Starting phenix.real_space_refine on Thu Mar 5 01:53:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o8s_70235/03_2026/9o8s_70235.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o8s_70235/03_2026/9o8s_70235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o8s_70235/03_2026/9o8s_70235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o8s_70235/03_2026/9o8s_70235.map" model { file = "/net/cci-nas-00/data/ceres_data/9o8s_70235/03_2026/9o8s_70235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o8s_70235/03_2026/9o8s_70235.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 84 5.16 5 C 10974 2.51 5 N 2991 2.21 5 O 3579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17628 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2471 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 19, 'TRANS': 296} Chain: "B" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1388 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "H" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 790 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "C" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2471 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 19, 'TRANS': 296} Chain: "E" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1388 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "G" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "J" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 790 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "D" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2471 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 19, 'TRANS': 296} Chain: "F" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1388 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "I" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "K" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 790 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" 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: "Q" 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "B" 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: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "E" 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: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.12, per 1000 atoms: 0.23 Number of scatterers: 17628 At special positions: 0 Unit cell: (127.804, 120.624, 145.036, 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 84 16.00 O 3579 8.00 N 2991 7.00 C 10974 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.05 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.06 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 98 " - pdb=" SG CYS H 100C" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS E 137 " distance=2.05 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.06 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 148 " distance=2.05 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 98 " - pdb=" SG CYS G 100C" distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS F 137 " distance=2.04 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 277 " distance=2.06 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 76 " distance=2.03 Simple disulfide: pdb=" SG CYS D 97 " - pdb=" SG CYS D 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 305 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 98 " - pdb=" SG CYS I 100C" distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 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=3, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " BETA1-6 " NAG N 1 " - " FUC N 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG X 1 " - " FUC X 3 " NAG-ASN " NAG A 401 " - " ASN A 22 " " NAG A 402 " - " ASN A 133 " " NAG A 403 " - " ASN A 158 " " NAG A 404 " - " ASN A 126 " " NAG A 405 " - " ASN A 45 " " NAG B 301 " - " ASN B 154 " " NAG C 401 " - " ASN C 22 " " NAG C 402 " - " ASN C 133 " " NAG C 403 " - " ASN C 158 " " NAG C 404 " - " ASN C 126 " " NAG C 405 " - " ASN C 45 " " NAG D 401 " - " ASN D 22 " " NAG D 402 " - " ASN D 133 " " NAG D 403 " - " ASN D 158 " " NAG D 404 " - " ASN D 126 " " NAG D 405 " - " ASN D 45 " " NAG E 301 " - " ASN E 154 " " NAG F 301 " - " ASN F 154 " " NAG M 1 " - " ASN A 38 " " NAG N 1 " - " ASN A 63 " " NAG O 1 " - " ASN A 246 " " NAG P 1 " - " ASN A 285 " " NAG Q 1 " - " ASN A 165 " " NAG R 1 " - " ASN C 38 " " NAG S 1 " - " ASN C 63 " " NAG T 1 " - " ASN C 246 " " NAG U 1 " - " ASN C 285 " " NAG V 1 " - " ASN C 165 " " NAG W 1 " - " ASN D 38 " " NAG X 1 " - " ASN D 63 " " NAG Y 1 " - " ASN D 246 " " NAG Z 1 " - " ASN D 285 " " NAG a 1 " - " ASN D 165 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 622.4 milliseconds 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3942 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 48 sheets defined 16.8% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 37 through 56 Processing helix chain 'B' and resid 75 through 126 Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'E' and resid 37 through 56 Processing helix chain 'E' and resid 75 through 126 Processing helix chain 'E' and resid 145 through 154 Processing helix chain 'E' and resid 162 through 171 Processing helix chain 'D' and resid 65 through 71 Processing helix chain 'D' and resid 104 through 116 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'F' and resid 37 through 56 Processing helix chain 'F' and resid 75 through 126 Processing helix chain 'F' and resid 145 through 154 Processing helix chain 'F' and resid 162 through 171 Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 36 removed outlier: 3.508A pdb=" N LYS B 139 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 3.608A pdb=" N ILE A 34 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.160A pdb=" N ILE A 51 " --> pdb=" O GLY A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 60 Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.649A pdb=" N ASN A 121 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR A 257 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.649A pdb=" N ASN A 121 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR A 257 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.716A pdb=" N LEU A 164 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.502A pdb=" N LYS B 62 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 19 through 22 removed outlier: 3.515A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.880A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR H 90 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.693A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU L 73 " --> pdb=" O PHE L 21 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR L 74 " --> pdb=" O SER L 63 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.567A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 33 through 36 Processing sheet with id=AB9, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.586A pdb=" N ILE C 34 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC2, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC3, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.158A pdb=" N ILE C 51 " --> pdb=" O GLY C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 58 through 60 Processing sheet with id=AC5, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.649A pdb=" N ASN C 121 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR C 257 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.649A pdb=" N ASN C 121 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR C 257 