Starting phenix.real_space_refine on Sat Feb 7 14:02:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pdn_71538/02_2026/9pdn_71538.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pdn_71538/02_2026/9pdn_71538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pdn_71538/02_2026/9pdn_71538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pdn_71538/02_2026/9pdn_71538.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pdn_71538/02_2026/9pdn_71538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pdn_71538/02_2026/9pdn_71538.map" } resolution = 3.04 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= 0.002 sd= 0.039 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 16 5.49 5 Mg 5 5.21 5 S 179 5.16 5 C 20828 2.51 5 N 5740 2.21 5 O 6346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 251 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33115 Number of models: 1 Model: "" Number of chains: 22 Chain: "C" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3051 Classifications: {'peptide': 386} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 369} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3040 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 362} Chain: "G" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1824 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 230} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1813 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain: "I" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1895 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 242} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1733 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 10, 'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 62 Chain: "L" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1850 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "M" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1856 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2269 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 277} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "v" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3199 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 22, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3107 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2701 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 325} Chain breaks: 1 Chain: "F" Number of atoms: 2801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2801 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1737 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.50, per 1000 atoms: 0.23 Number of scatterers: 33115 At special positions: 0 Unit cell: (128.904, 192.832, 142.528, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 179 16.00 P 16 15.00 Mg 5 11.99 O 6346 8.00 N 5740 7.00 C 20828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 154 " distance=2.04 Simple disulfide: pdb=" SG CYS H 137 " - pdb=" SG CYS H 213 " distance=2.03 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 186 " 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=0, symmetry=0 Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 501 " pdb="ZN ZN c 501 " - pdb=" NE2 HIS c 115 " pdb="ZN ZN c 501 " - pdb=" NE2 HIS c 113 " 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7924 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 28 sheets defined 46.1% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'C' and resid 21 through 67 removed outlier: 3.682A pdb=" N ILE C 28 " --> pdb=" O TYR C 24 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 33 " --> pdb=" O GLU C 29 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.619A pdb=" N LEU C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 154 through 166 removed outlier: 4.150A pdb=" N VAL C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 172 through 179 Processing helix chain 'C' and resid 197 through 206 Processing helix chain 'C' and resid 225 through 241 removed outlier: 3.586A pdb=" N ARG C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 256 removed outlier: 3.836A pdb=" N SER C 256 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 281 Processing helix chain 'C' and resid 321 through 332 removed outlier: 3.701A pdb=" N ASP C 327 " --> pdb=" O GLU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 350 removed outlier: 3.521A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 372 removed outlier: 3.850A pdb=" N LYS C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 391 removed outlier: 3.699A pdb=" N ALA C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS C 389 " --> pdb=" O MET C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 403 Processing helix chain 'D' and resid 40 through 82 removed outlier: 3.512A pdb=" N TYR D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.749A pdb=" N LEU D 123 " --> pdb=" O ASP D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 182 removed outlier: 3.621A pdb=" N ALA D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 187 through 193 removed outlier: 3.710A pdb=" N TYR D 191 " --> pdb=" O HIS D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 222 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 242 through 257 Processing helix chain 'D' and resid 267 through 270 Processing helix chain 'D' and resid 279 through 297 removed outlier: 3.530A pdb=" N VAL D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 350 removed outlier: 3.845A pdb=" N ARG D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 365 Processing helix chain 'D' and resid 371 through 389 Processing helix chain 'D' and resid 395 through 408 removed outlier: 3.619A pdb=" N THR D 405 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE D 407 " --> pdb=" O TYR D 403 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS D 408 " --> pdb=" O LYS D 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 33 removed outlier: 3.530A pdb=" N ALA G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE G 29 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 36 No H-bonds generated for 'chain 'G' and resid 34 through 36' Processing helix chain 'G' and resid 62 through 66 removed outlier: 3.609A pdb=" N VAL G 66 " --> pdb=" O SER G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 128 removed outlier: 3.675A pdb=" N CYS G 115 " --> pdb=" O VAL G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 183 removed outlier: 3.637A pdb=" N SER G 175 " --> pdb=" O LYS G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 211 through 213 No H-bonds generated for 'chain 'G' and resid 211 through 213' Processing helix chain 'G' and resid 231 through 244 Processing helix chain 'H' and resid 19 through 31 Processing helix chain 'H' and resid 79 through 102 removed outlier: 3.652A pdb=" N VAL H 85 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 121 removed outlier: 3.736A pdb=" N TYR H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 174 Processing helix chain 'H' and resid 183 through 197 removed outlier: 3.696A pdb=" N HIS H 189 " --> pdb=" O GLU H 185 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU H 197 " --> pdb=" O LEU H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 234 Processing helix chain 'I' and resid 18 through 27 Processing helix chain 'I' and resid 28 through 31 Processing helix chain 'I' and resid 79 through 102 Processing helix chain 'I' and resid 107 through 122 removed outlier: 3.644A pdb=" N TYR I 121 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR I 122 " --> pdb=" O LYS I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 178 Processing helix chain 'I' and resid 185 through 201 removed outlier: 3.863A pdb=" N LYS I 199 " --> pdb=" O LYS I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 209 No H-bonds generated for 'chain 'I' and resid 207 through 209' Processing helix chain 'I' and resid 229 through 248 removed outlier: 3.589A pdb=" N LYS I 246 " --> pdb=" O GLU I 242 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA I 247 " --> pdb=" O GLU I 243 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU I 248 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 251 No H-bonds generated for 'chain 'I' and resid 249 through 251' Processing helix chain 'J' and resid 16 through 29 removed outlier: 3.573A pdb=" N GLN J 23 " --> pdb=" O VAL J 19 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS J 27 " --> pdb=" O GLN J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 removed outlier: 3.991A pdb=" N THR J 58 " --> pdb=" O ASP J 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG J 60 " --> pdb=" O ARG J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 98 removed outlier: 3.520A pdb=" N ALA J 80 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 120 Processing helix chain 'J' and resid 164 through 176 removed outlier: 4.035A pdb=" N LYS J 174 " --> pdb=" O GLU J 170 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN J 175 " --> pdb=" O PHE J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 182 removed outlier: 3.590A pdb=" N ILE J 181 " --> pdb=" O THR J 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 196 Processing helix chain 'J' and resid 223 through 237 Processing helix chain 'J' and resid 238 through 240 No H-bonds generated for 'chain 'J' and resid 238 through 240' Processing helix chain 'L' and resid 19 through 32 removed outlier: 3.618A pdb=" N GLU L 27 " --> pdb=" O GLU L 23 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA L 28 " --> pdb=" O TYR L 24 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL L 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS L 30 " --> pdb=" O MET L 26 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN L 31 " --> pdb=" O GLU L 27 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 99 Processing helix chain 'L' and resid 104 through 118 removed outlier: 3.555A pdb=" N ILE L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 175 Processing helix chain 'L' and resid 176 through 180 removed outlier: 4.004A pdb=" N MET L 180 " --> pdb=" O SER L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 199 Processing helix chain 'L' and resid 229 through 234 Processing helix chain 'M' and resid 20 through 31 removed outlier: 3.655A pdb=" N GLU M 31 " --> pdb=" O MET M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 103 Processing helix chain 'M' and resid 107 through 122 removed outlier: 3.614A pdb=" N TYR M 122 " --> pdb=" O TYR M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 178 removed outlier: 3.804A pdb=" N GLU M 175 " --> pdb=" O ALA M 171 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 200 Processing helix chain 'M' and resid 228 through 241 Processing helix chain 'M' and resid 242 through 244 No H-bonds generated for 'chain 'M' and resid 242 through 244' Processing helix chain 'c' and resid 35 through 48 Processing helix chain 'c' and resid 88 through 103 removed outlier: 3.627A pdb=" N GLN c 101 " --> pdb=" O ASP c 97 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR c 102 " --> pdb=" O MET c 98 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY c 103 " --> pdb=" O LEU c 99 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 137 removed outlier: 3.971A pdb=" N LEU c 136 " --> pdb=" O SER c 132 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER