimal weight: 3.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- 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** E 425 ASN I 67 ASN J 590 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.206160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.154471 restraints weight = 29569.922| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 4.48 r_work: 0.3416 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1262 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= 0.165 Angle : 0.683 20.408 36313 Z= 0.319 Chirality : 0.049 0.625 4332 Planarity : 0.004 0.057 4383 Dihedral : 12.583 98.971 5830 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.76 % Allowed : 9.00 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3025 helix: 0.84 (0.28), residues: 401 sheet: -0.22 (0.17), residues: 909 loop : -0.48 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 427 HIS 0.014 0.001 HIS E 61 PHE 0.024 0.001 PHE M 100K TYR 0.016 0.001 TYR P 86 ARG 0.003 0.000 ARG E 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 61) link_NAG-ASN : angle 3.71042 ( 183) link_ALPHA1-6 : bond 0.00435 ( 8) link_ALPHA1-6 : angle 1.68651 ( 24) link_BETA1-4 : bond 0.00468 ( 37) link_BETA1-4 : angle 2.08061 ( 111) link_ALPHA1-2 : bond 0.00680 ( 10) link_ALPHA1-2 : angle 1.71515 ( 30) link_ALPHA1-3 : bond 0.01163 ( 6) link_ALPHA1-3 : angle 2.03481 ( 18) hydrogen bonds : bond 0.04082 ( 798) hydrogen bonds : angle 5.88920 ( 2175) SS BOND : bond 0.00363 ( 44) SS BOND : angle 1.14277 ( 88) covalent geometry : bond 0.00392 (26405) covalent geometry : angle 0.61579 (35859) *********************** 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 316 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 269 time to evaluate : 2.691 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: A 77 THR cc_start: 0.7799 (m) cc_final: 0.7251 (p) REVERT: A 217 TYR cc_start: 0.8913 (m-80) cc_final: 0.8493 (m-80) REVERT: A 439 ILE cc_start: 0.9111 (mm) cc_final: 0.8697 (mm) REVERT: E 64 GLU cc_start: 0.2325 (OUTLIER) cc_final: 0.1411 (tt0) REVERT: E 439 ILE cc_start: 0.9103 (mm) cc_final: 0.8725 (mm) REVERT: F 591 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7897 (tptt) REVERT: I 33 ASN cc_start: 0.6828 (p0) cc_final: 0.6510 (p0) REVERT: I 217 TYR cc_start: 0.8937 (m-80) cc_final: 0.8696 (m-80) REVERT: J 523 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8797 (pp) REVERT: M 100 MET cc_start: 0.3666 (mmt) cc_final: 0.3298 (mmt) REVERT: N 90 MET cc_start: 0.4992 (tpp) cc_final: 0.4592 (ttp) outliers start: 47 outliers final: 31 residues processed: 290 average time/residue: 0.3406 time to fit residues: 162.2909 Evaluate side-chains 283 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 250 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE 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 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 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 H residue 30 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 95 MET 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 I residue 499 THR 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 L residue 88 CYS 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 250 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 273 optimal weight: 7.9990 chunk 52 optimal weight: 0.4980 chunk 43 optimal weight: 9.9990 chunk 246 optimal weight: 1.9990 chunk 290 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN C 100FHIS D 31 ASN E 114 GLN I 67 ASN J 543 GLN J 590 GLN K 50 GLN ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.202283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.150597 restraints weight = 29818.382| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 5.03 r_work: 0.3339 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 26571 Z= 0.253 Angle : 0.749 21.640 36313 Z= 0.351 Chirality : 0.051 0.628 4332 Planarity : 0.005 0.057 4383 Dihedral : 11.339 102.510 5829 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.51 % Allowed : 10.87 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 3025 helix: 0.89 (0.28), residues: 387 sheet: -0.35 (0.17), residues: 921 loop : -0.58 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 427 HIS 0.011 0.001 HIS E 61 PHE 0.028 0.002 PHE M 100K TYR 0.020 0.002 TYR D 91 ARG 0.004 0.000 ARG E 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00581 ( 61) link_NAG-ASN : angle 3.94678 ( 183) link_ALPHA1-6 : bond 0.00429 ( 8) link_ALPHA1-6 : angle 1.78587 ( 24) link_BETA1-4 : bond 