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC8, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AC9, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.726A pdb=" N LEU C 164 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 303 through 304 removed outlier: 3.521A pdb=" N LYS E 62 " --> pdb=" O GLY C 303 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 19 through 22 removed outlier: 3.596A pdb=" N LEU G 80 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU G 78 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.885A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR G 90 " --> pdb=" O THR G 107 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR G 107 " --> pdb=" O TYR G 90 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.671A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU J 73 " --> pdb=" O PHE J 21 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS J 23 " --> pdb=" O PHE J 71 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE J 71 " --> pdb=" O CYS J 23 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR J 74 " --> pdb=" O SER J 63 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER J 63 " --> pdb=" O THR J 74 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.566A pdb=" N THR J 85 " --> pdb=" O GLN J 38 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 33 through 36 removed outlier: 3.510A pdb=" N LYS F 139 " --> pdb=" O GLU F 131 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 24 through 26 removed outlier: 3.596A pdb=" N ILE D 34 " --> pdb=" O VAL D 26 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 39 through 41 Processing sheet with id=AD9, first strand: chain 'D' and resid 43 through 44 Processing sheet with id=AE1, first strand: chain 'D' and resid 51 through 52 removed outlier: 6.161A pdb=" N ILE D 51 " --> pdb=" O GLY D 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 58 through 60 Processing sheet with id=AE3, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.645A pdb=" N ASN D 121 " --> pdb=" O TYR D 257 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR D 257 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLY D 256 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE D 179 " --> pdb=" O GLY D 256 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE D 179 " --> pdb=" O PRO D 254 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.645A pdb=" N ASN D 121 " --> pdb=" O TYR D 257 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR D 257 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLY D 256 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE D 179 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 130 through 131 Processing sheet with id=AE6, first strand: chain 'D' and resid 140 through 141 Processing sheet with id=AE7, first strand: chain 'D' and resid 164 through 169 removed outlier: 3.723A pdb=" N LEU D 164 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 303 through 304 removed outlier: 3.534A pdb=" N LYS F 62 " --> pdb=" O GLY D 303 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 19 through 22 removed outlier: 3.612A pdb=" N LEU I 80 " --> pdb=" O LEU I 20 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU I 78 " --> pdb=" O CYS I 22 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 57 through 59 removed outlier: 7.121A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR I 90 " --> pdb=" O THR I 107 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR I 107 " --> pdb=" O TYR I 90 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.556A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU K 73 " --> pdb=" O PHE K 21 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS K 23 " --> pdb=" O PHE K 71 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER K 63 " --> pdb=" O THR K 74 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.567A pdb=" N THR K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1626 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: 2.88 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 5769 1.36 - 1.51: 5381 1.51 - 1.66: 6724 1.66 - 1.80: 91 1.80 - 1.95: 23 Bond restraints: 17988 Sorted by residual: bond pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " ideal model delta sigma weight residual 1.808 1.951 -0.143 3.30e-02 9.18e+02 1.87e+01 bond pdb=" CB CYS A 52 " pdb=" SG CYS A 52 " ideal model delta sigma weight residual 1.808 1.950 -0.142 3.30e-02 9.18e+02 1.85e+01 bond pdb=" CB CYS D 52 " pdb=" SG CYS D 52 " ideal model delta sigma weight residual 1.808 1.950 -0.142 3.30e-02 9.18e+02 1.85e+01 bond pdb=" CB CYS C 277 " pdb=" SG CYS C 277 " ideal model delta sigma weight residual 1.808 1.685 0.123 3.30e-02 9.18e+02 1.40e+01 bond pdb=" CB CYS D 277 " pdb=" SG CYS D 277 " ideal model delta sigma weight residual 1.808 1.685 0.123 3.30e-02 9.18e+02 1.39e+01 ... (remaining 17983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 23996 3.69 - 7.38: 334 7.38 - 11.07: 25 11.07 - 14.76: 8 14.76 - 18.45: 3 Bond angle restraints: 24366 Sorted by residual: angle pdb=" CA CYS C 277 " pdb=" CB CYS C 277 " pdb=" SG CYS C 277 " ideal model delta sigma weight residual 114.40 132.85 -18.45 2.30e+00 1.89e-01 6.44e+01 angle pdb=" CA CYS D 277 " pdb=" CB CYS D 277 " pdb=" SG CYS D 277 " ideal model delta sigma weight residual 114.40 132.82 -18.42 2.30e+00 1.89e-01 6.41e+01 angle pdb=" CA CYS A 277 " pdb=" CB CYS A 277 " pdb=" SG CYS A 277 " ideal model delta sigma weight residual 114.40 132.73 -18.33 2.30e+00 1.89e-01 6.35e+01 angle pdb=" C CYS A 277 " pdb=" CA CYS A 277 " pdb=" CB CYS A 277 " ideal model delta sigma weight residual 111.71 98.42 13.29 2.23e+00 2.01e-01 3.55e+01 angle pdb=" C CYS D 277 " pdb=" CA CYS D 277 " pdb=" CB CYS D 277 " ideal model delta sigma weight residual 111.71 98.46 13.25 2.23e+00 2.01e-01 3.53e+01 ... (remaining 24361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.75: 10768 23.75 - 47.50: 484 47.50 - 71.25: 125 71.25 - 95.00: 53 95.00 - 118.75: 33 Dihedral angle restraints: 11463 sinusoidal: 5271 harmonic: 6192 Sorted by residual: 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 93.00 162.57 -69.57 1 1.00e+01 1.00e-02 6.25e+01 dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " pdb=" CB CYS J 88 " ideal model delta sinusoidal sigma weight residual 93.00 162.50 -69.50 1 1.00e+01 1.00e-02 6.24e+01 dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " pdb=" CB CYS K 88 " ideal model delta sinusoidal sigma weight residual 93.00 162.36 -69.36 1 1.00e+01 1.00e-02 6.22e+01 ... (remaining 11460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 2701 0.136 - 0.271: 96 0.271 - 0.407: 11 0.407 - 0.542: 0 0.542 - 0.677: 3 Chirality restraints: 2811 Sorted by residual: chirality pdb=" C1 NAG C 405 " pdb=" ND2 ASN C 45 " pdb=" C2 NAG C 405 " pdb=" O5 NAG C 405 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" C1 NAG D 405 " pdb=" ND2 ASN D 45 " pdb=" C2 NAG D 405 " pdb=" O5 NAG D 405 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" C1 NAG A 405 " pdb=" ND2 ASN A 45 " pdb=" C2 NAG A 405 " pdb=" O5 NAG A 405 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.14e+01 ... (remaining 2808 not shown) Planarity restraints: 3126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 229 " 0.945 9.50e-02 1.11e+02 4.24e-01 1.11e+02 pdb=" NE ARG C 229 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG C 229 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG C 229 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 229 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 229 " 0.940 9.50e-02 1.11e+02 4.22e-01 1.11e+02 pdb=" NE ARG D 229 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG D 229 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG D 229 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 229 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 229 " -0.923 9.50e-02 1.11e+02 4.14e-01 1.07e+02 pdb=" NE ARG A 229 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG A 229 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG A 229 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 229 " -0.011 2.00e-02 2.50e+03 ... (remaining 3123 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 29 2.35 - 2.99: 9316 2.99 - 3.63: 26026 3.63 - 4.26: 41730 4.26 - 4.90: 69855 Nonbonded interactions: 146956 Sorted by model distance: nonbonded pdb=" CZ ARG A 222 " pdb=" N2 NAG a 2 " model vdw 1.714 2.680 nonbonded pdb=" O3 NAG O 1 " pdb=" O5 NAG O 2 " model vdw 2.103 3.040 nonbonded pdb=" O3 NAG T 1 " pdb=" O5 NAG T 2 " model vdw 2.107 3.040 nonbonded pdb=" O3 NAG Y 1 " pdb=" O5 NAG Y 2 " model vdw 2.109 3.040 nonbonded pdb=" OD1 ASP H 86 " pdb=" OH TYR H 90 " model vdw 2.126 3.040 ... (remaining 146951 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'R' selection = chain 'T' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) } 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: 6.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 16.340 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 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 0.143 18075 Z= 0.333 Angle : 1.181 18.452 24591 Z= 0.596 Chirality : 0.067 0.677 2811 Planarity : 0.023 0.424 3093 Dihedral : 16.583 118.747 7440 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.16), residues: 2139 helix: 1.23 (0.24), residues: 348 sheet: 1.01 (0.24), residues: 474 loop : -0.80 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.074 0.004 ARG C 222 TYR 0.040 0.003 TYR A 195 PHE 0.034 0.004 PHE B 119 TRP 0.022 0.002 TRP I 47 HIS 0.020 0.003 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00742 (17988) covalent geometry : angle 1.10360 (24366) SS BOND : bond 0.01318 ( 27) SS BOND : angle 5.26006 ( 54) hydrogen bonds : bond 0.22577 ( 581) hydrogen bonds : angle 8.45773 ( 1626) Misc. bond : bond 0.06092 ( 3) link_BETA1-4 : bond 0.01068 ( 21) link_BETA1-4 : angle 4.07368 ( 63) link_BETA1-6 : bond 0.01753 ( 3) link_BETA1-6 : angle 4.37717 ( 9) link_NAG-ASN : bond 0.00839 ( 33) link_NAG-ASN : angle 4.38440 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7432 (mm-30) REVERT: A 123 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6723 (mt-10) REVERT: A 147 PHE cc_start: 0.8158 (t80) cc_final: 0.7932 (t80) REVERT: A 175 ASP cc_start: 0.7240 (p0) cc_final: 0.7008 (p0) REVERT: H 36 TRP cc_start: 0.5680 (m100) cc_final: 0.5195 (m100) REVERT: H 80 LEU cc_start: 0.8195 (tt) cc_final: 0.7584 (tm) REVERT: H 100 TYR cc_start: 0.7321 (m-80) cc_final: 0.7063 (m-80) REVERT: C 62 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7456 (mm-30) REVERT: C 188 ASP cc_start: 0.7556 (m-30) cc_final: 0.6655 (t0) REVERT: E 47 GLN cc_start: 0.8403 (mm110) cc_final: 0.8139 (mt0) REVERT: G 36 TRP cc_start: 0.5702 (m100) cc_final: 0.5233 (m100) REVERT: G 80 LEU cc_start: 0.8118 (tt) cc_final: 0.7567 (tm) REVERT: D 35 GLU cc_start: 0.8314 (tt0) cc_final: 0.8078 (tt0) REVERT: D 62 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7398 (mm-30) REVERT: D 119 GLU cc_start: 0.7690 (tt0) cc_final: 0.7366 (mt-10) REVERT: D 147 PHE cc_start: 0.8117 (t80) cc_final: 0.7870 (t80) REVERT: D 175 ASP cc_start: 0.7097 (p0) cc_final: 0.6853 (p0) REVERT: D 187 THR cc_start: 0.7479 (p) cc_final: 0.7274 (p) REVERT: F 105 GLN cc_start: 0.7656 (tp40) cc_final: 0.7404 (tp40) REVERT: F 109 ASP cc_start: 0.8031 (m-30) cc_final: 0.7807 (m-30) REVERT: I 36 TRP cc_start: 0.5035 (m100) cc_final: 0.4656 (m100) REVERT: I 80 LEU cc_start: 0.8129 (tt) cc_final: 0.7473 (tm) outliers start: 0 outliers final: 2 residues processed: 404 average time/residue: 0.5274 time to fit residues: 240.9402 Evaluate side-chains 298 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 296 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain I residue 100 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 56 HIS A 81 ASN A 96 ASN B 47 GLN H 35 ASN H 76 ASN L 56 ASN C 18 HIS C 56 HIS C 81 ASN C 295 GLN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 GLN E 105 GLN E 125 GLN G 35 ASN G 76 ASN J 56 ASN D 18 HIS D 56 HIS D 81 ASN D 295 GLN F 26 HIS F 42 GLN F 47 GLN F 125 GLN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN K 56 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.156013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.133606 restraints weight = 31024.132| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 3.17 r_work: 0.3828 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18075 Z= 0.185 Angle : 0.784 12.857 24591 Z= 0.377 Chirality : 0.050 0.526 2811 Planarity : 0.006 0.114 3093 Dihedral : 14.333 110.287 3535 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.16 % Allowed : 11.06 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.16), residues: 2139 helix: 1.58 (0.25), residues: 351 sheet: 0.82 (0.23), residues: 480 loop : -0.89 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG C 222 TYR 0.029 0.002 TYR H 100I PHE 0.014 0.002 PHE C 148 TRP 0.011 0.001 TRP C 153 HIS 0.008 0.001 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00400 (17988) covalent geometry : angle 0.72298 (24366) SS BOND : bond 0.00482 ( 27) SS BOND : angle 1.88979 ( 54) hydrogen bonds : bond 0.06037 ( 581) hydrogen bonds : angle 6.53317 ( 1626) Misc. bond : bond 0.00668 ( 3) link_BETA1-4 : bond 0.00782 ( 21) link_BETA1-4 : angle 3.47917 ( 63) link_BETA1-6 : bond 0.01780 ( 3) link_BETA1-6 : angle 3.17372 ( 9) link_NAG-ASN : bond 0.00764 ( 33) link_NAG-ASN : angle 3.66614 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 323 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8176 (tt0) cc_final: 0.7920 (tt0) REVERT: A 62 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7364 (mm-30) REVERT: A 119 GLU cc_start: 0.7735 (tt0) cc_final: 0.7462 (mt-10) REVERT: A 123 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6733 (mt-10) REVERT: A 147 PHE cc_start: 0.8162 (t80) cc_final: 0.7878 (t80) REVERT: A 220 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.6808 (mtm180) REVERT: B 145 ASP cc_start: 0.5852 (p0) cc_final: 0.5615 (p0) REVERT: H 34 MET cc_start: 0.7248 (mmt) cc_final: 0.7035 (mmm) REVERT: H 36 TRP cc_start: 0.5737 (m100) cc_final: 0.5394 (m100) REVERT: H 80 LEU cc_start: 0.8127 (tt) cc_final: 0.7264 (tm) REVERT: L 55 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.6432 (tt0) REVERT: L 56 ASN cc_start: 0.7869 (m-40) cc_final: 0.7217 (m110) REVERT: C 62 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7370 (mm-30) REVERT: C 119 GLU cc_start: 0.7779 (tt0) cc_final: 0.7478 (mt-10) REVERT: E 47 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8184 (mm-40) REVERT: E 145 ASP cc_start: 0.5893 (p0) cc_final: 0.5616 (p0) REVERT: G 4 LEU cc_start: 0.8487 (mp) cc_final: 0.8091 (tp) REVERT: J 11 LEU cc_start: 0.8552 (mp) cc_final: 0.8341 (mt) REVERT: D 35 GLU cc_start: 0.8444 (tt0) cc_final: 0.8207 (tt0) REVERT: D 62 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7231 (mm-30) REVERT: D 119 GLU cc_start: 0.7710 (tt0) cc_final: 0.7424 (mt-10) REVERT: F 145 ASP cc_start: 0.6014 (p0) cc_final: 0.5744 (p0) REVERT: I 36 TRP cc_start: 0.5671 (m100) cc_final: 0.5025 (m100) REVERT: I 71 ARG cc_start: 0.7899 (ptm160) cc_final: 0.7592 (ttm-80) REVERT: I 100 VAL cc_start: 0.9051 (m) cc_final: 0.8706 (t) REVERT: I 100 