Starting phenix.real_space_refine on Fri Oct 30 00:41:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36py_77749/10_2026/36py_77749.cif Found real_map, /net/cci-nas-00/data/ceres_data/36py_77749/10_2026/36py_77749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/36py_77749/10_2026/36py_77749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36py_77749/10_2026/36py_77749.map" model { file = "/net/cci-nas-00/data/ceres_data/36py_77749/10_2026/36py_77749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36py_77749/10_2026/36py_77749.cif" } resolution = 3.7 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= 0.004 sd= 0.041 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 20 6.06 5 P 10 5.49 5 Mg 10 5.21 5 S 70 5.16 5 C 20900 2.51 5 N 6090 2.21 5 O 6690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 274 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33790 Number of models: 1 Model: "" Number of chains: 20 Chain: "C" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3371 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain: "D" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3371 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain: "E" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3371 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain: "F" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3371 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain: "G" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3371 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain: "H" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3371 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain: "I" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3371 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain: "J" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3371 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain: "K" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3371 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain: "L" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3371 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 8 Unusual residues: {' MG': 1, ' ZN': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 8 Unusual residues: {' MG': 1, ' ZN': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 8 Unusual residues: {' MG': 1, ' ZN': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 8 Unusual residues: {' MG': 1, ' ZN': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 8 Unusual residues: {' MG': 1, ' ZN': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 8 Unusual residues: {' MG': 1, ' ZN': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 8 Unusual residues: {' MG': 1, ' ZN': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 8 Unusual residues: {' MG': 1, ' ZN': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 8 Unusual residues: {' MG': 1, ' ZN': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 8 Unusual residues: {' MG': 1, ' ZN': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" O1 PO4 C 504 " occ=0.72 ... (3 atoms not shown) pdb=" P PO4 C 504 " occ=0.72 residue: pdb=" O1 PO4 D 504 " occ=0.72 ... (3 atoms not shown) pdb=" P PO4 D 504 " occ=0.72 residue: pdb=" O1 PO4 E 504 " occ=0.72 ... (3 atoms not shown) pdb=" P PO4 E 504 " occ=0.72 residue: pdb=" O1 PO4 F 504 " occ=0.72 ... (3 atoms not shown) pdb=" P PO4 F 504 " occ=0.72 residue: pdb=" O1 PO4 G 504 " occ=0.72 ... (3 atoms not shown) pdb=" P PO4 G 504 " occ=0.72 residue: pdb=" O1 PO4 H 504 " occ=0.72 ... (3 atoms not shown) pdb=" P PO4 H 504 " occ=0.72 residue: pdb=" O1 PO4 I 504 " occ=0.72 ... (3 atoms not shown) pdb=" P PO4 I 504 " occ=0.72 residue: pdb=" O1 PO4 J 504 " occ=0.72 ... (3 atoms not shown) pdb=" P PO4 J 504 " occ=0.72 residue: pdb=" O1 PO4 K 504 " occ=0.72 ... (3 atoms not shown) pdb=" P PO4 K 504 " occ=0.72 residue: pdb=" O1 PO4 L 504 " occ=0.72 ... (3 atoms not shown) pdb=" P PO4 L 504 " occ=0.72 Time building chain proxies: 7.57, per 1000 atoms: 0.22 Number of scatterers: 33790 At special positions: 0 Unit cell: (132.06, 133.125, 224.715, 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 20 29.99 S 70 16.00 P 10 15.00 Mg 10 11.99 O 6690 8.00 N 6090 7.00 C 20900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 178 " distance=2.03 Simple disulfide: pdb=" SG CYS C 286 " - pdb=" SG CYS C 336 " distance=2.03 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 178 " distance=2.03 Simple disulfide: pdb=" SG CYS D 286 " - pdb=" SG CYS D 336 " distance=2.03 Simple disulfide: pdb=" SG CYS E 168 " - pdb=" SG CYS E 178 " distance=2.03 Simple disulfide: pdb=" SG CYS E 286 " - pdb=" SG CYS E 336 " distance=2.03 Simple disulfide: pdb=" SG CYS F 168 " - pdb=" SG CYS F 178 " distance=2.03 Simple disulfide: pdb=" SG CYS F 286 " - pdb=" SG CYS F 336 " distance=2.03 Simple disulfide: pdb=" SG CYS G 168 " - pdb=" SG CYS G 178 " distance=2.03 Simple disulfide: pdb=" SG CYS G 286 " - pdb=" SG CYS G 336 " distance=2.03 Simple disulfide: pdb=" SG CYS H 168 " - pdb=" SG CYS H 178 " distance=2.03 Simple disulfide: pdb=" SG CYS H 286 " - pdb=" SG CYS H 336 " distance=2.03 Simple disulfide: pdb=" SG CYS I 168 " - pdb=" SG CYS I 178 " distance=2.03 Simple disulfide: pdb=" SG CYS I 286 " - pdb=" SG CYS I 336 " distance=2.03 Simple disulfide: pdb=" SG CYS J 168 " - pdb=" SG CYS J 178 " distance=2.02 Simple disulfide: pdb=" SG CYS J 286 " - pdb=" SG CYS J 336 " distance=2.03 Simple disulfide: pdb=" SG CYS K 168 " - pdb=" SG CYS K 178 " distance=2.03 Simple disulfide: pdb=" SG CYS K 286 " - pdb=" SG CYS K 336 " distance=2.03 Simple disulfide: pdb=" SG CYS L 168 " - pdb=" SG CYS L 178 " distance=2.03 Simple disulfide: pdb=" SG CYS L 286 " - pdb=" SG CYS L 336 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 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 370 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 331 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 412 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 370 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 331 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 412 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 370 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 412 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 331 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 370 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" NE2 HIS F 331 " pdb="ZN ZN F 502 " - pdb=" NE2 HIS F 412 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 370 " pdb=" ZN G 502 " pdb="ZN ZN G 502 " - pdb=" NE2 HIS G 412 " pdb="ZN ZN G 502 " - pdb=" NE2 HIS G 331 " pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 370 " pdb="ZN ZN H 501 " - pdb="ZN ZN H 502 " pdb=" ZN H 502 " pdb="ZN ZN H 502 " - pdb=" NE2 HIS H 412 " pdb=" ZN I 501 " pdb="ZN ZN I 501 " - pdb=" NE2 HIS I 370 " pdb=" ZN I 502 " pdb="ZN ZN I 502 " - pdb=" NE2 HIS I 331 " pdb="ZN ZN I 502 " - pdb=" NE2 HIS I 412 " pdb=" ZN J 501 " pdb="ZN ZN J 501 " - pdb=" NE2 HIS J 370 " pdb=" ZN J 502 " pdb="ZN ZN J 502 " - pdb=" NE2 HIS J 412 " pdb="ZN ZN J 502 " - pdb=" NE2 HIS J 331 " pdb=" ZN K 501 " pdb="ZN ZN K 501 " - pdb=" NE2 HIS K 370 " pdb=" ZN K 502 " pdb="ZN ZN K 502 " - pdb=" NE2 HIS K 331 " pdb="ZN ZN K 502 " - pdb=" NE2 HIS K 412 " pdb=" ZN L 501 " pdb="ZN ZN L 501 " - pdb=" NE2 HIS L 370 " pdb=" ZN L 502 " pdb="ZN ZN L 502 " - pdb=" NE2 HIS L 412 " pdb="ZN ZN L 502 " - pdb=" NE2 HIS L 331 " 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8140 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 47 sheets defined 38.8% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'C' and resid 29 through 37 removed outlier: 3.865A pdb=" N GLN C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 67 Processing helix chain 'C' and resid 101 through 112 Processing helix chain 'C' and resid 131 through 139 Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.699A pdb=" N SER C 175 " --> pdb=" O PRO C 171 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LYS C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 186 removed outlier: 6.258A pdb=" N LEU C 183 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLU C 184 " --> pdb=" O ASN C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 199 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 217 through 221 removed outlier: 4.382A pdb=" N TYR C 220 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 239 through 244 Processing helix chain 'C' and resid 298 through 312 removed outlier: 4.229A pdb=" N ASP C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 332 removed outlier: 3.915A pdb=" N LYS C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA C 332 " --> pdb=" O LYS C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 360 removed outlier: 3.694A pdb=" N LYS C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 430 removed outlier: 