0.00504 ( 37) link_BETA1-4 : angle 2.27112 ( 111) link_ALPHA1-2 : bond 0.00666 ( 10) link_ALPHA1-2 : angle 1.90404 ( 30) link_ALPHA1-3 : bond 0.01144 ( 6) link_ALPHA1-3 : angle 2.21296 ( 18) hydrogen bonds : bond 0.04345 ( 798) hydrogen bonds : angle 5.83681 ( 2175) SS BOND : bond 0.00421 ( 44) SS BOND : angle 1.29603 ( 88) covalent geometry : bond 0.00622 (26405) covalent geometry : angle 0.67835 (35859) *********************** 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 319 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 252 time to evaluate : 2.895 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: 0.9003 (m-80) cc_final: 0.8469 (m-80) REVERT: A 439 ILE cc_start: 0.9184 (mm) cc_final: 0.8800 (mm) REVERT: E 64 GLU cc_start: 0.2397 (OUTLIER) cc_final: 0.1437 (tt0) REVERT: I 33 ASN cc_start: 0.6805 (p0) cc_final: 0.6554 (p0) REVERT: I 217 TYR cc_start: 0.9068 (m-80) cc_final: 0.8682 (m-80) REVERT: M 100 MET cc_start: 0.3241 (mmt) cc_final: 0.2955 (mmt) REVERT: N 90 MET cc_start: 0.4910 (tpp) cc_final: 0.4503 (ttp) REVERT: R 31 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6330 (ptt90) outliers start: 67 outliers final: 43 residues processed: 294 average time/residue: 0.3429 time to fit residues: 166.1205 Evaluate side-chains 293 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 248 time to evaluate : 2.726 ------------------------------------------------------------------------------- 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 265 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 501 CYS 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 244 SER Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 424 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 101 VAL 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 I residue 501 CYS 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 79 optimal weight: 4.9990 chunk 271 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 192 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 197 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 590 GLN D 31 ASN E 425 ASN I 490 GLN J 590 GLN K 50 GLN ** P 38 HIS ** 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 = 0.4264 r_free = 0.4264 target = 0.205743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.154177 restraints weight = 29623.091| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 4.92 r_work: 0.3407 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26571 Z= 0.145 Angle : 0.647 20.521 36313 Z= 0.302 Chirality : 0.048 0.586 4332 Planarity : 0.004 0.056 4383 Dihedral : 10.237 100.413 5829 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.14 % Allowed : 12.79 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 3025 helix: 1.00 (0.28), residues: 393 sheet: -0.32 (0.16), residues: 933 loop : -0.48 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 69 HIS 0.012 0.001 HIS E 61 PHE 0.029 0.001 PHE O 100K TYR 0.013 0.001 TYR D 91 ARG 0.002 0.000 ARG A 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 61) link_NAG-ASN : angle 3.56919 ( 183) link_ALPHA1-6 : bond 0.00496 ( 8) link_ALPHA1-6 : angle 1.77329 ( 24) link_BETA1-4 : bond 0.00437 ( 37) link_BETA1-4 : angle 1.89302 ( 111) link_ALPHA1-2 : bond 0.00718 ( 10) link_ALPHA1-2 : angle 1.71879 ( 30) link_ALPHA1-3 : bond 0.01239 ( 6) link_ALPHA1-3 : angle 2.16939 ( 18) hydrogen bonds : bond 0.03632 ( 798) hydrogen bonds : angle 5.52056 ( 2175) SS BOND : bond 0.00464 ( 44) SS BOND : angle 1.02337 ( 88) covalent geometry : bond 0.00343 (26405) covalent geometry : angle 0.58150 (35859) *********************** 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 317 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 260 time to evaluate : 3.006 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: A 217 TYR cc_start: 0.8920 (m-80) cc_final: 0.8379 (m-80) REVERT: A 439 ILE cc_start: 0.9142 (mm) cc_final: 0.8717 (mm) REVERT: E 439 ILE cc_start: 0.9102 (mm) cc_final: 0.8746 (mm) REVERT: F 591 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7686 (tptt) REVERT: I 33 ASN cc_start: 0.6740 (p0) cc_final: 0.6523 (p0) REVERT: I 217 TYR cc_start: 0.8941 (m-80) cc_final: 0.8674 (m-80) REVERT: M 100 MET cc_start: 0.3355 (mmt) cc_final: 0.3015 (mmt) REVERT: N 90 MET cc_start: 0.4943 (tpp) cc_final: 0.4568 (ttp) REVERT: R 31 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6369 (ptt90) outliers start: 57 outliers final: 38 residues processed: 292 average time/residue: 0.3466 time to fit residues: 165.3192 Evaluate