c 137 " --> pdb=" O PHE c 133 " (cutoff:3.500A) Processing helix chain 'c' and resid 164 through 169 removed outlier: 4.018A pdb=" N MET c 168 " --> pdb=" O ALA c 165 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL c 169 " --> pdb=" O ASN c 166 " (cutoff:3.500A) Processing helix chain 'c' and resid 188 through 193 removed outlier: 3.647A pdb=" N ILE c 193 " --> pdb=" O ILE c 189 " (cutoff:3.500A) Processing helix chain 'c' and resid 213 through 218 Processing helix chain 'c' and resid 219 through 222 removed outlier: 4.203A pdb=" N LYS c 222 " --> pdb=" O ASN c 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 219 through 222' Processing helix chain 'c' and resid 233 through 262 Processing helix chain 'c' and resid 266 through 274 removed outlier: 3.514A pdb=" N ILE c 272 " --> pdb=" O GLU c 268 " (cutoff:3.500A) Processing helix chain 'c' and resid 285 through 309 Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 41 through 64 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.552A pdb=" N GLN A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 134 removed outlier: 3.661A pdb=" N ILE A 134 " --> pdb=" O PRO A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 165 removed outlier: 3.723A pdb=" N MET A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 180 through 192 removed outlier: 3.945A pdb=" N VAL A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 199 through 204 removed outlier: 4.020A pdb=" N LEU A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 232 Processing helix chain 'A' and resid 251 through 267 Processing helix chain 'A' and resid 277 through 280 Processing helix chain 'A' and resid 291 through 307 removed outlier: 3.944A pdb=" N VAL A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.575A pdb=" N LEU A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 347 through 359 Processing helix chain 'A' and resid 369 through 376 removed outlier: 3.532A pdb=" N LEU A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 399 removed outlier: 3.602A pdb=" N ILE A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 removed outlier: 3.536A pdb=" N PHE A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 4.426A pdb=" N LYS A 422 " --> pdb=" O LYS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'B' and resid 58 through 86 removed outlier: 3.523A pdb=" N LEU B 62 " --> pdb=" O CYS B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.856A pdb=" N LYS B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.857A pdb=" N SER B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU B 202 " --> pdb=" O LYS B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.176A pdb=" N TYR B 211 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET B 214 " --> pdb=" O TYR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 261 through 277 removed outlier: 3.560A pdb=" N LYS B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 299 through 317 removed outlier: 3.608A pdb=" N ILE B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 369 Processing helix chain 'B' and resid 380 through 385 Processing helix chain 'B' and resid 391 through 409 Processing helix chain 'B' and resid 415 through 427 removed outlier: 3.755A pdb=" N PHE B 419 " --> pdb=" O THR B 415 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 52 removed outlier: 3.708A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 125 removed outlier: 4.223A pdb=" N HIS E 124 " --> pdb=" O ASN E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 155 removed outlier: 4.162A pdb=" N LEU E 151 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 156 through 163 Processing helix chain 'E' and resid 179 through 191 Processing helix chain 'E' and resid 199 through 204 removed outlier: 3.850A pdb=" N VAL E 204 " --> pdb=" O SER E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 225 removed outlier: 3.719A pdb=" N ILE E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP E 224 " --> pdb=" O ASN E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 238 removed outlier: 4.024A pdb=" N ALA E 237 " --> pdb=" O GLU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 265 removed outlier: 3.607A pdb=" N ILE E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 307 through 318 removed outlier: 3.668A pdb=" N ASP E 311 " --> pdb=" O GLN E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 335 removed outlier: 3.724A pdb=" N ILE E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 356 removed outlier: 3.564A pdb=" N LEU E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG E 344 " --> pdb=" O GLY E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 377 removed outlier: 4.268A pdb=" N PHE E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 85 removed outlier: 3.545A pdb=" N THR F 85 " --> pdb=" O LYS F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 145 Processing helix chain 'F' and resid 171 through 176 removed outlier: 3.986A pdb=" N GLU F 176 " --> pdb=" O LYS F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 202 Processing helix chain 'F' and resid 203 through 208 Processing helix chain 'F' and resid 208 through 216 removed outlier: 4.051A pdb=" N PHE F 212 " --> pdb=" O HIS F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 243 Processing helix chain 'F' and resid 263 through 278 Processing helix chain 'F' and resid 288 through 293 removed outlier: 3.640A pdb=" N THR F 293 " --> pdb=" O ASP F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 304 removed outlier: 3.731A pdb=" N ARG F 304 " --> pdb=" O ALA F 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 301 through 304' Processing helix chain 'F' and resid 305 through 320 removed outlier: 3.521A pdb=" N PHE F 320 " --> pdb=" O GLN F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 369 Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 392 through 411 removed outlier: 4.321A pdb=" N CYS F 400 " --> pdb=" O CYS F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 428 removed outlier: 3.916A pdb=" N GLN F 428 " --> pdb=" O ILE F 424 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 30 Processing helix chain 'K' and resid 31 through 34 Processing helix chain 'K' and resid 81 through 104 Processing helix chain 'K' and resid 108 through 121 Processing helix chain 'K' and resid 173 through 185 removed outlier: 3.754A pdb=" N GLU K 183 " --> pdb=" O SER K 179 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 206 Processing helix chain 'K' and resid 233 through 240 Processing sheet with id=AA1, first strand: chain 'D' and resid 111 through 112 removed outlier: 6.602A pdb=" N ALA C 115 " --> pdb=" O HIS C 124 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N LEU C 123 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASP C 98 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LYS C 125 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG C 78 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS C 88 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL C 76 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.021A pdb=" N LEU C 188 " --> pdb=" O THR C 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 210 through 213 removed outlier: 6.377A pdb=" N THR C 210 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE C 247 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE C 212 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 337 through 338 removed outlier: 7.144A pdb=" N ASN C 337 " --> pdb=" O VAL C 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 87 through 91 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 104 through 105 current: chain 'D' and resid 139 through 141 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 139 through 141 current: chain 'A' and resid 111 through 114 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 120 through 123 current: chain 'A' and resid 149 through 152 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 149 through 152 current: chain 'B' and resid 120 through 124 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 131 through 134 current: chain 'B' and resid 159 through 162 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 159 through 162 current: chain 'E' and resid 69 through 73 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 78 through 83 current: chain 'E' and resid 106 through 111 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 106 through 111 current: chain 'F' and resid 121 through 126 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 131 through 133 current: chain 'F' and resid 160 through 163 Processing sheet with id=AA6, first strand: chain 'D' and resid 201 through 205 Processing sheet with id=AA7, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.952A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 69 through 73 removed outlier: 3.675A pdb=" N ILE G 72 " --> pdb=" O ILE G 76 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE G 139 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR G 81 " --> pdb=" O CYS G 137 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY G 142 " --> pdb=" O GLN G 150 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS G 153 " --> pdb=" O CYS G 161 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS G 161 " --> pdb=" O LYS G 153 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY G 162 " --> pdb=" O ASP H 58 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 160 through 163 Processing sheet with id=AB1, first strand: chain 'H' and resid 66 through 69 removed outlier: 6.704A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY H 73 " --> pdb=" O CYS H 137 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN H 140 " --> pdb=" O ARG H 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 34 through 36 Processing sheet with id=AB3, first strand: chain 'I' and resid 43 through 48 Processing sheet with id=AB4, first strand: chain 'I' and resid 65 through 69 removed outlier: 6.307A pdb=" N MET I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU I 135 " --> pdb=" O SER I 75 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY I 138 " --> pdb=" O GLN I 146 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU I 147 " --> pdb=" O TRP I 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 77 through 78 Processing sheet with id=AB6, first strand: chain 'J' and resid 158 through 161 Processing sheet with id=AB7, first strand: chain 'J' and resid 62 through 63 removed outlier: 3.700A pdb=" N ARG J 143 " --> pdb=" O GLY J 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 158 through 161 removed outlier: 3.529A pdb=" N ILE L 214 " --> pdb=" O THR L 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 63 through 65 removed outlier: 3.522A pdb=" N GLY L 136 " --> pdb=" O HIS L 143 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP L 138 " --> pdb=" O GLY L 141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 162 through 165 Processing sheet with id=AC2, first strand: chain 'M' and resid 66 through 67 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 74 through 76 current: chain 'M' and resid 133 through 141 removed outlier: 3.762A pdb=" N PHE M 135 " --> pdb=" O ILE M 151 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET M 150 " --> pdb=" O TYR M 158 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR M 158 " --> pdb=" O MET M 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'c' and resid 30 through 34 removed outlier: 6.377A pdb=" N GLN c 30 " --> pdb=" O VAL c 67 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL c 69 " --> pdb=" O GLN c 30 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N TYR c 32 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ASP c 71 " --> pdb=" O TYR c 32 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N SER c 34 " --> pdb=" O ASP c 71 " (cutoff:3.500A) removed outlier: 11.509A pdb=" N PHE c 73 " --> pdb=" O SER c 34 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR c 66 " --> pdb=" O VAL c 62 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL c 62 " --> pdb=" O THR c 66 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU c 58 " --> pdb=" O ILE c 70 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N VAL c 72 " --> pdb=" O LEU c 56 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU c 56 " --> pdb=" O VAL c 72 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ALA c 74 " --> pdb=" O MET c 54 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N MET c 54 " --> pdb=" O ALA c 74 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLY c 59 " --> pdb=" O VAL c 108 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL c 108 " --> pdb=" O GLY c 59 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL c 145 " --> pdb=" O HIS c 113 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N ILE c 157 " --> pdb=" O ILE c 205 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE c 205 " --> pdb=" O ILE c 157 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA c 159 " --> pdb=" O ILE c 203 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL c 31 " --> pdb=" O ASN c 206 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG c 208 " --> pdb=" O VAL c 31 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE c 33 " --> pdb=" O ARG c 208 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 211 through 215 removed outlier: 6.560A pdb=" N CYS A 270 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LEU A 318 " --> pdb=" O CYS A 270 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE A 272 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ALA A 320 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE A 274 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N CYS A 236 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N PHE A 273 " --> pdb=" O CYS A 236 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE A 238 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP A 275 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL A 240 " --> pdb=" O ASP A 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 246 through 250 removed outlier: 6.445A pdb=" N THR B 246 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N PHE B 283 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU B 248 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER B 280 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE B 328 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL B 282 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ALA B 330 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE B 284 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 278 through 279 removed outlier: 7.403A pdb=" N THR E 279 " --> pdb=" O CYS E 170 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU E 172 " --> pdb=" O THR E 279 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU E 171 " --> pdb=" O ILE E 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 194 through 198 Processing sheet with id=AC8, first strand: chain 'F' and resid 249 through 250 removed outlier: 6.540A pdb=" N LEU F 249 " --> pdb=" O PHE F 284 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ASP F 286 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE F 283 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ALA F 331 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE F 285 " --> pdb=" O ALA F 331 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 167 through 170 Processing sheet with id=AD1, first strand: chain 'K' and resid 74 through 80 1500 hydrogen bonds defined for protein. 4290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.58 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11123 1.34 - 1.47: 7012 1.47 - 1.59: 15205 1.59 - 1.72: 11 1.72 - 1.84: 300 Bond restraints: 33651 Sorted by residual: bond pdb=" C ALA B 278 " pdb=" N PRO B 279 " ideal model delta sigma weight residual 1.330 1.368 -0.038 1.19e-02 7.06e+03 1.02e+01 bond pdb=" C ALA F 279 " pdb=" N PRO F 280 " ideal model delta sigma weight residual 1.330 1.356 -0.026 1.19e-02 7.06e+03 4.88e+00 bond pdb=" C LEU B 203 " pdb=" N PRO B 204 " ideal model delta sigma weight residual 1.336 1.351 -0.016 1.08e-02 8.57e+03 2.06e+00 bond pdb=" CB LYS A 268 " pdb=" CG LYS A 268 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.95e+00 bond pdb=" N ASP I 41 " pdb=" CA ASP I 41 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.81e+00 ... (remaining 33646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 45126 3.11 - 6.21: 344 6.21 - 9.32: 27 9.32 - 12.42: 5 12.42 - 15.53: 1 Bond angle restraints: 45503 Sorted by residual: angle pdb=" N PRO c 23 " pdb=" CA PRO c 23 " pdb=" CB PRO c 23 " ideal model delta sigma weight residual 103.35 110.65 -7.30 8.70e-01 1.32e+00 7.04e+01 angle pdb=" C LYS M 207 " pdb=" CA LYS M 207 " pdb=" CB LYS M 207 " ideal model delta sigma weight residual 116.54 110.02 6.52 1.15e+00 7.56e-01 3.21e+01 angle pdb=" C LEU G 114 " pdb=" N CYS G 115 " pdb=" CA CYS G 115 " ideal model delta sigma weight residual 122.65 113.95 8.70 1.60e+00 3.91e-01 2.95e+01 angle pdb=" N LYS C 82 " pdb=" CA LYS C 82 " pdb=" C LYS C 82 " ideal model delta sigma weight residual 114.64 107.18 7.46 1.52e+00 4.33e-01 2.41e+01 angle pdb=" N VAL G 66 " pdb=" CA VAL G 66 " pdb=" C VAL G 66 " ideal model delta sigma weight residual 112.80 107.44 5.36 1.15e+00 7.56e-01 2.17e+01 ... (remaining 45498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 17500 18.02 - 36.05: 2479 36.05 - 54.07: 641 54.07 - 72.10: 91 72.10 - 90.12: 46 Dihedral angle restraints: 20757 sinusoidal: 8483 harmonic: 12274 Sorted by residual: dihedral pdb=" CA ILE D 85 " pdb=" C ILE D 85 " pdb=" N PRO D 86 " pdb=" CA PRO D 86 " ideal model delta harmonic sigma weight residual 180.00 134.29 45.71 0 5.00e+00 4.00e-02 8.36e+01 dihedral pdb=" CB CYS M 41 " pdb=" SG CYS M 41 " pdb=" SG CYS M 186 " pdb=" CB CYS M 186 " ideal model delta sinusoidal sigma weight residual -86.00 -12.44 -73.56 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CA THR B 53 " pdb=" C THR B 53 " pdb=" N PRO B 54 " pdb=" CA PRO B 54 " ideal model delta harmonic sigma weight residual 180.00 140.04 39.96 0 5.00e+00 4.00e-02 6.39e+01 ... (remaining 20754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 4800 0.084 - 0.168: 377 0.168 - 0.252: 6 0.252 - 0.337: 2 0.337 - 0.421: 3 Chirality restraints: 5188 Sorted by residual: chirality pdb=" CG LEU I 114 " pdb=" CB LEU I 114 " pdb=" CD1 LEU I 114 " pdb=" CD2 LEU I 114 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CG LEU D 73 " pdb=" CB LEU D 73 " pdb=" CD1 LEU D 73 " pdb=" CD2 LEU D 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CG LEU G 179 " pdb=" CB LEU G 179 " pdb=" CD1 LEU G 179 " pdb=" CD2 LEU G 179 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 5185 not shown) Planarity restraints: 5888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 53 " 0.058 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO B 54 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 54 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 54 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 85 " -0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO D 86 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO D 86 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 86 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN M 221 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C ASN M 221 " -0.041 2.00e-02 2.50e+03 pdb=" O ASN M 221 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY M 222 " 0.014 2.00e-02 2.50e+03 ... (remaining 5885 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 315 2.55 - 3.14: 26822 3.14 - 3.73: 54035 3.73 - 4.31: 72548 4.31 - 4.90: 120713 Nonbonded interactions: 274433 Sorted by model distance: nonbonded pdb=" OG1 THR C 197 " pdb="MG MG C 502 " model vdw 1.968 2.170 nonbonded pdb=" O2G ATP C 501 " pdb="MG MG C 502 " model vdw 1.993 2.170 nonbonded pdb=" O2G ATP B 501 " pdb="MG MG B 502 " model vdw 2.005 2.170 nonbonded pdb=" OG1 THR A 223 " pdb="MG MG A 502 " model vdw 2.007 2.170 nonbonded pdb=" OD2 ASP C 249 " pdb="MG MG C 502 " model vdw 2.008 2.170 ... (remaining 274428 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 34.600 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 : 0.003 0.153 33656 Z= 0.156 Angle : 0.729 15.527 45509 Z= 0.411 Chirality : 0.045 0.421 5188 Planarity : 0.005 0.087 5888 Dihedral : 17.768 90.119 12824 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.57 % Favored : 94.17 % Rotamer: Outliers : 2.91 % Allowed : 29.06 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.02 % 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: -0.43 (0.13), residues: 4184 helix: 0.60 (0.13), residues: 1748 sheet: -0.68 (0.20), residues: 657 loop : -0.93 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 80 TYR 0.025 0.001 TYR E 40 PHE 0.023 0.001 PHE H 173 TRP 0.036 0.003 TRP I 159 HIS 0.024 0.001 HIS E 271 Details of bonding type rmsd covalent geometry : bond 0.00304 (33651) covalent geometry : angle 0.72655 (45503) SS BOND : bond 0.00746 ( 3) SS BOND : angle 4.96907 ( 6) hydrogen bonds : bond 0.18440 ( 1500) hydrogen bonds : angle 6.81318 ( 4290) metal coordination : bond 0.12788 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 705 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8375 (tm-30) REVERT: C 139 MET cc_start: 0.9152 (ttm) cc_final: 0.8854 (ttp) REVERT: C 180 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8681 (pt) REVERT: D 58 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8254 (tm-30) REVERT: D 60 TYR cc_start: 0.4379 (OUTLIER) cc_final: 0.2996 (t80) REVERT: D 252 ARG cc_start: 0.8062 (ttp80) cc_final: 0.7788 (ttm-80) REVERT: D 398 ASP cc_start: 0.8297 (m-30) cc_final: 0.7947 (m-30) REVERT: G 159 TYR cc_start: 0.8907 (t80) cc_final: 0.8654 (t80) REVERT: G 180 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8537 (mm-30) REVERT: I 93 ILE cc_start: 0.8826 (mt) cc_final: 0.8530 (mt) REVERT: I 220 ASN cc_start: 0.7684 (t0) cc_final: 0.7442 (t0) REVERT: J 136 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6511 (t80) REVERT: M 169 ARG cc_start: 0.8347 (mtp85) cc_final: 0.8025 (mmm-85) REVERT: c 149 GLN cc_start: 0.7949 (mt0) cc_final: 0.7727 (mm-40) REVERT: c 167 MET cc_start: 0.6714 (mmt) cc_final: 0.6351 (mmp) REVERT: c 286 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8061 (pp20) REVERT: A 371 GLU cc_start: 0.8373 (tp30) cc_final: 0.8129 (mm-30) REVERT: B 71 TYR cc_start: 0.9092 (m-80) cc_final: 0.8744 (m-80) REVERT: B 75 GLU cc_start: 0.6302 (OUTLIER) cc_final: 0.5299 (mp0) REVERT: B 165 ASP cc_start: 0.8578 (t70) cc_final: 0.7749 (t0) REVERT: E 232 MET cc_start: 0.8821 (ttm) cc_final: 