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.6239 (mtt) REVERT: K 4 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7686 (mtp) REVERT: K 55 GLN cc_start: 0.7221 (tm-30) cc_final: 0.6478 (tt0) outliers start: 40 outliers final: 16 residues processed: 341 average time/residue: 0.5109 time to fit residues: 197.8285 Evaluate side-chains 296 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 276 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain E residue 9 PHE Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain K residue 4 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 165 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN B 105 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN C 96 ASN C 122 ASN C 295 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN E 125 GLN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN J 6 GLN J 56 ASN D 96 ASN D 122 ASN D 295 GLN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS F 47 GLN F 125 GLN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN K 6 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.145776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.122355 restraints weight = 31132.363| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.12 r_work: 0.3666 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 18075 Z= 0.307 Angle : 0.885 14.469 24591 Z= 0.425 Chirality : 0.054 0.536 2811 Planarity : 0.007 0.141 3093 Dihedral : 12.258 109.018 3533 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 5.39 % Allowed : 12.68 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.16), residues: 2139 helix: 1.31 (0.25), residues: 351 sheet: 0.09 (0.23), residues: 483 loop : -1.03 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG C 222 TYR 0.028 0.002 TYR H 100I PHE 0.034 0.003 PHE D 147 TRP 0.043 0.003 TRP G 36 HIS 0.010 0.002 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00692 (17988) covalent geometry : angle 0.82841 (24366) SS BOND : bond 0.00711 ( 27) SS BOND : angle 1.59327 ( 54) hydrogen bonds : bond 0.06286 ( 581) hydrogen bonds : angle 6.30953 ( 1626) Misc. bond : bond 0.00526 ( 3) link_BETA1-4 : bond 0.01039 ( 21) link_BETA1-4 : angle 3.72182 ( 63) link_BETA1-6 : bond 0.01673 ( 3) link_BETA1-6 : angle 3.00294 ( 9) link_NAG-ASN : bond 0.00698 ( 33) link_NAG-ASN : angle 3.80782 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 300 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7299 (mm-30) REVERT: A 123 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6980 (mt-10) REVERT: A 147 PHE cc_start: 0.8461 (t80) cc_final: 0.8159 (t80) REVERT: A 232 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7917 (mp) REVERT: B 74 GLU cc_start: 0.6301 (pm20) cc_final: 0.6004 (pm20) REVERT: B 76 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6504 (ttt-90) REVERT: B 115 MET cc_start: 0.8752 (mmm) cc_final: 0.8504 (tpt) REVERT: L 21 PHE cc_start: 0.7579 (m-80) cc_final: 0.7214 (m-80) REVERT: C 62 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7308 (mm-30) REVERT: C 123 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6236 (mt-10) REVERT: C 201 ARG cc_start: 0.8143 (ttp-110) cc_final: 0.7936 (ttp-110) REVERT: E 47 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8311 (mm-40) REVERT: E 76 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6361 (ttt-90) REVERT: E 145 ASP cc_start: 0.6453 (OUTLIER) cc_final: 0.6249 (p0) REVERT: G 4 LEU cc_start: 0.8600 (mp) cc_final: 0.8321 (tp) REVERT: D 35 GLU cc_start: 0.8523 (tt0) cc_final: 0.8304 (tt0) REVERT: D 62 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7166 (mm-30) REVERT: F 74 GLU cc_start: 0.6342 (pm20) cc_final: 0.6082 (pm20) REVERT: F 145 ASP cc_start: 0.6502 (OUTLIER) cc_final: 0.6286 (p0) REVERT: I 6 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6433 (mm-30) REVERT: I 36 TRP cc_start: 0.6063 (m100) cc_final: 0.5804 (m100) REVERT: I 100 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.6480 (mtt) REVERT: K 4 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7696 (mtp) REVERT: K 55 GLN cc_start: 0.7564 (tm-30) cc_final: 0.7023 (tt0) outliers start: 100 outliers final: 53 residues processed: 357 average time/residue: 0.4788 time to fit residues: 195.3819 Evaluate side-chains 326 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 266 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 58 TYR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 58 TYR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 150 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 153 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 156 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN B 105 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 81 GLN H 100BASN L 6 GLN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN E 125 GLN G 35 ASN G 76 ASN J 56 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN D 295 GLN F 105 GLN F 125 GLN I 35 ASN I 76 ASN I 81 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.149260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.126360 restraints weight = 30825.568| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 3.13 r_work: 0.3717 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18075 Z= 0.163 Angle : 0.778 12.972 24591 Z= 0.369 Chirality : 0.050 0.490 2811 Planarity : 0.005 0.112 3093 Dihedral : 11.175 108.676 3531 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.23 % Favored : 96.73 % Rotamer: Outliers : 4.37 % Allowed : 16.13 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.16), residues: 2139 helix: 1.22 (0.26), residues: 351 sheet: -0.02 (0.23), residues: 474 loop : -1.01 (0.15), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG C 222 TYR 0.028 0.001 TYR I 100I PHE 0.044 0.002 PHE D 147 TRP 0.033 0.001 TRP H 36 HIS 0.010 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00354 (17988) covalent geometry : angle 0.71935 (24366) SS BOND : bond 0.00238 ( 27) SS BOND : angle 2.69920 ( 54) hydrogen bonds : bond 0.05504 ( 581) hydrogen bonds : angle 6.03364 ( 1626) Misc. bond : bond 0.00475 ( 3) link_BETA1-4 : bond 0.00753 ( 21) link_BETA1-4 : angle 3.14108 ( 63) link_BETA1-6 : bond 0.01723 ( 3) link_BETA1-6 : angle 3.09956 ( 9) link_NAG-ASN : bond 0.00616 ( 33) link_NAG-ASN : angle 3.42208 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 301 time to evaluate : 0.685 Fit side-chains REVERT: A 62 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7229 (mm-30) REVERT: A 75 GLN cc_start: 0.7832 (mp10) cc_final: 0.7582 (pt0) REVERT: A 119 GLU cc_start: 0.7794 (tt0) cc_final: 0.7445 (mt-10) REVERT: A 123 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6968 (mt-10) REVERT: A 147 PHE cc_start: 0.8241 (t80) cc_final: 0.7972 (t80) REVERT: B 115 MET cc_start: 0.8707 (mmm) cc_final: 0.8466 (tpt) REVERT: H 80 LEU cc_start: 0.8534 (tt) cc_final: 0.8260 (tt) REVERT: L 21 PHE cc_start: 0.7484 (m-80) cc_final: 0.7080 (m-80) REVERT: L 53 SER cc_start: 0.7397 (OUTLIER) cc_final: 0.6848 (p) REVERT: L 55 GLN cc_start: 0.7635 (tm-30) cc_final: 0.6756 (tt0) REVERT: C 62 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7204 (mm-30) REVERT: C 201 ARG cc_start: 0.8021 (ttp-110) cc_final: 0.7761 (ttp-110) REVERT: E 47 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8295 (mm110) REVERT: E 105 GLN cc_start: 0.8106 (tp40) cc_final: 0.7696 (tp-100) REVERT: E 145 ASP cc_start: 0.5764 (OUTLIER) cc_final: 0.5545 (p0) REVERT: G 80 LEU cc_start: 0.8497 (tt) cc_final: 0.8214 (tt) REVERT: J 53 SER cc_start: 0.7405 (OUTLIER) cc_final: 0.6878 (p) REVERT: D 62 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7131 (mm-30) REVERT: D 119 GLU cc_start: 0.7837 (tt0) cc_final: 0.7456 (mt-10) REVERT: D 201 ARG cc_start: 0.8057 (ttp-110) cc_final: 0.7855 (ttp-110) REVERT: F 74 GLU cc_start: 0.6057 (pm20) cc_final: 0.5736 (pm20) REVERT: I 6 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6200 (mm-30) REVERT: I 36 TRP cc_start: 0.5967 (m100) cc_final: 0.5515 (m100) REVERT: I 100 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.6267 (mtt) REVERT: K 4 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7512 (mtp) REVERT: K 21 PHE cc_start: 0.7014 (m-80) cc_final: 0.6564 (m-80) REVERT: K 55 GLN cc_start: 0.7369 (tm-30) cc_final: 0.6972 (tt0) REVERT: K 56 ASN cc_start: 0.7909 (m-40) cc_final: 0.7408 (m110) outliers start: 81 outliers final: 40 residues processed: 351 average time/residue: 0.4616 time to fit residues: 185.9629 Evaluate side-chains 309 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 264 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain E residue 9 PHE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 58 TYR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 58 TYR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 67 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 79 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 162 optimal weight: 0.2980 chunk 176 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 195 optimal weight: 0.0270 chunk 83 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 54 optimal weight: 10.0000 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS B 47 GLN B 105 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN C 295 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN E 125 GLN G 76 ASN J 56 ASN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 HIS F 47 GLN F 105 GLN F 125 GLN I 35 ASN I 76 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.146865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.124035 restraints weight = 30612.024| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 3.11 r_work: 0.3641 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 18075 Z= 0.212 Angle : 0.771 12.513 24591 Z= 0.369 Chirality : 0.049 0.482 2811 Planarity : 0.007 0.215 3093 Dihedral : 10.744 108.029 3531 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.91 % Allowed : 17.26 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.16), residues: 2139 helix: 1.23 (0.26), residues: 351 sheet: -0.20 (0.23), residues: 483 loop : -1.01 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 222 TYR 0.027 0.002 TYR I 100I PHE 0.046 0.002 PHE D 147 TRP 0.025 0.002 TRP H 36 HIS 0.008 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00479 (17988) covalent geometry : angle 0.71299 (24366) SS BOND : bond 0.00315 ( 27) SS BOND : angle 2.92652 ( 54) hydrogen bonds : bond 0.05606 ( 581) hydrogen bonds : angle 5.97880 ( 1626) Misc. bond : bond 0.01148 ( 3) link_BETA1-4 : bond 0.00673 ( 21) link_BETA1-4 : angle 2.89453 ( 63) link_BETA1-6 : bond 0.01731 ( 3) link_BETA1-6 : angle 3.00207 ( 9) link_NAG-ASN : bond 0.00617 ( 33) link_NAG-ASN : angle 3.41749 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 285 time to evaluate : 0.686 Fit side-chains REVERT: A 62 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7132 (mm-30) REVERT: A 75 GLN cc_start: 0.7854 (mp10) cc_final: 0.7572 (pt0) REVERT: A 119 GLU cc_start: 0.7896 (tt0) cc_final: 0.7523 (mt-10) REVERT: A 147 PHE cc_start: 0.8368 (t80) cc_final: 0.8154 (t80) REVERT: A 173 GLN cc_start: 0.7809 (mp-120) cc_final: 0.7172 (tm-30) REVERT: H 80 LEU cc_start: 0.8609 (tt) cc_final: 0.8367 (tt) REVERT: L 21 PHE cc_start: 0.7323 (m-80) cc_final: 0.7013 (m-80) REVERT: L 53 SER cc_start: 0.7479 (OUTLIER) cc_final: 0.6910 (p) REVERT: L 55 GLN cc_start: 0.7628 (tm-30) cc_final: 0.6994 (tt0) REVERT: L 97 THR cc_start: 0.7141 (p) cc_final: 0.6933 (p) REVERT: C 62 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7191 (mm-30) REVERT: C 201 ARG cc_start: 0.8108 (ttp-110) cc_final: 0.7823 (ttp-110) REVERT: E 47 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8232 (mt0) REVERT: E 74 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6297 (pm20) REVERT: E 76 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6273 (ttt-90) REVERT: E 109 ASP cc_start: 0.8209 (m-30) cc_final: 0.7719 (p0) REVERT: E 145 ASP cc_start: 0.6068 (p0) cc_final: 0.5838 (p0) REVERT: G 4 LEU cc_start: 0.8698 (mp) cc_final: 0.8396 (tp) REVERT: G 80 LEU cc_start: 0.8566 (tt) cc_final: 0.8179 (tt) REVERT: J 53 SER cc_start: 0.7577 (OUTLIER) cc_final: 0.6995 (p) REVERT: D 35 GLU cc_start: 0.8469 (tt0) cc_final: 0.8166 (tt0) REVERT: D 62 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7140 (mm-30) REVERT: D 119 GLU cc_start: 0.7883 (tt0) cc_final: 0.7480 (mt-10) REVERT: D 173 GLN cc_start: 0.7767 (mp-120) cc_final: 0.7078 (tm-30) REVERT: D 201 ARG cc_start: 0.8124 (ttp-110) cc_final: 0.7903 (ttp-110) REVERT: D 220 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.6569 (mtm180) REVERT: D 268 MET cc_start: 0.7158 (ttm) cc_final: 0.6826 (ttm) REVERT: F 74 GLU cc_start: 0.6120 (pm20) cc_final: 0.5687 (pm20) REVERT: I 4 LEU cc_start: 0.8578 (mp) cc_final: 0.8183 (tp) REVERT: I 6 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6233 (mm-30) REVERT: I 36 TRP cc_start: 0.6139 (m100) cc_final: 0.5584 (m100) REVERT: I 80 LEU cc_start: 0.8323 (tt) cc_final: 0.7972 (tt) REVERT: K 4 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7533 (mtp) REVERT: K 21 PHE cc_start: 0.7077 (m-80) cc_final: 0.6650 (m-80) REVERT: K 55 GLN cc_start: 0.7467 (tm-30) cc_final: 0.7077 (tt0) outliers start: 91 outliers final: 52 residues processed: 341 average time/residue: 0.4681 time to fit residues: 182.9771 Evaluate side-chains 328 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 270 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain E residue 9 PHE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 58 TYR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 277 CYS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 58 TYR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 19 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 138 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 209 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 161 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN B 105 GLN H 35 ASN H 76 ASN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN E 125 GLN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN J 56 ASN D 311 HIS F 47 GLN F 105 GLN F 125 GLN I 76 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.148710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.126580 restraints weight = 30584.881| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.06 r_work: 0.3724 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18075 Z= 0.160 Angle : 0.729 9.917 24591 Z= 0.348 Chirality : 0.047 0.378 2811 Planarity : 0.007 0.232 3093 Dihedral : 11.522 113.822 3531 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.56 % Allowed : 18.77 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.17), residues: 2139 helix: 1.27 (0.26), residues: 351 sheet: -0.26 (0.23), residues: 480 loop : -1.01 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A 222 TYR 0.028 0.001 TYR I 100I PHE 0.050 0.002 PHE D 147 TRP 0.030 0.001 TRP H 36 HIS 0.009 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00351 (17988) covalent geometry : angle 0.69181 (24366) SS BOND : bond 0.00244 ( 27) SS BOND : angle 2.35657 ( 54) hydrogen bonds : bond 0.05298 ( 581) hydrogen bonds : angle 5.86403 ( 1626) Misc. bond : bond 0.00757 ( 3) link_BETA1-4 : bond 0.00627 ( 