side-chains 287 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 248 time to evaluate : 2.504 ------------------------------------------------------------------------------- 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 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 244 SER Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 475 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 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 303 THR Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 457 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 128 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 122 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 590 GLN H 6 GLN I 33 ASN I 490 GLN J 590 GLN ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.207510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.155667 restraints weight = 29343.617| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 4.34 r_work: 0.3399 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26571 Z= 0.150 Angle : 0.644 19.287 36313 Z= 0.301 Chirality : 0.048 0.592 4332 Planarity : 0.004 0.055 4383 Dihedral : 9.788 99.870 5829 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.40 % Allowed : 13.46 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 3025 helix: 1.18 (0.29), residues: 381 sheet: -0.30 (0.17), residues: 935 loop : -0.47 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 69 HIS 0.011 0.001 HIS E 61 PHE 0.032 0.001 PHE O 100K TYR 0.015 0.001 TYR O 32 ARG 0.002 0.000 ARG J 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 61) link_NAG-ASN : angle 3.48282 ( 183) link_ALPHA1-6 : bond 0.00475 ( 8) link_ALPHA1-6 : angle 1.75420 ( 24) link_BETA1-4 : bond 0.00446 ( 37) link_BETA1-4 : angle 1.88265 ( 111) link_ALPHA1-2 : bond 0.00722 ( 10) link_ALPHA1-2 : angle 1.76517 ( 30) link_ALPHA1-3 : bond 0.01231 ( 6) link_ALPHA1-3 : angle 2.20066 ( 18) hydrogen bonds : bond 0.03592 ( 798) hydrogen bonds : angle 5.43292 ( 2175) SS BOND : bond 0.00291 ( 44) SS BOND : angle 0.99625 ( 88) covalent geometry : bond 0.00358 (26405) covalent geometry : angle 0.58117 (35859) *********************** 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 321 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 257 time to evaluate : 3.018 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: 0.8902 (m-80) cc_final: 0.8371 (m-80) REVERT: A 432 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.6936 (mt0) REVERT: A 439 ILE cc_start: 0.9134 (mm) cc_final: 0.8698 (mm) REVERT: E 64 GLU cc_start: 0.2145 (OUTLIER) cc_final: 0.1276 (tt0) REVERT: E 439 ILE cc_start: 0.9110 (mm) cc_final: 0.8751 (mm) REVERT: F 591 LYS cc_start: 0.8157 (ttmt) cc_final: 0.7761 (tptt) REVERT: I 217 TYR cc_start: 0.8962 (m-80) cc_final: 0.8695 (m-80) REVERT: M 100 MET cc_start: 0.3375 (mmt) cc_final: 0.3019 (mmt) REVERT: N 90 MET cc_start: 0.4943 (tpp) cc_final: 0.4528 (ttp) REVERT: R 31 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.6460 (ptt90) outliers start: 64 outliers final: 46 residues processed: 297 average time/residue: 0.3471 time to fit residues: 169.6395 Evaluate side-chains 296 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 247 time to evaluate : 2.525 ------------------------------------------------------------------------------- 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 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 244 SER Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 333 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 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 77 THR Chi-restraints excluded: chain I residue 303 THR 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 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 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 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 11 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 197 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 255 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 590 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.210644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.157186 restraints weight = 29695.819| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 4.44 r_work: 0.3440 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26571 Z= 0.118 Angle : 0.608 20.314 36313 Z= 0.284 Chirality : 0.047 0.569 4332 Planarity : 0.004 0.055 4383 Dihedral : 9.196 98.133 5829 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.10 % Allowed : 