0.8403 (mtp) REVERT: E 320 ILE cc_start: 0.8047 (mm) cc_final: 0.7694 (mp) REVERT: E 368 MET cc_start: 0.5466 (mpp) cc_final: 0.4418 (tpp) REVERT: E 372 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7436 (mtt-85) REVERT: F 200 GLU cc_start: 0.7425 (pt0) cc_final: 0.7113 (pt0) REVERT: F 236 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8376 (tt) REVERT: F 286 ASP cc_start: 0.6436 (t70) cc_final: 0.6205 (t0) REVERT: F 347 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.5710 (mpp80) REVERT: F 356 MET cc_start: 0.8999 (tpp) cc_final: 0.8575 (tpp) REVERT: K 10 ARG cc_start: 0.8701 (ttm-80) cc_final: 0.7090 (mpt180) REVERT: K 95 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7708 (tm-30) REVERT: K 164 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8549 (tm-30) REVERT: K 182 GLN cc_start: 0.8467 (mt0) cc_final: 0.8225 (mt0) REVERT: K 224 GLN cc_start: 0.8337 (tt0) cc_final: 0.7817 (tm-30) REVERT: K 228 MET cc_start: 0.5751 (mmm) cc_final: 0.5339 (mmp) outliers start: 103 outliers final: 80 residues processed: 767 average time/residue: 0.2131 time to fit residues: 266.7915 Evaluate side-chains 725 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 637 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 206 HIS Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain I residue 74 CYS Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 228 TYR Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 154 PHE Chi-restraints excluded: chain L residue 214 ILE Chi-restraints excluded: chain M residue 63 ASN Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 180 ASN Chi-restraints excluded: chain c residue 204 THR Chi-restraints excluded: chain c residue 261 GLU Chi-restraints excluded: chain c residue 286 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 155 ASN Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 347 ARG Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 229 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 197 optimal weight: 0.0270 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 106 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN D 414 HIS ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS I 220 ASN ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 214 GLN ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN E 220 ASN ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 ASN F 325 GLN F 436 GLN K 23 GLN K 204 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.122630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.098631 restraints weight = 66343.444| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.64 r_work: 0.3321 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33656 Z= 0.145 Angle : 0.627 13.497 45509 Z= 0.324 Chirality : 0.044 0.257 5188 Planarity : 0.005 0.077 5888 Dihedral : 8.974 88.081 4906 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.00 % Favored : 94.72 % Rotamer: Outliers : 4.67 % Allowed : 24.96 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 1.16 % 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: -0.24 (0.13), residues: 4184 helix: 0.83 (0.12), residues: 1784 sheet: -0.82 (0.19), residues: 693 loop : -0.82 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 80 TYR 0.014 0.001 TYR M 25 PHE 0.016 0.001 PHE H 173 TRP 0.021 0.002 TRP I 159 HIS 0.018 0.001 HIS E 271 Details of bonding type rmsd covalent geometry : bond 0.00323 (33651) covalent geometry : angle 0.62620 (45503) SS BOND : bond 0.00871 ( 3) SS BOND : angle 2.73947 ( 6) hydrogen bonds : bond 0.04361 ( 1500) hydrogen bonds : angle 5.07380 ( 4290) metal coordination : bond 0.02194 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 709 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8287 (mt-10) REVERT: C 139 MET cc_start: 0.9171 (ttm) cc_final: 0.8892 (ttp) REVERT: C 180 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8710 (pt) REVERT: D 60 TYR cc_start: 0.4448 (OUTLIER) cc_final: 0.3034 (t80) REVERT: D 252 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7960 (ttp80) REVERT: D 398 ASP cc_start: 0.8393 (m-30) cc_final: 0.8144 (m-30) REVERT: G 88 ARG cc_start: 0.8492 (tpp80) cc_final: 0.8119 (mtt90) REVERT: G 152 TYR cc_start: 0.8062 (m-80) cc_final: 0.7821 (m-80) REVERT: G 180 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8493 (mm-30) REVERT: G 244 GLU cc_start: 0.5622 (mp0) cc_final: 0.5269 (mp0) REVERT: H 58 ASP cc_start: 0.8660 (t0) cc_final: 0.8416 (t0) REVERT: H 72 ILE cc_start: 0.8922 (mt) cc_final: 0.8658 (mt) REVERT: H 79 MET cc_start: 0.8219 (mtp) cc_final: 0.7544 (mtt) REVERT: I 93 ILE cc_start: 0.8803 (mt) cc_final: 0.8497 (mt) REVERT: I 167 ASN cc_start: 0.9048 (m110) cc_final: 0.8830 (m110) REVERT: I 220 ASN cc_start: 0.7711 (t0) cc_final: 0.7398 (t0) REVERT: J 136 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6588 (t80) REVERT: L 176 MET cc_start: 0.7642 (tmm) cc_final: 0.7346 (tmm) REVERT: c 29 GLU cc_start: 0.8312 (tt0) cc_final: 0.7920 (tt0) REVERT: c 148 ILE cc_start: 0.9060 (mm) cc_final: 0.8762 (mm) REVERT: c 283 HIS cc_start: 0.8055 (m-70) cc_final: 0.7750 (m-70) REVERT: c 285 GLU cc_start: 0.8532 (pp20) cc_final: 0.7471 (tp30) REVERT: c 286 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8377 (tm-30) REVERT: B 71 TYR cc_start: 0.9055 (m-80) cc_final: 0.8587 (m-80) REVERT: B 75 GLU cc_start: 0.6246 (OUTLIER) cc_final: 0.5212 (mp0) REVERT: B 165 ASP cc_start: 0.8684 (t70) cc_final: 0.8007 (t0) REVERT: B 324 ASP cc_start: 0.8677 (t0) cc_final: 0.8345 (t0) REVERT: B 372 MET cc_start: 0.8705 (mmm) cc_final: 0.8465 (mtt) REVERT: B 385 MET cc_start: 0.7553 (ppp) cc_final: 0.7311 (ppp) REVERT: E 66 GLU cc_start: 0.8993 (pt0) cc_final: 0.8528 (pp20) REVERT: E 110 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7429 (p90) REVERT: E 298 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7835 (mtpt) REVERT: E 368 MET cc_start: 0.5652 (mpp) cc_final: 0.4446 (tpp) REVERT: E 372 ARG cc_start: 0.7866 (mtm-85) cc_final: 0.7337 (mtt-85) REVERT: F 121 CYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7139 (p) REVERT: F 336 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8104 (p0) REVERT: K 10 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8469 (mmm-85) REVERT: K 93 ARG cc_start: 0.5083 (ttt180) cc_final: 0.4432 (mtt180) REVERT: K 95 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7725 (tm-30) REVERT: K 104 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8545 (t0) REVERT: K 118 ASN cc_start: 0.8989 (m-40) cc_final: 0.8573 (m-40) REVERT: K 224 GLN cc_start: 0.8386 (tt0) cc_final: 0.8136 (tt0) outliers start: 165 outliers final: 84 residues processed: 814 average time/residue: 0.2115 time to fit residues: 282.8928 Evaluate side-chains 700 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 606 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 206 HIS Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 74 CYS Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 228 TYR Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 261 GLU Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 286 GLU Chi-restraints excluded: chain c residue 294 SER Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 121 CYS Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain K residue 10 ARG Chi-restraints excluded: chain K residue 83 LYS Chi-restraints excluded: chain K residue 104 ASN Chi-restraints excluded: chain K residue 165 CYS Chi-restraints excluded: chain K residue 229 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 256 optimal weight: 30.0000 chunk 35 optimal weight: 0.9980 chunk 299 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 275 optimal weight: 5.9990 chunk 315 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 407 optimal weight: 3.9990 chunk 265 optimal weight: 3.9990 chunk 230 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS D 57 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 GLN D 414 HIS ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 GLN J 221 ASN L 175 HIS ** M 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 254 ASN ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN A 433 ASN B 119 ASN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN E 345 ASN ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.117876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.094502 restraints weight = 66448.284| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.55 r_work: 0.3230 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 33656 Z= 0.209 Angle : 0.640 12.448 45509 Z= 0.329 Chirality : 0.045 0.267 5188 Planarity : 0.005 0.080 5888 Dihedral : 8.619 89.099 4812 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.38 % Favored : 94.41 % Rotamer: Outliers : 5.46 % Allowed : 24.08 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 1.16 % 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: -0.23 (0.13), residues: 4184 helix: 0.84 (0.12), residues: 1816 sheet: -0.93 (0.19), residues: 694 loop : -0.79 (0.16), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 43 TYR 0.016 0.002 TYR F 437 PHE 0.017 0.002 PHE H 173 TRP 0.015 0.002 TRP H 158 HIS 0.016 0.001 HIS E 271 Details of bonding type rmsd covalent geometry : bond 0.00486 (33651) covalent geometry : angle 0.63908 (45503) SS BOND : bond 0.01013 ( 3) SS BOND : angle 3.30996 ( 6) hydrogen bonds : bond 0.04207 ( 1500) hydrogen bonds : angle 4.82287 ( 4290) metal coordination : bond 0.00820 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 621 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8237 (mt-10) REVERT: C 83 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8121 (mtmt) REVERT: C 139 MET cc_start: 0.9225 (ttm) cc_final: 0.8815 (ttp) REVERT: C 180 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8817 (pt) REVERT: D 60 TYR cc_start: 0.4714 (OUTLIER) cc_final: 0.3208 (t80) REVERT: D 77 GLU cc_start: 0.8170 (tp30) cc_final: 0.7896 (tp30) REVERT: D 91 GLN cc_start: 0.8166 (mp10) cc_final: 0.7793 (mp10) REVERT: G 88 ARG cc_start: 0.8543 (tpp80) cc_final: 0.8209 (mtt90) REVERT: G 180 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8521 (mm-30) REVERT: H 58 ASP cc_start: 0.8705 (t0) cc_final: 0.8428 (t0) REVERT: H 79 MET cc_start: 0.8540 (mtp) cc_final: 0.7918 (mtp) REVERT: I 151 ASP cc_start: 0.8646 (t0) cc_final: 0.8364 (t0) REVERT: I 220 ASN cc_start: 0.7708 (t0) cc_final: 0.7464 (t0) REVERT: J 136 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.6499 (t80) REVERT: L 100 ASP cc_start: 0.8256 (t0) cc_final: 0.7808 (t0) REVERT: M 32 ASN cc_start: 0.8181 (t0) cc_final: 0.7931 (t0) REVERT: M 86 SER cc_start: 0.9151 (t) cc_final: 0.8865 (m) REVERT: M 158 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.6976 (p90) REVERT: c 107 MET cc_start: 0.8007 (ttp) cc_final: 0.7714 (ttp) REVERT: c 148 ILE cc_start: 0.9319 (mm) cc_final: 0.9014 (mm) REVERT: c 283 HIS cc_start: 0.8088 (m-70) cc_final: 0.7814 (m-70) REVERT: A 85 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 138 MET cc_start: 0.8192 (ptt) cc_final: 0.7953 (ptp) REVERT: A 252 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8533 (tp30) REVERT: A 263 MET cc_start: 0.8449 (ttm) cc_final: 0.8244 (ttt) REVERT: A 296 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: B 71 TYR cc_start: 0.9096 (m-80) cc_final: 0.8741 (m-80) REVERT: B 83 GLU