21) link_BETA1-4 : angle 2.69586 ( 63) link_BETA1-6 : bond 0.01712 ( 3) link_BETA1-6 : angle 2.96871 ( 9) link_NAG-ASN : bond 0.00616 ( 33) link_NAG-ASN : angle 2.40769 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 287 time to evaluate : 0.730 Fit side-chains REVERT: A 62 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7090 (mm-30) REVERT: A 75 GLN cc_start: 0.7834 (mp10) cc_final: 0.7559 (pt0) REVERT: A 119 GLU cc_start: 0.7840 (tt0) cc_final: 0.7510 (mt-10) REVERT: A 123 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6994 (mt-10) REVERT: A 173 GLN cc_start: 0.7868 (mp-120) cc_final: 0.7225 (tm-30) REVERT: H 80 LEU cc_start: 0.8681 (tt) cc_final: 0.8468 (tt) REVERT: L 21 PHE cc_start: 0.7344 (m-80) cc_final: 0.7068 (m-80) REVERT: L 53 SER cc_start: 0.7417 (OUTLIER) cc_final: 0.6902 (p) REVERT: L 55 GLN cc_start: 0.7621 (tm-30) cc_final: 0.7078 (tt0) REVERT: L 97 THR cc_start: 0.7134 (p) cc_final: 0.6926 (p) REVERT: C 62 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7133 (mm-30) REVERT: C 201 ARG cc_start: 0.8097 (ttp-110) cc_final: 0.7835 (ttp-110) REVERT: E 45 ILE cc_start: 0.8346 (mm) cc_final: 0.8107 (mm) REVERT: E 47 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8189 (mt0) REVERT: E 74 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6278 (pm20) REVERT: E 109 ASP cc_start: 0.8118 (m-30) cc_final: 0.7807 (p0) REVERT: E 145 ASP cc_start: 0.6008 (p0) cc_final: 0.5795 (p0) REVERT: G 80 LEU cc_start: 0.8555 (tt) cc_final: 0.8031 (tm) REVERT: J 53 SER cc_start: 0.7475 (OUTLIER) cc_final: 0.6935 (p) REVERT: D 35 GLU cc_start: 0.8476 (tt0) cc_final: 0.8265 (tt0) REVERT: D 62 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7113 (mm-30) REVERT: D 75 GLN cc_start: 0.7816 (mp10) cc_final: 0.7547 (mt0) REVERT: D 119 GLU cc_start: 0.7879 (tt0) cc_final: 0.7557 (mt-10) REVERT: D 173 GLN cc_start: 0.7911 (mp-120) cc_final: 0.7210 (tm-30) REVERT: D 201 ARG cc_start: 0.8089 (ttp-110) cc_final: 0.7846 (ttp-110) REVERT: F 74 GLU cc_start: 0.5982 (pm20) cc_final: 0.5700 (pm20) REVERT: I 4 LEU cc_start: 0.8586 (mp) cc_final: 0.8227 (tp) REVERT: I 6 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6228 (mm-30) REVERT: I 36 TRP cc_start: 0.6073 (m100) cc_final: 0.5518 (m100) REVERT: I 80 LEU cc_start: 0.8376 (tt) cc_final: 0.8022 (tt) REVERT: K 4 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7642 (mtp) REVERT: K 21 PHE cc_start: 0.7202 (m-80) cc_final: 0.6773 (m-80) REVERT: K 55 GLN cc_start: 0.7402 (tm-30) cc_final: 0.7184 (tt0) outliers start: 66 outliers final: 38 residues processed: 326 average time/residue: 0.4566 time to fit residues: 171.1269 Evaluate side-chains 314 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 272 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain E residue 9 PHE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 58 TYR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 58 TYR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 19 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 137 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN H 35 ASN H 76 ASN C 210 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN E 125 GLN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN J 56 ASN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 HIS F 47 GLN F 125 GLN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.144935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.122015 restraints weight = 31035.431| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 3.13 r_work: 0.3652 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 18075 Z= 0.248 Angle : 0.791 10.096 24591 Z= 0.382 Chirality : 0.047 0.223 2811 Planarity : 0.008 0.252 3093 Dihedral : 11.215 107.422 3531 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.31 % Allowed : 19.09 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.16), residues: 2139 helix: 1.32 (0.26), residues: 351 sheet: -0.40 (0.22), residues: 480 loop : -1.15 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 222 TYR 0.025 0.002 TYR I 100I PHE 0.045 0.003 PHE D 147 TRP 0.028 0.002 TRP G 36 HIS 0.008 0.002 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00562 (17988) covalent geometry : angle 0.75331 (24366) SS BOND : bond 0.00371 ( 27) SS BOND : angle 2.64945 ( 54) hydrogen bonds : bond 0.05693 ( 581) hydrogen bonds : angle 5.96429 ( 1626) Misc. bond : bond 0.00793 ( 3) link_BETA1-4 : bond 0.00624 ( 21) link_BETA1-4 : angle 2.70005 ( 63) link_BETA1-6 : bond 0.01551 ( 3) link_BETA1-6 : angle 2.89472 ( 9) link_NAG-ASN : bond 0.00505 ( 33) link_NAG-ASN : angle 2.54041 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 282 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7120 (mm-30) REVERT: A 123 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6988 (mt-10) REVERT: A 232 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7704 (mp) REVERT: B 76 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6381 (ttt-90) REVERT: B 115 MET cc_start: 0.8796 (mmm) cc_final: 0.8545 (tpt) REVERT: H 80 LEU cc_start: 0.8780 (tt) cc_final: 0.8567 (tt) REVERT: L 21 PHE cc_start: 0.7375 (m-80) cc_final: 0.7075 (m-80) REVERT: L 53 SER cc_start: 0.7600 (OUTLIER) cc_final: 0.6979 (p) REVERT: L 55 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7283 (tt0) REVERT: L 97 THR cc_start: 0.6999 (p) cc_final: 0.6789 (p) REVERT: C 62 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7166 (mm-30) REVERT: C 201 ARG cc_start: 0.8175 (ttp-110) cc_final: 0.7811 (ttp-110) REVERT: E 47 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8259 (mt0) REVERT: E 74 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6151 (pm20) REVERT: E 76 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6333 (ttt-90) REVERT: E 109 ASP cc_start: 0.8148 (m-30) cc_final: 0.7818 (p0) REVERT: E 145 ASP cc_start: 0.6285 (p0) cc_final: 0.6052 (p0) REVERT: G 4 LEU cc_start: 0.8721 (mp) cc_final: 0.8458 (tp) REVERT: G 36 TRP cc_start: 0.6238 (m100) cc_final: 0.5985 (m100) REVERT: G 80 LEU cc_start: 0.8669 (tt) cc_final: 0.8133 (tm) REVERT: D 35 GLU cc_start: 0.8480 (tt0) cc_final: 0.8246 (tt0) REVERT: D 62 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7115 (mm-30) REVERT: D 75 GLN cc_start: 0.7759 (mp10) cc_final: 0.7495 (pt0) REVERT: D 119 GLU cc_start: 0.7889 (tt0) cc_final: 0.7547 (mt-10) REVERT: D 201 ARG cc_start: 0.8202 (ttp-110) cc_final: 0.7953 (ttp-110) REVERT: I 4 LEU cc_start: 0.8638 (mp) cc_final: 0.8187 (tp) REVERT: I 6 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6492 (mm-30) REVERT: I 36 TRP cc_start: 0.6360 (m100) cc_final: 0.6013 (m100) REVERT: I 80 LEU cc_start: 0.8502 (tt) cc_final: 0.8119 (tt) REVERT: K 4 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7581 (mtp) REVERT: K 21 PHE cc_start: 0.7232 (m-80) cc_final: 0.6824 (m-80) outliers start: 80 outliers final: 50 residues processed: 329 average time/residue: 0.4714 time to fit residues: 177.5688 Evaluate side-chains 321 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 265 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain E residue 9 PHE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 58 TYR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 58 TYR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 67 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 174 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 145 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 296 ASN B 47 GLN B 105 GLN H 35 ASN H 76 ASN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN E 125 GLN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN J 56 ASN F 12 