14.29 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3025 helix: 1.19 (0.28), residues: 392 sheet: -0.25 (0.16), residues: 954 loop : -0.44 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 69 HIS 0.011 0.001 HIS E 61 PHE 0.035 0.001 PHE O 100K TYR 0.011 0.001 TYR D 91 ARG 0.002 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 61) link_NAG-ASN : angle 3.34327 ( 183) link_ALPHA1-6 : bond 0.00501 ( 8) link_ALPHA1-6 : angle 1.69004 ( 24) link_BETA1-4 : bond 0.00456 ( 37) link_BETA1-4 : angle 1.74671 ( 111) link_ALPHA1-2 : bond 0.00796 ( 10) link_ALPHA1-2 : angle 1.67903 ( 30) link_ALPHA1-3 : bond 0.01240 ( 6) link_ALPHA1-3 : angle 2.13143 ( 18) hydrogen bonds : bond 0.03299 ( 798) hydrogen bonds : angle 5.22299 ( 2175) SS BOND : bond 0.00232 ( 44) SS BOND : angle 0.85051 ( 88) covalent geometry : bond 0.00275 (26405) covalent geometry : angle 0.54747 (35859) *********************** 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 323 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 267 time to evaluate : 2.811 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: 0.8859 (m-80) cc_final: 0.8344 (m-80) REVERT: A 432 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.6901 (mt0) REVERT: A 439 ILE cc_start: 0.9096 (mm) cc_final: 0.8635 (mm) REVERT: E 64 GLU cc_start: 0.2123 (OUTLIER) cc_final: 0.1310 (tt0) REVERT: E 166 ARG cc_start: 0.8308 (ttp80) cc_final: 0.8078 (ttp80) REVERT: E 439 ILE cc_start: 0.9098 (mm) cc_final: 0.8739 (mm) REVERT: F 591 LYS cc_start: 0.8058 (ttmt) cc_final: 0.7705 (tptt) REVERT: I 217 TYR cc_start: 0.8902 (m-80) cc_final: 0.8687 (m-80) REVERT: M 100 MET cc_start: 0.3397 (mmt) cc_final: 0.3026 (mmt) REVERT: N 90 MET cc_start: 0.4946 (tpp) cc_final: 0.4512 (ttp) outliers start: 56 outliers final: 44 residues processed: 302 average time/residue: 0.3565 time to fit residues: 174.0552 Evaluate side-chains 306 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 260 time to evaluate : 2.491 ------------------------------------------------------------------------------- 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 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 208 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 333 ILE 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 125 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 J residue 598 CYS 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 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 R residue 93 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 250 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 590 GLN D 31 ASN G 105 GLN H 31 ASN I 490 GLN ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.209985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.156591 restraints weight = 29636.588| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 4.64 r_work: 0.3439 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26571 Z= 0.133 Angle : 0.614 19.157 36313 Z= 0.287 Chirality : 0.047 0.560 4332 Planarity : 0.004 0.055 4383 Dihedral : 9.002 98.432 5825 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.21 % Allowed : 14.51 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3025 helix: 1.25 (0.29), residues: 389 sheet: -0.22 (0.16), residues: 958 loop : -0.43 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 69 HIS 0.011 0.001 HIS E 61 PHE 0.034 0.001 PHE O 100K TYR 0.013 0.001 TYR D 91 ARG 0.005 0.000 ARG R 31 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 61) link_NAG-ASN : angle 3.30208 ( 183) link_ALPHA1-6 : bond 0.00468 ( 8) link_ALPHA1-6 : angle 1.67654 ( 24) link_BETA1-4 : bond 0.00456 ( 37) link_BETA1-4 : angle 1.77626 ( 111) link_ALPHA1-2 : bond 0.00800 ( 10) link_ALPHA1-2 : angle 1.68181 ( 30) link_ALPHA1-3 : bond 0.01204 ( 6) link_ALPHA1-3 : angle 2.13120 ( 18) hydrogen bonds : bond 0.03372 ( 798) hydrogen bonds : angle 5.17893 ( 2175) SS BOND : bond 0.00269 ( 44) SS BOND : angle 0.89891 ( 88) covalent geometry : bond 0.00316 (26405) covalent geometry : angle 0.55437 (35859) *********************** 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 319 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 260 time to evaluate : 2.742 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 217 TYR cc_start: 0.8895 (m-80) cc_final: 0.8362 (m-80) REVERT: A 432 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.6924 (mt0) REVERT: A 439 ILE cc_start: 0.9097 (mm) cc_final: 0.8636 (mm) REVERT: E 64 GLU cc_start: 0.2107 (OUTLIER) cc_final: 0.1333 (tt0) REVERT: E 439 ILE