cc_start: 0.8582 (tp30) cc_final: 0.8078 (mt-10) REVERT: B 165 ASP cc_start: 0.8901 (t70) cc_final: 0.8386 (t0) REVERT: B 295 TYR cc_start: 0.8981 (p90) cc_final: 0.8752 (p90) REVERT: B 324 ASP cc_start: 0.8791 (t0) cc_final: 0.8405 (t0) REVERT: E 66 GLU cc_start: 0.8944 (pt0) cc_final: 0.8515 (pp20) REVERT: E 110 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7536 (p90) REVERT: E 275 MET cc_start: 0.9072 (ptp) cc_final: 0.8735 (ptp) REVERT: E 361 PHE cc_start: 0.5144 (t80) cc_final: 0.4793 (t80) REVERT: E 372 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7446 (mtt-85) REVERT: K 93 ARG cc_start: 0.5072 (ttt180) cc_final: 0.4419 (mtt180) REVERT: K 95 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7787 (tm-30) REVERT: K 118 ASN cc_start: 0.9079 (m-40) cc_final: 0.8649 (m-40) REVERT: K 196 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8985 (ttpp) REVERT: K 224 GLN cc_start: 0.8319 (tt0) cc_final: 0.7964 (tt0) outliers start: 193 outliers final: 121 residues processed: 750 average time/residue: 0.2148 time to fit residues: 264.6668 Evaluate side-chains 691 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 562 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 206 HIS Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 215 GLN Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain c residue 170 LEU Chi-restraints excluded: chain c residue 261 GLU Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 286 GLU Chi-restraints excluded: chain c residue 294 SER Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 83 LYS Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 147 ASP Chi-restraints excluded: chain K residue 196 LYS Chi-restraints excluded: chain K residue 229 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 413 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 204 optimal weight: 0.6980 chunk 260 optimal weight: 1.9990 chunk 377 optimal weight: 2.9990 chunk 241 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 369 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS G 127 GLN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 221 ASN ** M 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 241 ASN A 54 GLN A 296 GLN ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 GLN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 23 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.116667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.093292 restraints weight = 65546.238| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.57 r_work: 0.3225 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 33656 Z= 0.137 Angle : 0.592 12.952 45509 Z= 0.302 Chirality : 0.043 0.333 5188 Planarity : 0.004 0.076 5888 Dihedral : 8.446 88.432 4802 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.21 % Favored : 94.57 % Rotamer: Outliers : 4.87 % Allowed : 24.45 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.02 % 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: -0.09 (0.13), residues: 4184 helix: 0.95 (0.12), residues: 1821 sheet: -0.90 (0.19), residues: 710 loop : -0.71 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 309 TYR 0.018 0.001 TYR G 152 PHE 0.014 0.001 PHE H 173 TRP 0.016 0.001 TRP H 158 HIS 0.016 0.001 HIS E 271 Details of bonding type rmsd covalent geometry : bond 0.00316 (33651) covalent geometry : angle 0.59072 (45503) SS BOND : bond 0.00597 ( 3) SS BOND : angle 3.39132 ( 6) hydrogen bonds : bond 0.03707 ( 1500) hydrogen bonds : angle 4.62578 ( 4290) metal coordination : bond 0.00246 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 631 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8172 (mt-10) REVERT: C 139 MET cc_start: 0.9201 (ttm) cc_final: 0.8908 (ttp) REVERT: C 180 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8682 (pt) REVERT: D 60 TYR cc_start: 0.4638 (OUTLIER) cc_final: 0.3103 (t80) REVERT: D 77 GLU cc_start: 0.8217 (tp30) cc_final: 0.7855 (tp30) REVERT: D 78 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7615 (mm-30) REVERT: D 82 ILE cc_start: 0.9123 (tp) cc_final: 0.8808 (tp) REVERT: D 94 GLU cc_start: 0.8450 (tt0) cc_final: 0.8247 (tt0) REVERT: G 39 SER cc_start: 0.9008 (m) cc_final: 0.8624 (p) REVERT: G 88 ARG cc_start: 0.8517 (tpp80) cc_final: 0.8134 (mtt90) REVERT: G 105 TYR cc_start: 0.8167 (m-80) cc_final: 0.7571 (m-80) REVERT: G 180 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8443 (mm-30) REVERT: H 58 ASP cc_start: 0.8648 (t0) cc_final: 0.8366 (t0) REVERT: H 72 ILE cc_start: 0.8985 (mt) cc_final: 0.8749 (mt) REVERT: H 79 MET cc_start: 0.8473 (mtp) cc_final: 0.7919 (mtp) REVERT: I 151 ASP cc_start: 0.8731 (t0) cc_final: 0.8476 (t0) REVERT: I 176 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7316 (mmtt) REVERT: J 52 LYS cc_start: 0.8797 (pttt) cc_final: 0.8247 (ptmm) REVERT: J 136 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6604 (t80) REVERT: J 172 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8860 (tt) REVERT: L 100 ASP cc_start: 0.8286 (t0) cc_final: 0.7902 (t0) REVERT: M 8 ASP cc_start: 0.8300 (t0) cc_final: 0.8070 (t0) REVERT: M 31 GLU cc_start: 0.7609 (pp20) cc_final: 0.7085 (pp20) REVERT: M 63 ASN cc_start: 0.9067 (p0) cc_final: 0.8810 (p0) REVERT: M 86 SER cc_start: 0.9152 (t) cc_final: 0.8836 (m) REVERT: M 101 ASN cc_start: 0.9307 (m-40) cc_final: 0.8941 (m-40) REVERT: M 150 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7177 (tpp) REVERT: M 158 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.6913 (p90) REVERT: M 161 TRP cc_start: 0.8648 (m100) cc_final: 0.8205 (m100) REVERT: c 107 MET cc_start: 0.8060 (ttp) cc_final: 0.7812 (ttp) REVERT: c 148 ILE cc_start: 0.9291 (mm) cc_final: 0.9010 (mm) REVERT: c 283 HIS cc_start: 0.7973 (m-70) cc_final: 0.7701 (m-70) REVERT: A 85 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 120 LYS cc_start: 0.8505 (tttt) cc_final: 0.8210 (ttpt) REVERT: A 256 MET cc_start: 0.8759 (ttm) cc_final: 0.8556 (ttm) REVERT: B 71 TYR cc_start: 0.9050 (m-80) cc_final: 0.8552 (m-80) REVERT: B 75 GLU cc_start: 0.6220 (OUTLIER) cc_final: 0.5072 (mp0) REVERT: B 83 GLU cc_start: 0.8591 (tp30) cc_final: 0.8194 (mp0) REVERT: B 165 ASP cc_start: 0.8890 (t70) cc_final: 0.8349 (t0) REVERT: B 262 ASP cc_start: 0.7027 (t0) cc_final: 0.6807 (t0) REVERT: B 295 TYR cc_start: 0.9065 (p90) cc_final: 0.8864 (p90) REVERT: B 309 MET cc_start: 0.8974 (tmm) cc_final: 0.8648 (tmm) REVERT: B 324 ASP cc_start: 0.8763 (t0) cc_final: 0.8361 (t0) REVERT: E 66 GLU cc_start: 0.8984 (pt0) cc_final: 0.8233 (pp20) REVERT: E 67 GLU cc_start: 0.8582 (mm-30) cc_final: 0.7765 (mm-30) REVERT: E 110 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7545 (p90) REVERT: E 275 MET cc_start: 0.9121 (ptp) cc_final: 0.8787 (ptp) REVERT: E 322 LYS cc_start: 0.6368 (OUTLIER) cc_final: 0.5218 (tptt) REVERT: E 372 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7519 (mtt-85) REVERT: F 69 MET cc_start: 0.5932 (ttt) cc_final: 0.5696 (ttt) REVERT: F 71 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7369 (p0) REVERT: F 316 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8659 (mm110) REVERT: K 93 ARG cc_start: 0.5026 (ttt180) cc_final: 0.4312 (mtt180) REVERT: K 95 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7768 (tm-30) REVERT: K 118 ASN cc_start: 0.9132 (m-40) cc_final: 0.8703 (m-40) outliers start: 172 outliers final: 107 residues processed: 747 average time/residue: 0.2061 time to fit residues: 252.9138 Evaluate side-chains 698 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 580 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 206 HIS Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 176 LYS Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 215 GLN Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain c residue 170 LEU Chi-restraints excluded: chain c residue 241 ASN Chi-restraints excluded: chain c residue 251 LEU Chi-restraints excluded: chain c residue 261 GLU Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 286 GLU Chi-restraints excluded: chain c residue 291 LEU Chi-restraints excluded: chain c residue 294 SER Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 146 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 229 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 300 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 292 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 344 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 410 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS I 198 ASN ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 HIS A 296 GLN B 131 HIS B 332 ASN ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.116281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.093112 restraints weight = 65941.873| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.57 r_work: 0.3187 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33656 Z= 0.178 Angle : 0.606 13.057 45509 Z= 0.309 Chirality : 0.044 0.343 5188 Planarity : 0.004 0.096 5888 Dihedral : 8.480 87.878 4800 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.09 % Favored : 94.72 % Rotamer: Outliers : 5.04 % Allowed : 24.70 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.02 % 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: -0.03 (0.13), residues: 4184 helix: 1.00 (0.12), residues: 1823 sheet: -0.90 (0.19), residues: 716 loop : -0.64 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 297 TYR 0.014 0.001 TYR G 152 PHE 0.014 0.001 PHE H 173 TRP 0.016 0.001 TRP H 158 HIS 0.014 0.001 HIS E 271 Details of bonding type rmsd covalent geometry : bond 0.00414 (33651) covalent geometry : angle 0.60416 (45503) SS BOND : bond 0.00821 ( 3) SS BOND : angle 4.06754 ( 6) hydrogen bonds : bond 0.03726 ( 1500) hydrogen bonds : angle 4.56986 ( 4290) metal coordination : bond 0.00367 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 591 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8197 (mt-10) REVERT: C 139 MET cc_start: 0.9223 (ttm) cc_final: 0.8888 (ttp) REVERT: C 369 TYR cc_start: 0.9257 (m-80) cc_final: 0.9020 (m-10) REVERT: D 60 TYR cc_start: 0.4686 (OUTLIER) cc_final: 0.2903 (t80) REVERT: D 77 GLU cc_start: 0.8302 (tp30) cc_final: 0.7936 (tp30) REVERT: D 78 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7655 (mm-30) REVERT: D 82 ILE cc_start: 0.9198 (tp) cc_final: 0.8877 (tp) REVERT: D 91 GLN cc_start: 0.8143 (mp10) cc_final: 0.7837 (mp10) REVERT: D 94 GLU cc_start: 0.8434 (tt0) cc_final: 0.8215 (tt0) REVERT: G 88 ARG cc_start: 0.8527 (tpp80) cc_final: 0.8157 (mtt90) REVERT: G 178 PHE cc_start: 0.9029 (t80) cc_final: 0.8804 (t80) REVERT: G 180 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8457 (mm-30) REVERT: H 42 ASN cc_start: 0.8574 (t0) cc_final: 0.8240 (m-40) REVERT: H 58 ASP cc_start: 0.8645 (t0) cc_final: 0.8326 (t0) REVERT: H 76 TYR cc_start: 0.8979 (p90) cc_final: 0.8399 (p90) REVERT: H 79 MET cc_start: 0.8545 (mtp) cc_final: 0.8296 (mtt) REVERT: H 141 GLU cc_start: 0.8255 (mp0) cc_final: 0.8016 (pm20) REVERT: I 151 ASP cc_start: 0.8671 (t0) cc_final: 0.8344 (t0) REVERT: L 100 ASP cc_start: 0.8329 (t0) cc_final: 0.7920 (t0) REVERT: M 8 ASP cc_start: 0.8335 (t0) cc_final: 0.8084 (t0) REVERT: M 17 ASP cc_start: 0.8673 (t0) cc_final: 0.8417 (t0) REVERT: M 86 SER cc_start: 0.9177 (t) cc_final: 0.8913 (p) REVERT: M 93 GLU cc_start: 0.8929 (tp30) cc_final: 