ASN F 47 GLN F 125 GLN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.147715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.125019 restraints weight = 30685.808| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.11 r_work: 0.3645 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18075 Z= 0.184 Angle : 0.758 11.626 24591 Z= 0.363 Chirality : 0.046 0.227 2811 Planarity : 0.009 0.323 3093 Dihedral : 10.990 107.505 3531 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.99 % Allowed : 20.17 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.17), residues: 2139 helix: 1.25 (0.26), residues: 357 sheet: -0.40 (0.23), residues: 480 loop : -1.14 (0.15), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 222 TYR 0.026 0.001 TYR I 100I PHE 0.044 0.002 PHE C 147 TRP 0.035 0.001 TRP H 36 HIS 0.009 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00407 (17988) covalent geometry : angle 0.72261 (24366) SS BOND : bond 0.00303 ( 27) SS BOND : angle 2.41906 ( 54) hydrogen bonds : bond 0.05370 ( 581) hydrogen bonds : angle 5.91471 ( 1626) Misc. bond : bond 0.01237 ( 3) link_BETA1-4 : bond 0.00632 ( 21) link_BETA1-4 : angle 2.56135 ( 63) link_BETA1-6 : bond 0.01560 ( 3) link_BETA1-6 : angle 2.88990 ( 9) link_NAG-ASN : bond 0.00466 ( 33) link_NAG-ASN : angle 2.47479 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 283 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7052 (mm-30) REVERT: A 119 GLU cc_start: 0.7908 (tt0) cc_final: 0.7507 (mt-10) REVERT: B 76 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6855 (ttt-90) REVERT: B 103 GLU cc_start: 0.8548 (mp0) cc_final: 0.8250 (mp0) REVERT: B 115 MET cc_start: 0.8735 (mmm) cc_final: 0.8493 (tpt) REVERT: H 80 LEU cc_start: 0.8789 (tt) cc_final: 0.8546 (tt) REVERT: L 21 PHE cc_start: 0.7323 (m-80) cc_final: 0.6997 (m-80) REVERT: L 53 SER cc_start: 0.7597 (OUTLIER) cc_final: 0.7001 (p) REVERT: L 55 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7205 (tt0) REVERT: L 73 LEU cc_start: 0.7904 (tp) cc_final: 0.7666 (tm) REVERT: L 97 THR cc_start: 0.6902 (p) cc_final: 0.6675 (p) REVERT: C 62 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7038 (mm-30) REVERT: C 188 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.6614 (t0) REVERT: C 201 ARG cc_start: 0.8110 (ttp-110) cc_final: 0.7732 (ttp-110) REVERT: E 47 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8172 (mt0) REVERT: E 74 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6096 (pm20) REVERT: E 76 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6267 (ttt-90) REVERT: E 109 ASP cc_start: 0.8079 (m-30) cc_final: 0.7830 (p0) REVERT: G 4 LEU cc_start: 0.8699 (mp) cc_final: 0.8465 (tp) REVERT: G 80 LEU cc_start: 0.8669 (tt) cc_final: 0.8236 (tm) REVERT: D 35 GLU cc_start: 0.8511 (tt0) cc_final: 0.8134 (tt0) REVERT: D 62 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7026 (mm-30) REVERT: D 75 GLN cc_start: 0.7714 (mp10) cc_final: 0.7465 (pt0) REVERT: D 119 GLU cc_start: 0.7892 (tt0) cc_final: 0.7537 (mt-10) REVERT: D 188 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.6608 (t0) REVERT: D 201 ARG cc_start: 0.8123 (ttp-110) cc_final: 0.7704 (ttp-110) REVERT: F 74 GLU cc_start: 0.6168 (pm20) cc_final: 0.5893 (pm20) REVERT: F 103 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8137 (mp0) REVERT: I 4 LEU cc_start: 0.8592 (mp) cc_final: 0.8158 (tp) REVERT: I 6 GLU cc_start: 0.6759 (mm-30) cc_final: 0.6270 (mm-30) REVERT: I 36 TRP cc_start: 0.6340 (m100) cc_final: 0.5837 (m100) REVERT: I 80 LEU cc_start: 0.8500 (tt) cc_final: 0.8074 (tt) REVERT: K 4 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7539 (mtp) REVERT: K 21 PHE cc_start: 0.7141 (m-80) cc_final: 0.6747 (m-80) outliers start: 74 outliers final: 53 residues processed: 328 average time/residue: 0.4771 time to fit residues: 179.6929 Evaluate side-chains 323 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 263 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain E residue 9 PHE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 58 TYR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 277 CYS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain I residue 58 TYR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 67 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 16 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 205 optimal weight: 0.0070 chunk 105 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS B 12 ASN B 47 GLN B 105 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN E 125 GLN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN G 81 GLN F 125 GLN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN K 56 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.149149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.126594 restraints weight = 30731.940| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 3.11 r_work: 0.3667 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18075 Z= 0.166 Angle : 0.750 13.103 24591 Z= 0.357 Chirality : 0.045 0.228 2811 Planarity : 0.011 0.473 3093 Dihedral : 10.801 107.410 3531 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.56 % Allowed : 20.87 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.17), residues: 2139 helix: 1.33 (0.27), residues: 357 sheet: -0.35 (0.23), residues: 477 loop : -1.06 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG C 222 TYR 0.027 0.001 TYR I 100I PHE 0.046 0.002 PHE C 147 TRP 0.038 0.001 TRP H 36 HIS 0.009 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00366 (17988) covalent geometry : angle 0.71330 (24366) SS BOND : bond 0.00260 ( 27) SS BOND : angle 2.56469 ( 54) hydrogen bonds : bond 0.05225 ( 581) hydrogen bonds : angle 5.84638 ( 1626) Misc. bond : bond 0.01548 ( 3) link_BETA1-4 : bond 0.00627 ( 21) link_BETA1-4 : angle 2.46361 ( 63) link_BETA1-6 : bond 0.01569 ( 3) link_BETA1-6 : angle 2.83469 ( 9) link_NAG-ASN : bond 0.00454 ( 33) link_NAG-ASN : angle 2.51605 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 285 time to evaluate : 0.513 Fit side-chains REVERT: A 62 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7038 (mm-30) REVERT: A 119 GLU cc_start: 0.7884 (tt0) cc_final: 0.7520 (mt-10) REVERT: A 123 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6954 (mt-10) REVERT: B 115 MET cc_start: 0.8760 (mmm) cc_final: 0.8488 (tpt) REVERT: H 80 LEU cc_start: 0.8778 (tt) cc_final: 0.8557 (tt) REVERT: L 21 PHE cc_start: 0.7364 (m-80) cc_final: 0.7066 (m-80) REVERT: L 53 SER cc_start: 0.7554 (OUTLIER) cc_final: 0.6973 (p) REVERT: L 55 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7188 (tt0) REVERT: L 73 LEU cc_start: 0.7898 (tp) cc_final: 0.7673 (tm) REVERT: L 97 THR cc_start: 0.6869 (p) cc_final: 0.6631 (p) REVERT: C 62 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7061 (mm-30) REVERT: C 172 GLU cc_start: 0.8143 (mp0) cc_final: 0.7337 (mp0) REVERT: C 201 ARG cc_start: 0.8117 (ttp-110) cc_final: 0.7630 (ttp-110) REVERT: E 47 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8156 (mt0) REVERT: E 74 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6012 (pm20) REVERT: E 76 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6190 (ttt-90) REVERT: E 103 GLU cc_start: 0.8461 (mp0) cc_final: 0.8070 (mp0) REVERT: G 4 LEU cc_start: 0.8645 (mp) cc_final: 0.8418 (tp) REVERT: G 80 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8324 (tt) REVERT: D 35 GLU cc_start: 0.8492 (tt0) cc_final: 0.8120 (tt0) REVERT: D 62 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7023 (mm-30) REVERT: D 75 GLN cc_start: 0.7696 (mp10) cc_final: 0.7408 (pt0) REVERT: D 119 GLU cc_start: 0.7831 (tt0) cc_final: 0.7504 (mt-10) REVERT: D 188 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.6592 (t0) REVERT: D 201 ARG cc_start: 0.8105 (ttp-110) cc_final: 0.7686 (ttp-110) REVERT: F 74 GLU cc_start: 0.6110 (pm20) cc_final: 0.5529 (pm20) REVERT: F 103 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8094 (mp0) REVERT: I 4 LEU cc_start: 0.8593 (mp) cc_final: 0.8164 (tp) REVERT: I 6 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6188 (mm-30) REVERT: I 36 TRP cc_start: 0.6288 (m100) cc_final: 0.5695 (m100) REVERT: I 80 LEU cc_start: 0.8512 (tt) cc_final: 0.7977 (tt) REVERT: K 4 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7547 (mtp) REVERT: K 21 PHE cc_start: 0.7149 (m-80) cc_final: 0.6766 (m-80) outliers start: 66 outliers final: 52 residues processed: 325 average time/residue: 0.4655 time to fit residues: 173.4780 Evaluate side-chains 322 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 264 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain E residue 9 PHE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 58 TYR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 277 CYS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain I residue 58 TYR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 5 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 146 optimal weight: 0.8980 chunk 85 optimal weight: 0.4980 chunk 64 optimal weight: 0.2980 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 47 GLN B 105 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** E 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN E 125 GLN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN J 56 ASN F 12 ASN F 47 GLN F 125 GLN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN K 56 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.149122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.126730 restraints weight = 30722.273| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 3.13 r_work: 0.3690 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 18075 Z= 0.161 Angle : 0.763 14.157 24591 Z= 0.362 Chirality : 0.045 0.229 2811 Planarity : 0.009 0.385 3093 Dihedral : 10.782 175.231 3531 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.51 % Allowed : 21.20 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.17), residues: 2139 helix: 1.43 (0.27), residues: 357 sheet: -0.28 (0.23), residues: 480 loop : -1.06 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG D 222 TYR 0.025 0.001 TYR G 100I PHE 0.050 0.002 PHE C 147 TRP 0.048 0.001 TRP G 36 HIS 0.009 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00362 (17988) covalent geometry : angle 0.72761 (24366) SS BOND : bond 0.00339 ( 27) SS BOND : angle 2.47991 ( 54) hydrogen bonds : bond 0.05139 ( 581) hydrogen bonds : angle 5.75923 ( 1626) Misc. bond : bond 0.00798 ( 3) link_BETA1-4 : bond 0.00641 ( 21) link_BETA1-4 : angle 2.36789 ( 63) link_BETA1-6 : bond 0.01557 ( 3) link_BETA1-6 : angle 2.73051 ( 9) link_NAG-ASN : bond 0.00438 ( 33) link_NAG-ASN : angle 2.60962 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 289 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7034 (mm-30) REVERT: A 119 GLU cc_start: 0.7848 (tt0) cc_final: 0.7551 (mt-10) REVERT: A 168 MET cc_start: 0.7242 (mmm) cc_final: 0.6881 (ttm) REVERT: B 115 MET cc_start: 0.8761 (mmm) cc_final: 0.8478 (tpt) REVERT: H 80 LEU cc_start: 0.8776 (tt) cc_final: 0.8517 (tt) REVERT: L 21 PHE cc_start: 0.7402 (m-80) cc_final: 0.7155 (m-80) REVERT: L 53 SER cc_start: 0.7539 (OUTLIER) cc_final: 0.6973 (p) REVERT: L 55 GLN cc_start: 0.7654 (tm-30) cc_final: 0.7214 (tt0) REVERT: L 73 LEU cc_start: 0.7949 (tp) cc_final: 0.7746 (tm) REVERT: L 97 THR cc_start: 0.6869 (p) cc_final: 0.6640 (p) REVERT: C 62 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7064 (mm-30) REVERT: C 119 GLU cc_start: 0.7905 (tt0) cc_final: 0.7571 (mt-10) REVERT: C 172 GLU cc_start: 0.8169 (mp0) cc_final: 0.7377 (mp0) REVERT: C 201 ARG cc_start: 0.8120 (ttp-110) cc_final: 0.7645 (ttp-110) REVERT: E 47 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8204 (mt0) REVERT: E 74 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.5839 (pm20) REVERT: E 76 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6445 (ttt-90) REVERT: E 103 GLU cc_start: 0.8488 (mp0) cc_final: 0.8127 (mp0) REVERT: G 80 LEU cc_start: 0.8652 (tt) cc_final: 0.8170 (tt) REVERT: D 35 GLU cc_start: 0.8486 (tt0) cc_final: 0.8124 (tt0) REVERT: D 62 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7041 (mm-30) REVERT: D 119 GLU cc_start: 0.7809 (tt0) cc_final: 0.7542 (mt-10) REVERT: D 188 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.6611 (t0) REVERT: D 201 ARG cc_start: 0.8096 (ttp-110) cc_final: 0.7691 (ttp-110) REVERT: F 103 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8124 (mp0) REVERT: F 109 ASP cc_start: 0.8271 (m-30) cc_final: 0.7609 (p0) REVERT: I 4 LEU cc_start: 0.8597 (mp) cc_final: 0.8164 (tp) REVERT: I 6 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6499 (mm-30) REVERT: I 36 TRP cc_start: 0.6221 (m100) cc_final: 0.5582 (m100) REVERT: I 80 LEU cc_start: 0.8500 (tt) cc_final: 0.8046 (tt) REVERT: K 4 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7575 (mtp) REVERT: K 21 PHE cc_start: 0.7211 (m-80) cc_final: 0.6808 (m-80) outliers start: 65 outliers final: 44 residues processed: 331 average time/residue: 0.4593 time to fit residues: 174.5048 Evaluate side-chains 320 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 14 CYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain G residue 58 TYR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain I residue 58 TYR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 30 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 117 optimal weight: 1.9990 chunk 203 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 201 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS B 12 ASN B 47 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN E 12 ASN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN E 125 GLN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN J 56 ASN F 47 GLN F 105 GLN F 125 GLN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN K 56 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.148341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.125637 restraints weight = 30880.367| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.11 r_work: 0.3695 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 18075 Z= 0.205 Angle : 0.810 14.527 24591 Z= 0.387 Chirality : 0.046 0.217 2811 Planarity : 0.011 0.401 3093 Dihedral : 10.673 159.364 3531 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.24 % Allowed : 22.06 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.17), residues: 2139 helix: 1.48 (0.27), residues: 357 sheet: -0.31 (0.23), residues: 480 loop : -1.10 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.001 ARG D 222 TYR 0.026 0.001 TYR G 100I PHE 0.057 0.002 PHE A 147 TRP 0.039 0.002 TRP G 36 HIS 0.009 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00465 (17988) covalent geometry : angle 0.77233 (24366) SS BOND : bond 0.00331 ( 27) SS BOND : angle 2.92253 ( 54) hydrogen bonds : bond 0.05323 ( 581) hydrogen bonds : angle 5.78468 ( 1626) Misc. bond : bond 0.01090 ( 3) link_BETA1-4 : bond 0.00742 ( 21) link_BETA1-4 : angle 2.37241 ( 63) link_BETA1-6 : bond 0.01446 ( 3) link_BETA1-6 : angle 2.67069 ( 9) link_NAG-ASN : bond 0.00439 ( 33) link_NAG-ASN : angle 2.69163 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5447.69 seconds wall clock time: 94 minutes 29.80 seconds (5669.80 seconds total)