cc_start: 0.9103 (mm) cc_final: 0.8755 (mm) REVERT: F 591 LYS cc_start: 0.8056 (ttmt) cc_final: 0.7670 (tptt) REVERT: I 217 TYR cc_start: 0.8952 (m-80) cc_final: 0.8724 (m-80) REVERT: M 100 MET cc_start: 0.3287 (mmt) cc_final: 0.2962 (mmt) REVERT: N 90 MET cc_start: 0.4930 (tpp) cc_final: 0.4475 (ttp) outliers start: 59 outliers final: 50 residues processed: 298 average time/residue: 0.3427 time to fit residues: 167.6231 Evaluate side-chains 305 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 253 time to evaluate : 2.633 ------------------------------------------------------------------------------- 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 488 VAL 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 208 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 333 ILE 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 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 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 P residue 93 SER 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 73 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 171 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 590 GLN E 425 ASN H 31 ASN J 590 GLN ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.209870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.156730 restraints weight = 29761.470| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 4.77 r_work: 0.3415 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26571 Z= 0.136 Angle : 0.609 18.496 36313 Z= 0.286 Chirality : 0.047 0.533 4332 Planarity : 0.004 0.056 4383 Dihedral : 8.766 101.016 5825 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.06 % Allowed : 15.07 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 3025 helix: 1.28 (0.29), residues: 392 sheet: -0.20 (0.17), residues: 958 loop : -0.42 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 69 HIS 0.011 0.001 HIS E 61 PHE 0.034 0.001 PHE O 100K TYR 0.012 0.001 TYR D 91 ARG 0.004 0.000 ARG D 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 61) link_NAG-ASN : angle 3.25143 ( 183) link_ALPHA1-6 : bond 0.00470 ( 8) link_ALPHA1-6 : angle 1.66727 ( 24) link_BETA1-4 : bond 0.00461 ( 37) link_BETA1-4 : angle 1.78224 ( 111) link_ALPHA1-2 : bond 0.00869 ( 10) link_ALPHA1-2 : angle 1.60982 ( 30) link_ALPHA1-3 : bond 0.01113 ( 6) link_ALPHA1-3 : angle 1.97311 ( 18) hydrogen bonds : bond 0.03383 ( 798) hydrogen bonds : angle 5.14274 ( 2175) SS BOND : bond 0.00277 ( 44) SS BOND : angle 0.91613 ( 88) covalent geometry : bond 0.00323 (26405) covalent geometry : angle 0.55115 (35859) *********************** 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 307 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 252 time to evaluate : 2.782 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: 0.8904 (m-80) cc_final: 0.8292 (m-80) REVERT: A 432 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.6905 (mt0) REVERT: A 439 ILE cc_start: 0.9104 (mm) cc_final: 0.8644 (mm) REVERT: E 64 GLU cc_start: 0.2290 (OUTLIER) cc_final: 0.1285 (tt0) REVERT: E 166 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7942 (ttp80) REVERT: E 439 ILE cc_start: 0.9106 (mm) cc_final: 0.8742 (mm) REVERT: F 591 LYS cc_start: 0.8072 (ttmt) cc_final: 0.7675 (tptt) REVERT: I 217 TYR cc_start: 0.8949 (m-80) cc_final: 0.8723 (m-80) REVERT: M 100 MET cc_start: 0.3287 (mmt) cc_final: 0.2972 (mmt) REVERT: N 90 MET cc_start: 0.4869 (tpp) cc_final: 0.4402 (ttp) outliers start: 55 outliers final: 50 residues processed: 288 average time/residue: 0.3465 time to fit residues: 163.4451 Evaluate side-chains 300 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 248 time to evaluate : 2.754 ------------------------------------------------------------------------------- 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 488 VAL 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 208 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 333 ILE 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 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 51 ILE 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 93 SER 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 183 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 254 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 69 optimal weight: 40.0000 chunk 63 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 590 GLN I 490 GLN J 590 GLN ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4275 r_free = 0.4275 target = 0.206991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.155772 