0.8592 (tp30) REVERT: M 101 ASN cc_start: 0.9305 (m-40) cc_final: 0.8956 (m-40) REVERT: M 158 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.6918 (p90) REVERT: c 107 MET cc_start: 0.8219 (ttp) cc_final: 0.7994 (ttp) REVERT: c 148 ILE cc_start: 0.9313 (mm) cc_final: 0.9062 (mm) REVERT: c 283 HIS cc_start: 0.7977 (m-70) cc_final: 0.7768 (m-70) REVERT: c 305 ASP cc_start: 0.8914 (m-30) cc_final: 0.8585 (m-30) REVERT: A 85 GLN cc_start: 0.8368 (tm-30) cc_final: 0.7960 (tm-30) REVERT: A 120 LYS cc_start: 0.8496 (tttt) cc_final: 0.8195 (ttpt) REVERT: A 394 MET cc_start: 0.9174 (mmm) cc_final: 0.8861 (mmm) REVERT: B 71 TYR cc_start: 0.9046 (m-80) cc_final: 0.8510 (m-80) REVERT: B 75 GLU cc_start: 0.5724 (OUTLIER) cc_final: 0.4527 (mp0) REVERT: B 83 GLU cc_start: 0.8707 (tp30) cc_final: 0.8438 (tp30) REVERT: B 165 ASP cc_start: 0.8901 (t70) cc_final: 0.8341 (t0) REVERT: B 262 ASP cc_start: 0.7208 (t0) cc_final: 0.6995 (t0) REVERT: B 309 MET cc_start: 0.8958 (tmm) cc_final: 0.8622 (tmm) REVERT: B 324 ASP cc_start: 0.8797 (t0) cc_final: 0.8411 (t0) REVERT: E 66 GLU cc_start: 0.8984 (pt0) cc_final: 0.8530 (pp20) REVERT: E 110 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.7548 (p90) REVERT: E 275 MET cc_start: 0.9123 (ptp) cc_final: 0.8831 (ptp) REVERT: E 322 LYS cc_start: 0.6463 (OUTLIER) cc_final: 0.5262 (tptt) REVERT: E 372 ARG cc_start: 0.8010 (mtm-85) cc_final: 0.7562 (mtt-85) REVERT: F 71 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7347 (p0) REVERT: F 353 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7480 (pp20) REVERT: K 86 LYS cc_start: 0.8606 (mtpp) cc_final: 0.8240 (mtmm) REVERT: K 93 ARG cc_start: 0.4988 (ttt180) cc_final: 0.4257 (mtt180) REVERT: K 95 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7783 (tm-30) REVERT: K 118 ASN cc_start: 0.9150 (m-40) cc_final: 0.8719 (m-40) REVERT: K 224 GLN cc_start: 0.8356 (tt0) cc_final: 0.7965 (tt0) outliers start: 178 outliers final: 124 residues processed: 710 average time/residue: 0.2077 time to fit residues: 241.9276 Evaluate side-chains 687 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 556 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 206 HIS Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 228 ARG Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 215 GLN Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 170 LEU Chi-restraints excluded: chain c residue 261 GLU Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 286 GLU Chi-restraints excluded: chain c residue 291 LEU Chi-restraints excluded: chain c residue 294 SER Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 146 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 229 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 127 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 350 optimal weight: 8.9990 chunk 385 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 405 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 310 optimal weight: 10.0000 chunk 341 optimal weight: 0.4980 chunk 351 optimal weight: 8.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS I 198 ASN ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.116182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.092976 restraints weight = 65406.303| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.56 r_work: 0.3195 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33656 Z= 0.160 Angle : 0.604 12.966 45509 Z= 0.307 Chirality : 0.044 0.353 5188 Planarity : 0.005 0.097 5888 Dihedral : 8.413 89.637 4796 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.33 % Favored : 94.46 % Rotamer: Outliers : 4.75 % Allowed : 25.01 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.02 % 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: 0.02 (0.13), residues: 4184 helix: 1.03 (0.12), residues: 1828 sheet: -0.86 (0.19), residues: 715 loop : -0.62 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 157 TYR 0.022 0.001 TYR E 132 PHE 0.011 0.001 PHE E 195 TRP 0.018 0.001 TRP H 158 HIS 0.016 0.001 HIS E 271 Details of bonding type rmsd covalent geometry : bond 0.00375 (33651) covalent geometry : angle 0.60280 (45503) SS BOND : bond 0.01305 ( 3) SS BOND : angle 3.85392 ( 6) hydrogen bonds : bond 0.03656 ( 1500) hydrogen bonds : angle 4.52247 ( 4290) metal coordination : bond 0.00324 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 594 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8216 (mt-10) REVERT: C 139 MET cc_start: 0.9230 (ttm) cc_final: 0.8883 (ttp) REVERT: D 60 TYR cc_start: 0.4659 (OUTLIER) cc_final: 0.2830 (t80) REVERT: D 77 GLU cc_start: 0.8340 (tp30) cc_final: 0.7992 (tp30) REVERT: D 78 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7650 (mm-30) REVERT: D 91 GLN cc_start: 0.8169 (mp10) cc_final: 0.7858 (mp10) REVERT: D 94 GLU cc_start: 0.8430 (tt0) cc_final: 0.8225 (tt0) REVERT: G 88 ARG cc_start: 0.8556 (tpp80) cc_final: 0.8183 (mtt90) REVERT: G 180 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8451 (mm-30) REVERT: H 42 ASN cc_start: 0.8557 (t0) cc_final: 0.8305 (m-40) REVERT: H 58 ASP cc_start: 0.8659 (t0) cc_final: 0.8324 (t0) REVERT: H 141 GLU cc_start: 0.8248 (mp0) cc_final: 0.7894 (pm20) REVERT: I 151 ASP cc_start: 0.8658 (t0) cc_final: 0.8315 (t0) REVERT: J 193 LYS cc_start: 0.9265 (mtmm) cc_final: 0.8823 (mtmt) REVERT: L 100 ASP cc_start: 0.8327 (t0) cc_final: 0.7918 (t0) REVERT: M 8 ASP cc_start: 0.8331 (t0) cc_final: 0.8035 (t0) REVERT: M 17 ASP cc_start: 0.8663 (t0) cc_final: 0.8384 (t0) REVERT: M 93 GLU cc_start: 0.8943 (tp30) cc_final: 0.8584 (tp30) REVERT: M 101 ASN cc_start: 0.9308 (m-40) cc_final: 0.8960 (m-40) REVERT: M 158 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.6886 (p90) REVERT: c 107 MET cc_start: 0.8300 (ttp) cc_final: 0.7752 (ttt) REVERT: c 148 ILE cc_start: 0.9311 (mm) cc_final: 0.9066 (mm) REVERT: c 283 HIS cc_start: 0.7915 (m-70) cc_final: 0.7664 (m-70) REVERT: c 305 ASP cc_start: 0.8862 (m-30) cc_final: 0.8523 (m-30) REVERT: A 85 GLN cc_start: 0.8398 (tm-30) cc_final: 0.7975 (tm-30) REVERT: A 120 LYS cc_start: 0.8421 (tttt) cc_final: 0.8103 (ttpt) REVERT: A 394 MET cc_start: 0.9191 (mmm) cc_final: 0.8887 (mmm) REVERT: B 71 TYR cc_start: 0.9047 (m-80) cc_final: 0.8511 (m-80) REVERT: B 75 GLU cc_start: 0.5696 (OUTLIER) cc_final: 0.4500 (mp0) REVERT: B 165 ASP cc_start: 0.8921 (t70) cc_final: 0.8350 (t0) REVERT: B 262 ASP cc_start: 0.7239 (t0) cc_final: 0.7027 (t0) REVERT: B 309 MET cc_start: 0.8980 (tmm) cc_final: 0.8665 (tmm) REVERT: B 324 ASP cc_start: 0.8786 (t0) cc_final: 0.8405 (t0) REVERT: E 66 GLU cc_start: 0.8961 (pt0) cc_final: 0.8203 (pp20) REVERT: E 67 GLU cc_start: 0.8647 (mm-30) cc_final: 0.7789 (mm-30) REVERT: E 110 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.7540 (p90) REVERT: E 147 GLU cc_start: 0.8269 (tm-30) cc_final: 0.8019 (tm-30) REVERT: E 275 MET cc_start: 0.9142 (ptp) cc_final: 0.8856 (ptp) REVERT: E 322 LYS cc_start: 0.6436 (OUTLIER) cc_final: 0.5342 (tptt) REVERT: E 372 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7767 (mtt-85) REVERT: F 205 PRO cc_start: 0.8565 (Cg_exo) cc_final: 0.8332 (Cg_endo) REVERT: F 353 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7511 (pp20) REVERT: K 86 LYS cc_start: 0.8549 (mtpp) cc_final: 0.8220 (mtmm) REVERT: K 93 ARG cc_start: 0.5017 (ttt180) cc_final: 0.4247 (mtt180) REVERT: K 95 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7772 (tm-30) REVERT: K 118 ASN cc_start: 0.9223 (m-40) cc_final: 0.8776 (m-40) REVERT: K 225 ASN cc_start: 0.8430 (m-40) cc_final: 0.8209 (m-40) outliers start: 168 outliers final: 126 residues processed: 708 average time/residue: 0.2022 time to fit residues: 235.5850 Evaluate side-chains 686 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 554 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 206 HIS Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 228 ARG Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 170 LEU Chi-restraints excluded: chain c residue 261 GLU Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 286 GLU Chi-restraints excluded: chain c residue 291 LEU Chi-restraints excluded: chain c residue 294 SER Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 146 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 229 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 153 optimal weight: 1.9990 chunk 283 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 8 optimal weight: 5.9990 chunk 246 optimal weight: 0.0980 chunk 179 optimal weight: 0.8980 chunk 249 optimal weight: 9.9990 chunk 335 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 233 optimal weight: 8.9990 chunk 331 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 198 ASN I 235 GLN J 54 GLN ** M 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 HIS ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.118193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.095007 restraints weight = 65439.190| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.58 r_work: 0.3230 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 33656 Z= 0.118 Angle : 0.591 13.107 45509 Z= 0.301 Chirality : 0.043 0.329 5188 Planarity : 0.004 0.098 5888 Dihedral : 8.221 89.778 4796 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.02 % Favored : 94.81 % Rotamer: Outliers : 4.13 % Allowed : 26.29 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.02 % 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: 0.13 (0.13), residues: 4184 helix: 1.16 (0.12), residues: 1819 sheet: -0.80 (0.19), residues: 703 loop : -0.61 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG c 139 TYR 0.027 0.001 TYR E 40 PHE 0.011 0.001 PHE G 9 TRP 0.020 0.001 TRP H 158 HIS 0.014 0.001 HIS E 271 Details of bonding type rmsd covalent geometry : bond 0.00269 (33651) covalent geometry : angle 0.58999 (45503) SS BOND : bond 0.00998 ( 3) SS BOND : angle 3.32161 ( 6) hydrogen bonds : bond 0.03451 ( 1500) hydrogen bonds : angle 4.42581 ( 4290) metal coordination : bond 0.00148 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 618 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8213 (mt-10) REVERT: C 139 MET cc_start: 0.9203 (ttm) cc_final: 0.8903 (ttp) REVERT: D 60 TYR cc_start: 0.4576 (OUTLIER) cc_final: 0.2755 (t80) REVERT: D 77 GLU cc_start: 0.8332 (tp30) cc_final: 0.7965 (tp30) REVERT: D 78 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7573 (mm-30) REVERT: D 91 GLN cc_start: 0.8176 (mp10) cc_final: 0.7773 (mp10) REVERT: D 399 PHE cc_start: 0.9394 (OUTLIER) cc_final: 0.8946 (t80) REVERT: G 39 SER cc_start: 0.8978 (m) cc_final: 0.8631 (p) REVERT: G 88 ARG cc_start: 0.8483 (tpp80) cc_final: 0.8127 (mtt90) REVERT: G 180 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8449 (mm-30) REVERT: H 42 ASN cc_start: 0.8501 (t0) cc_final: 0.8269 (m-40) REVERT: H 58 ASP cc_start: 0.8587 (t0) cc_final: 0.8236 (t0) REVERT: H 76 TYR cc_start: 0.8965 (p90) cc_final: 0.8308 (p90) REVERT: I 30 HIS cc_start: 0.8573 (m170) cc_final: 0.8290 (m170) REVERT: I 93 ILE cc_start: 0.8854 (mt) cc_final: 0.8523 (mt) REVERT: I 151 ASP cc_start: 0.8609 (t0) cc_final: 0.8247 (t0) REVERT: J 136 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.6560 (t80) REVERT: J 193 LYS cc_start: 0.9242 (mtmm) cc_final: 0.8798 (mtmt) REVERT: L 100 ASP cc_start: 0.8357 (t0) cc_final: 0.7990 (t0) REVERT: M 8 ASP cc_start: 0.8364 (t0) cc_final: 0.8049 (t0) REVERT: M 17 ASP cc_start: 0.8625 (t0) cc_final: 0.8348 (t0) REVERT: M 86 SER cc_start: 0.9169 (t) cc_final: 0.8888 (p) REVERT: M 93 GLU cc_start: 0.8999 (tp30) cc_final: 0.8641 (tp30) REVERT: M 101 ASN cc_start: 0.9287 (m-40) cc_final: 0.8957 (m-40) REVERT: M 151 ILE cc_start: 0.9157 (mt) cc_final: 0.8942 (mt) REVERT: M 158 TYR cc_start: 0.7627 (OUTLIER) cc_final: 0.6917 (p90) REVERT: c 107 MET cc_start: 0.8278 (ttp) cc_final: 0.7888 (ttt) REVERT: c 284 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7099 (mm) REVERT: c 286 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8443 (pp20) REVERT: c 305 ASP cc_start: 0.8827 (m-30) cc_final: 0.8380 (m-30) REVERT: A 85 GLN cc_start: 0.8468 (tm-30) cc_final: 0.7745 (tm-30) REVERT: A 120 LYS cc_start: 0.8392 (tttt) cc_final: 0.8079 (ttpt) REVERT: A 394 MET cc_start: 0.9209 (mmm) cc_final: 0.8980 (mmm) REVERT: B 71 TYR cc_start: 0.9033 (m-80) cc_final: 0.8527 (m-80) REVERT: B 75 GLU cc_start: 0.5689 (OUTLIER) cc_final: 0.4624 (mp0) REVERT: B 83 GLU cc_start: 0.8741 (tp30) cc_final: 0.8087 (pt0) REVERT: B 165 ASP cc_start: 0.8881 (t70) cc_final: 0.8137 (t0) REVERT: B 262 ASP cc_start: 0.7190 (t0) cc_final: 0.6966 (t0) REVERT: B 309 MET cc_start: 0.8978 (tmm) cc_final: 0.8714 (tmm) REVERT: B 324 ASP cc_start: 0.8724 (t0) cc_final: 0.8360 (t0) REVERT: E 41 GLU cc_start: 0.8686 (mm-30) cc_final: 0.7198 (tt0) REVERT: E 66 GLU cc_start: 0.8965 (pt0) cc_final: 0.8111 (pp20) REVERT: E 67 GLU cc_start: 0.8626 (mm-30) cc_final: 0.7626 (mm-30) REVERT: E 110 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7533 (p90) REVERT: E 275 MET cc_start: 0.9116 (ptp) cc_final: 0.8819 (ptp) REVERT: E 298 LYS cc_start: 0.8296 (mtpt) cc_final: 0.7857 (mtpp) REVERT: E 322 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.5414 (tptt) REVERT: E 372 ARG cc_start: 0.8093 (mtm-85) cc_final: 0.7737 (mtt-85) REVERT: F 205 PRO cc_start: 0.8532 (Cg_exo) cc_final: 0.8280 (Cg_endo) REVERT: F 353 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7573 (pp20) REVERT: K 86 LYS cc_start: 0.8508 (mtpp) cc_final: 0.8217 (mtmt) REVERT: K 93 ARG cc_start: 0.4985 (ttt180) cc_final: 0.4195 (mtt180) REVERT: K 95 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7711 (tm-30) REVERT: K 118 ASN cc_start: 0.9053 (m-40) cc_final: 0.8625 (m-40) REVERT: K 224 GLN cc_start: 0.8349 (tt0) cc_final: 0.7927 (tt0) REVERT: K 225 ASN cc_start: 0.8354 (m-40) cc_final: 0.8108 (m-40) outliers start: 146 outliers final: 93 residues processed: 714 average time/residue: 0.1839 time to fit residues: 216.9082 Evaluate side-chains 673 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 570 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 228 ARG Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 235 GLN Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 170 LEU Chi-restraints excluded: chain c residue 261 GLU Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 286 GLU Chi-restraints excluded: chain c residue 291 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 146 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 229 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 295 optimal weight: 0.0040 chunk 67 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 296 optimal weight: 1.9990 chunk 396 optimal weight: 3.9990 chunk 311 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 160 optimal weight: 8.9990 chunk 301 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 198 ASN ** I 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.117408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.094397 restraints weight = 65183.845| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.56 r_work: 0.3226 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33656 Z= 0.131 Angle : 0.601 13.173 45509 Z= 0.305 Chirality : 0.043 0.342 5188 Planarity : 0.004 0.101 5888 Dihedral : 8.187 89.621 4793 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.90 % Favored : 94.91 % Rotamer: Outliers : 3.96 % Allowed : 26.43 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.02 % 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: 0.16 (0.13), residues: 4184 helix: 1.16 (0.12), residues: 1831 sheet: -0.75 (0.19), residues: 701 loop : -0.61 (0.16), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 252 TYR 0.027 0.001 TYR E 40 PHE 0.027 0.001 PHE c 91 TRP 0.022 0.001 TRP H 158 HIS 0.009 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00305 (33651) covalent geometry : angle 0.60001 (45503) SS BOND : bond 0.01067 ( 3) SS BOND : angle 3.71081 ( 6) hydrogen bonds : bond 0.03429 ( 1500) hydrogen bonds : angle 4.41908 ( 4290) metal coordination : bond 0.00188 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 588 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8209 (mt-10) REVERT: C 139 MET cc_start: 0.9217 (ttm) cc_final: 0.8877 (ttp) REVERT: D 60 TYR cc_start: 0.4585 (OUTLIER) cc_final: 0.2751 (t80) REVERT: D 77 GLU cc_start: 0.8348 (tp30) cc_final: 0.8008 (tp30) REVERT: D 78 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7639 (mm-30) REVERT: D 91 GLN cc_start: 0.8156 (mp10) cc_final: 0.7747 (mp10) REVERT: D 399 PHE cc_start: 0.9411 (OUTLIER) cc_final: 0.9016 (t80) REVERT: G 88 ARG cc_start: 0.8466 (tpp80) cc_final: 0.8130 (mtt90) REVERT: G 180 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8446 (mm-30) REVERT: H 58 ASP cc_start: 0.8573 (t0) cc_final: 0.8223 (t0) REVERT: H 76 TYR cc_start: 0.8972 (p90) cc_final: 0.8305 (p90) REVERT: I 30 HIS cc_start: 0.8564 (m170) cc_final: 0.8248 (m170) REVERT: I 93 ILE cc_start: 0.8732 (mt) cc_final: 0.8475 (mt) REVERT: I 151 ASP cc_start: 0.8639 (t0) cc_final: 0.8272 (t0) REVERT: J 136 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.6619 (t80) REVERT: J 193 LYS cc_start: 0.9248 (mtmm) cc_final: 0.8795 (mtmt) REVERT: L 100 ASP cc_start: 0.8322 (t0) cc_final: 0.7956 (t0) REVERT: M 8 ASP cc_start: 0.8366 (t0) cc_final: 0.8010 (t0) REVERT: M 17 ASP cc_start: 0.8667 (t0) cc_final: 0.8384 (t0) REVERT: M 86 SER cc_start: 0.9168 (t) cc_final: 0.8898 (p) REVERT: M 93 GLU cc_start: 0.9000 (tp30) cc_final: 0.8635 (tp30) REVERT: M 101 ASN cc_start: 0.9281 (m-40) cc_final: 0.8933 (m-40) REVERT: M 151 ILE cc_start: 0.9064 (mt) cc_final: 0.8857 (mt) REVERT: M 158 TYR cc_start: 0.7633 (OUTLIER) cc_final: 0.6934 (p90) REVERT: c 107 MET cc_start: 0.8319 (ttp) cc_final: 0.7995 (ttt) REVERT: c 162 LEU cc_start: 0.8584 (mt) cc_final: 0.8278 (tp) REVERT: c 284 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7222 (mm) REVERT: c 286 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8372 (pp20) REVERT: c 305 ASP cc_start: 0.8829 (m-30) cc_final: 0.8376 (m-30) REVERT: A 85 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8020 (tm-30) REVERT: A 120 LYS cc_start: 0.8373 (tttt) cc_final: 0.8080 (ttpt) REVERT: A 394 MET cc_start: 0.9179 (mmm) cc_final: 0.8941 (mmm) REVERT: B 71 TYR cc_start: 0.9012 (m-80) cc_final: 0.8629 (m-80) REVERT: B 96 ARG cc_start: 0.7837 (mpp-170) cc_final: 0.7550 (mpp-170) REVERT: B 165 ASP cc_start: 0.8863 (t70) cc_final: 0.8119 (t0) REVERT: B 262 ASP cc_start: 0.7193 (t0) cc_final: 0.6968 (t0) REVERT: B 309 MET cc_start: 0.8968 (tmm) cc_final: 0.8704 (tmm) REVERT: B 324 ASP cc_start: 0.8747 (t0) cc_final: 0.8399 (t0) REVERT: E 41 GLU cc_start: 0.8722 (mm-30) cc_final: 0.7263 (tt0) REVERT: E 66 GLU cc_start: 0.8935 (pt0) cc_final: 0.8080 (pp20) REVERT: E 67 GLU cc_start: 0.8630 (mm-30) cc_final: 0.7632 (mm-30) REVERT: E 110 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.7529 (p90) REVERT: E 275 MET cc_start: 0.9124 (ptp) cc_final: 0.8817 (ptp) REVERT: E 298 LYS cc_start: 0.8295 (mtpt) cc_final: 0.7865 (mtpp) REVERT: E 322 LYS cc_start: 0.6660 (OUTLIER) cc_final: 0.5717 (tptt) REVERT: E 372 ARG cc_start: 0.8108 (mtm-85) cc_final: 0.7740 (mtt-85) REVERT: F 175 MET cc_start: 0.7162 (mmt) cc_final: 0.6442 (mtt) REVERT: F 205 PRO cc_start: 0.8506 (Cg_exo) cc_final: 0.8244 (Cg_endo) REVERT: F 353 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7380 (pp20) REVERT: K 86 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8251 (mtmt) REVERT: K 93 ARG cc_start: 0.4653 (ttt180) cc_final: 0.3997 (mtt180) REVERT: K 95 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7753 (tm-30) REVERT: K 118 ASN cc_start: 0.9093 (m-40) cc_final: 0.8639 (m-40) REVERT: K 224 GLN cc_start: 0.8328 (tt0) cc_final: 0.7818 (tt0) outliers start: 140 outliers final: 98 residues processed: 683 average time/residue: 0.1876 time to fit residues: 212.0305 Evaluate side-chains 672 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 565 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 228 ARG Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 170 LEU Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 286 GLU Chi-restraints excluded: chain c residue 291 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 146 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 229 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 200 optimal weight: 6.9990 chunk 58 optimal weight: 0.0970 chunk 4 optimal weight: 0.9990 chunk 331 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 391 optimal weight: 5.9990 chunk 361 optimal weight: 6.9990 chunk 204 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 263 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 ASN I 69 ASN I 198 ASN I 235 GLN ** M 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.116676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.093188 restraints weight = 65367.857| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.60 r_work: 0.3222 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33656 Z= 0.133 Angle : 0.608 13.045 45509 Z= 0.308 Chirality : 0.043 0.349 5188 Planarity : 0.004 0.103 5888 Dihedral : 8.097 88.815 4788 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.00 % Favored : 94.81 % Rotamer: Outliers : 3.74 % Allowed : 26.49 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 1.16 % 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: 0.18 (0.13), residues: 4184 helix: 1.20 (0.12), residues: 1833 sheet: -0.79 (0.19), residues: 723 loop : -0.58 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 252 TYR 0.027 0.001 TYR E 40 PHE 0.024 0.001 PHE G 178 TRP 0.025 0.001 TRP H 158 HIS 0.009 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00311 (33651) covalent geometry : angle 0.60683 (45503) SS BOND : bond 0.00948 ( 3) SS BOND : angle 3.91712 ( 6) hydrogen bonds : bond 0.03399 ( 1500) hydrogen bonds : angle 4.39618 ( 4290) metal coordination : bond 0.00220 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 600 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8233 (mt-10) REVERT: C 139 MET cc_start: 0.9227 (ttm) cc_final: 0.8889 (ttp) REVERT: D 60 TYR cc_start: 0.4598 (OUTLIER) cc_final: 0.2755 (t80) REVERT: D 77 GLU cc_start: 0.8337 (tp30) cc_final: 0.8001 (tp30) REVERT: D 78 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7675 (mm-30) REVERT: D 91 GLN cc_start: 0.8128 (mp10) cc_final: 0.7738 (mp10) REVERT: D 399 PHE cc_start: 0.9402 (OUTLIER) cc_final: 0.9008 (t80) REVERT: G 88 ARG cc_start: 0.8458 (tpp80) cc_final: 0.8137 (mtt90) REVERT: H 42 ASN cc_start: 0.8401 (m-40) cc_final: 0.8185 (m110) REVERT: H 58 ASP cc_start: 0.8640 (t70) cc_final: 0.8282 (t0) REVERT: H 76 TYR cc_start: 0.8989 (p90) cc_final: 0.8322 (p90) REVERT: I 30 HIS cc_start: 0.8544 (m170) cc_final: 0.8215 (m170) REVERT: I 93 ILE cc_start: 0.8645 (mt) cc_final: 0.8431 (mt) REVERT: I 151 ASP cc_start: 0.8621 (t0) cc_final: 0.8243 (t0) REVERT: J 136 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.6857 (t80) REVERT: L 100 ASP cc_start: 0.8268 (t0) cc_final: 0.7921 (t0) REVERT: M 8 ASP cc_start: 0.8361 (t0) cc_final: 0.8006 (t0) REVERT: M 17 ASP cc_start: 0.8685 (t0) cc_final: 0.8396 (t0) REVERT: M 93 GLU cc_start: 0.9004 (tp30) cc_final: 0.8665 (tp30) REVERT: M 101 ASN cc_start: 0.9276 (m-40) cc_final: 0.8931 (m-40) REVERT: M 151 ILE cc_start: 0.9085 (mt) cc_final: 0.8812 (mt) REVERT: M 158 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.6850 (p90) REVERT: c 107 MET cc_start: 0.8251 (ttp) cc_final: 0.7946 (ttt) REVERT: c 162 LEU cc_start: 0.8630 (mt) cc_final: 0.8336 (tp) REVERT: c 196 LEU cc_start: 0.8836 (mt) cc_final: 0.8446 (mt) REVERT: c 284 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7382 (mm) REVERT: c 286 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8425 (pp20) REVERT: c 305 ASP cc_start: 0.8823 (m-30) cc_final: 0.8379 (m-30) REVERT: A 85 GLN cc_start: 0.8398 (tm-30) cc_final: 0.7880 (tm-30) REVERT: A 88 GLN cc_start: 0.8230 (pp30) cc_final: 0.7902 (pp30) REVERT: A 120 LYS cc_start: 0.8372 (tttt) cc_final: 0.8094 (ttpt) REVERT: A 394 MET cc_start: 0.9199 (mmm) cc_final: 0.8966 (mmm) REVERT: B 71 TYR cc_start: 0.9008 (m-80) cc_final: 0.8487 (m-80) REVERT: B 75 GLU cc_start: 0.5750 (OUTLIER) cc_final: 0.4661 (mp0) REVERT: B 165 ASP cc_start: 0.8867 (t70) cc_final: 0.8131 (t0) REVERT: B 262 ASP cc_start: 0.7210 (t0) cc_final: 0.6994 (t0) REVERT: B 309 MET cc_start: 0.8946 (tmm) cc_final: 0.8680 (tmm) REVERT: B 324 ASP cc_start: 0.8749 (t0) cc_final: 0.8423 (t0) REVERT: E 41 GLU cc_start: 0.8560 (mm-30) cc_final: 0.7214 (tt0) REVERT: E 66 GLU cc_start: 0.8926 (pt0) cc_final: 0.8113 (pp20) REVERT: E 67 GLU cc_start: 0.8623 (mm-30) cc_final: 0.7693 (mm-30) REVERT: E 110 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7483 (p90) REVERT: E 147 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7621 (tm-30) REVERT: E 257 LEU cc_start: 0.8851 (tp) cc_final: 0.8586 (tp) REVERT: E 275 MET cc_start: 0.9129 (ptp) cc_final: 0.8852 (ptp) REVERT: E 298 LYS cc_start: 0.8328 (mtpt) cc_final: 0.7881 (mtpp) REVERT: F 97 LEU cc_start: 0.9016 (tp) cc_final: 0.8727 (tt) REVERT: F 205 PRO cc_start: 0.8548 (Cg_exo) cc_final: 0.8316 (Cg_endo) REVERT: F 353 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7532 (pp20) REVERT: K 86 LYS cc_start: 0.8502 (mtpp) cc_final: 0.8251 (mtmt) REVERT: K 93 ARG cc_start: 0.4622 (ttt180) cc_final: 0.3952 (mtt180) REVERT: K 95 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7778 (tm-30) REVERT: K 118 ASN cc_start: 0.9099 (m-40) cc_final: 0.8640 (m-40) REVERT: K 147 ASP cc_start: 0.8015 (m-30) cc_final: 0.7795 (m-30) REVERT: K 224 GLN cc_start: 0.8280 (tt0) cc_final: 0.7977 (tt0) outliers start: 132 outliers final: 107 residues processed: 686 average time/residue: 0.1877 time to fit residues: 213.9425 Evaluate side-chains 688 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 572 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 228 ARG Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 170 LEU Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 286 GLU Chi-restraints excluded: chain c residue 291 LEU Chi-restraints excluded: chain c residue 294 SER Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 146 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 104 ASN Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 229 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 164 optimal weight: 2.9990 chunk 313 optimal weight: 0.9990 chunk 363 optimal weight: 3.9990 chunk 252 optimal weight: 8.9990 chunk 208 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 336 optimal weight: 4.9990 chunk 357 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 198 ASN ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.117193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.094409 restraints weight = 65806.452| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.54 r_work: 0.3215 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.171 33656 Z= 0.196 Angle : 0.720 59.200 45509 Z= 0.392 Chirality : 0.045 0.357 5188 Planarity : 0.005 0.106 5888 Dihedral : 8.063 88.797 4786 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.09 % Favored : 94.74 % Rotamer: Outliers : 3.54 % Allowed : 26.85 % Favored : 69.61 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 1.16 % 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: 0.18 (0.13), residues: 4184 helix: 1.20 (0.12), residues: 1833 sheet: -0.79 (0.19), residues: 723 loop : -0.59 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 252 TYR 0.051 0.001 TYR A 429 PHE 0.020 0.001 PHE c 91 TRP 0.022 0.001 TRP H 158 HIS 0.009 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00455 (33651) covalent geometry : angle 0.71887 (45503) SS BOND : bond 0.01693 ( 3) SS BOND : angle 4.28017 ( 6) hydrogen bonds : bond 0.03410 ( 1500) hydrogen bonds : angle 4.40052 ( 4290) metal coordination : bond 0.00343 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 573 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8231 (mt-10) REVERT: C 139 MET cc_start: 0.9237 (ttm) cc_final: 0.8896 (ttp) REVERT: D 60 TYR cc_start: 0.4598 (OUTLIER) cc_final: 0.2753 (t80) REVERT: D 77 GLU cc_start: 0.8334 (tp30) cc_final: 0.8000 (tp30) REVERT: D 78 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7671 (mm-30) REVERT: D 91 GLN cc_start: 0.8137 (mp10) cc_final: 0.7739 (mp10) REVERT: D 399 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.9002 (t80) REVERT: G 88 ARG cc_start: 0.8470 (tpp80) cc_final: 0.8132 (mtt90) REVERT: H 42 ASN cc_start: 0.8419 (m-40) cc_final: 0.8201 (m110) REVERT: H 58 ASP cc_start: 0.8633 (t70) cc_final: 0.8275 (t0) REVERT: H 76 TYR cc_start: 0.8993 (p90) cc_final: 0.8325 (p90) REVERT: I 30 HIS cc_start: 0.8537 (m170) cc_final: 0.8204 (m170) REVERT: I 151 ASP cc_start: 0.8611 (t0) cc_final: 0.8240 (t0) REVERT: J 136 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.6862 (t80) REVERT: L 100 ASP cc_start: 0.8266 (t0) cc_final: 0.7922 (t0) REVERT: M 8 ASP cc_start: 0.8373 (t0) cc_final: 0.8013 (t0) REVERT: M 17 ASP cc_start: 0.8679 (t0) cc_final: 0.8389 (t0) REVERT: M 93 GLU cc_start: 0.8999 (tp30) cc_final: 0.8655 (tp30) REVERT: M 101 ASN cc_start: 0.9280 (m-40) cc_final: 0.8933 (m-40) REVERT: M 151 ILE cc_start: 0.9040 (mt) cc_final: 0.8817 (mt) REVERT: M 158 TYR cc_start: 0.7648 (OUTLIER) cc_final: 0.6852 (p90) REVERT: c 107 MET cc_start: 0.8274 (ttp) cc_final: 0.7968 (ttt) REVERT: c 162 LEU cc_start: 0.8612 (mt) cc_final: 0.8345 (tp) REVERT: c 196 LEU cc_start: 0.8844 (mt) cc_final: 0.8434 (mt) REVERT: c 284 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7383 (mm) REVERT: c 286 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8428 (pp20) REVERT: c 305 ASP cc_start: 0.8824 (m-30) cc_final: 0.8379 (m-30) REVERT: A 85 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7880 (tm-30) REVERT: A 88 GLN cc_start: 0.8224 (pp30) cc_final: 0.7898 (pp30) REVERT: A 120 LYS cc_start: 0.8361 (tttt) cc_final: 0.8088 (ttpt) REVERT: A 394 MET cc_start: 0.9209 (mmm) cc_final: 0.8977 (mmm) REVERT: B 71 TYR cc_start: 0.9004 (m-80) cc_final: 0.8482 (m-80) REVERT: B 75 GLU cc_start: 0.5750 (OUTLIER) cc_final: 0.4664 (mp0) REVERT: B 165 ASP cc_start: 0.8860 (t70) cc_final: 0.8122 (t0) REVERT: B 262 ASP cc_start: 0.7218 (t0) cc_final: 0.7003 (t0) REVERT: B 309 MET cc_start: 0.8956 (tmm) cc_final: 0.8688 (tmm) REVERT: B 324 ASP cc_start: 0.8754 (t0) cc_final: 0.8429 (t0) REVERT: E 41 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7219 (tt0) REVERT: E 66 GLU cc_start: 0.8963 (pt0) cc_final: 0.8120 (pp20) REVERT: E 67 GLU cc_start: 0.8687 (mm-30) cc_final: 0.7704 (mm-30) REVERT: E 110 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7517 (p90) REVERT: E 147 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7608 (tm-30) REVERT: E 257 LEU cc_start: 0.8847 (tp) cc_final: 0.8595 (tp) REVERT: E 275 MET cc_start: 0.9152 (ptp) cc_final: 0.8855 (ptp) REVERT: E 298 LYS cc_start: 0.8344 (mtpt) cc_final: 0.7898 (mtpp) REVERT: F 97 LEU cc_start: 0.9020 (tp) cc_final: 0.8728 (tt) REVERT: F 205 PRO cc_start: 0.8577 (Cg_exo) cc_final: 0.8349 (Cg_endo) REVERT: F 353 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7520 (pp20) REVERT: K 86 LYS cc_start: 0.8499 (mtpp) cc_final: 0.8247 (mtmt) REVERT: K 93 ARG cc_start: 0.4610 (ttt180) cc_final: 0.3931 (mtt180) REVERT: K 95 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7785 (tm-30) REVERT: K 118 ASN cc_start: 0.9097 (m-40) cc_final: 0.8636 (m-40) REVERT: K 147 ASP cc_start: 0.8006 (m-30) cc_final: 0.7803 (m-30) REVERT: K 224 GLN cc_start: 0.8295 (tt0) cc_final: 0.7973 (tt0) outliers start: 125 outliers final: 110 residues processed: 655 average time/residue: 0.2009 time to fit residues: 219.0072 Evaluate side-chains 691 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 572 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 228 ARG Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 170 LEU Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 286 GLU Chi-restraints excluded: chain c residue 291 LEU Chi-restraints excluded: chain c residue 294 SER Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain E residue 40 TYR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 146 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 229 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 186 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 351 optimal weight: 5.9990 chunk 209 optimal weight: 7.9990 chunk 324 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 216 optimal weight: 20.0000 chunk 211 optimal weight: 0.8980 chunk 262 optimal weight: 8.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 198 ASN ** M 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.116715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.093426 restraints weight = 65541.044| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.57 r_work: 0.3222 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.344 33656 Z= 0.217 Angle : 0.721 59.200 45509 Z= 0.392 Chirality : 0.045 0.357 5188 Planarity : 0.005 0.108 5888 Dihedral : 8.063 88.797 4786 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.09 % Favored : 94.74 % Rotamer: Outliers : 3.42 % Allowed : 26.91 % Favored : 69.67 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 1.16 % 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: 0.18 (0.13), residues: 4184 helix: 1.20 (0.12), residues: 1833 sheet: -0.79 (0.19), residues: 723 loop : -0.59 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 252 TYR 0.051 0.001 TYR A 429 PHE 0.020 0.001 PHE c 91 TRP 0.022 0.001 TRP H 158 HIS 0.009 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00455 (33651) covalent geometry : angle 0.71890 (45503) SS BOND : bond 0.19842 ( 3) SS BOND : angle 4.85962 ( 6) hydrogen bonds : bond 0.03410 ( 1500) hydrogen bonds : angle 4.40052 ( 4290) metal coordination : bond 0.00343 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8421.93 seconds wall clock time: 145 minutes 18.04 seconds (8718.04 seconds total)