restraints weight = 29513.384| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 5.06 r_work: 0.3430 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26571 Z= 0.140 Angle : 0.624 21.079 36313 Z= 0.290 Chirality : 0.047 0.415 4332 Planarity : 0.004 0.056 4383 Dihedral : 8.719 101.984 5825 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.02 % Allowed : 15.52 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 3025 helix: 1.28 (0.29), residues: 392 sheet: -0.16 (0.17), residues: 950 loop : -0.44 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 69 HIS 0.011 0.001 HIS E 61 PHE 0.033 0.001 PHE O 100K TYR 0.013 0.001 TYR D 91 ARG 0.004 0.000 ARG D 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 61) link_NAG-ASN : angle 3.68863 ( 183) link_ALPHA1-6 : bond 0.00456 ( 8) link_ALPHA1-6 : angle 1.65938 ( 24) link_BETA1-4 : bond 0.00457 ( 37) link_BETA1-4 : angle 1.79049 ( 111) link_ALPHA1-2 : bond 0.00775 ( 10) link_ALPHA1-2 : angle 1.58607 ( 30) link_ALPHA1-3 : bond 0.01064 ( 6) link_ALPHA1-3 : angle 1.92498 ( 18) hydrogen bonds : bond 0.03406 ( 798) hydrogen bonds : angle 5.13218 ( 2175) SS BOND : bond 0.00274 ( 44) SS BOND : angle 0.92932 ( 88) covalent geometry : bond 0.00335 (26405) covalent geometry : angle 0.55413 (35859) ********************** 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 309 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 255 time to evaluate : 2.918 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: 0.8904 (m-80) cc_final: 0.8297 (m-80) REVERT: A 432 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.6942 (mt0) REVERT: A 439 ILE cc_start: 0.9112 (mm) cc_final: 0.8649 (mm) REVERT: E 64 GLU cc_start: 0.2275 (OUTLIER) cc_final: 0.1283 (tt0) REVERT: E 439 ILE cc_start: 0.9112 (mm) cc_final: 0.8746 (mm) REVERT: F 591 LYS cc_start: 0.8107 (ttmt) cc_final: 0.7712 (tptt) REVERT: M 100 MET cc_start: 0.3265 (mmt) cc_final: 0.2948 (mmt) REVERT: N 90 MET cc_start: 0.4955 (tpp) cc_final: 0.4472 (ttp) outliers start: 54 outliers final: 50 residues processed: 290 average time/residue: 0.3492 time to fit residues: 167.2741 Evaluate side-chains 301 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 249 time to evaluate : 2.477 ------------------------------------------------------------------------------- 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 488 VAL 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 208 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 333 ILE 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 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 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 P residue 93 SER 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 44 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 296 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 163 optimal weight: 0.0970 chunk 224 optimal weight: 4.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 590 GLN D 31 ASN I 490 GLN J 590 GLN ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.206165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.154810 restraints weight = 29554.517| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 4.98 r_work: 0.3398 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26571 Z= 0.155 Angle : 0.632 20.411 36313 Z= 0.295 Chirality : 0.047 0.423 4332 Planarity : 0.004 0.056 4383 Dihedral : 8.707 102.765 5825 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.10 % Allowed : 15.64 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 3025 helix: 1.33 (0.29), residues: 386 sheet: -0.16 (0.17), residues: 938 loop : -0.47 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 69 HIS 0.011 0.001 HIS E 61 PHE 0.033 0.001 PHE O 100K TYR 0.014 0.001 TYR D 91 ARG 0.004 0.000 ARG D 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 61) link_NAG-ASN : angle 3.60085 ( 183) link_ALPHA1-6 : bond 0.00436 ( 8) link_ALPHA1-6 : angle 1.67095 ( 24) link_BETA1-4 : bond 0.00469 ( 37) link_BETA1-4 : angle 1.83523 ( 111) link_ALPHA1-2 : bond 0.00719 ( 10) link_ALPHA1-2 : angle 1.59608 ( 30) link_ALPHA1-3 : bond 0.01040 ( 6) link_ALPHA1-3 : angle 1.87277 ( 18) hydrogen bonds : bond 0.03507 ( 798) hydrogen bonds : angle 5.14573 ( 2175) SS BOND : bond 0.00288 ( 44) SS BOND : angle 1.04834 ( 88) covalent geometry : bond 0.00373 (26405) covalent geometry : angle 0.56470 (35859) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12571.03 seconds wall clock time: 218 minutes 54.82 seconds (13134.82 seconds total)