3.561A pdb=" N ASN C 428 " --> pdb=" O GLN C 425 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 429 " --> pdb=" O ALA C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 447 removed outlier: 3.529A pdb=" N PHE C 440 " --> pdb=" O THR C 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 9 removed outlier: 4.292A pdb=" N PHE D 8 " --> pdb=" O ASP D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 37 Processing helix chain 'D' and resid 54 through 67 Processing helix chain 'D' and resid 101 through 112 removed outlier: 3.711A pdb=" N SER D 105 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 153 through 158 Processing helix chain 'D' and resid 170 through 178 removed outlier: 4.753A pdb=" N LYS D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 190 through 199 Processing helix chain 'D' and resid 208 through 213 Processing helix chain 'D' and resid 224 through 233 Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 276 through 281 Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 324 through 332 removed outlier: 4.029A pdb=" N LYS D 328 " --> pdb=" O ALA D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 360 removed outlier: 3.721A pdb=" N LYS D 351 " --> pdb=" O GLU D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 430 removed outlier: 3.637A pdb=" N ASN D 428 " --> pdb=" O GLN D 425 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D 429 " --> pdb=" O ALA D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 447 removed outlier: 3.968A pdb=" N PHE D 439 " --> pdb=" O GLN D 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 9 removed outlier: 4.130A pdb=" N PHE E 8 " --> pdb=" O ASP E 4 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN E 9 " --> pdb=" O PRO E 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4 through 9' Processing helix chain 'E' and resid 29 through 37 Processing helix chain 'E' and resid 54 through 66 Processing helix chain 'E' and resid 74 through 78 removed outlier: 3.708A pdb=" N LEU E 78 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 131 through 139 Processing helix chain 'E' and resid 153 through 158 Processing helix chain 'E' and resid 170 through 178 removed outlier: 4.912A pdb=" N LYS E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 186 Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 217 through 221 removed outlier: 4.312A pdb=" N TYR E 220 " --> pdb=" O ALA E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 233 Processing helix chain 'E' and resid 239 through 246 Processing helix chain 'E' and resid 298 through 311 Processing helix chain 'E' and resid 324 through 332 removed outlier: 3.925A pdb=" N LYS E 328 " --> pdb=" O ALA E 324 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA E 332 " --> pdb=" O LYS E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 360 Processing helix chain 'E' and resid 425 through 430 Processing helix chain 'E' and resid 436 through 447 Processing helix chain 'F' and resid 4 through 9 removed outlier: 4.240A pdb=" N PHE F 8 " --> pdb=" O ASP F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 37 Processing helix chain 'F' and resid 54 through 66 Processing helix chain 'F' and resid 101 through 112 removed outlier: 3.685A pdb=" N SER F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 139 Processing helix chain 'F' and resid 153 through 161 removed outlier: 5.050A pdb=" N LEU F 159 " --> pdb=" O THR F 155 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU F 160 " --> pdb=" O PRO F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 178 removed outlier: 3.527A pdb=" N SER F 175 " --> pdb=" O PRO F 171 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS F 176 " --> pdb=" O GLU F 172 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 182 Processing helix chain 'F' and resid 190 through 199 Processing helix chain 'F' and resid 207 through 213 removed outlier: 3.582A pdb=" N THR F 210 " --> pdb=" O GLY F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 233 Processing helix chain 'F' and resid 239 through 245 Processing helix chain 'F' and resid 276 through 281 removed outlier: 3.535A pdb=" N GLN F 281 " --> pdb=" O GLY F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 311 Processing helix chain 'F' and resid 324 through 332 removed outlier: 4.010A pdb=" N LYS F 328 " --> pdb=" O ALA F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 360 removed outlier: 3.768A pdb=" N LYS F 351 " --> pdb=" O GLU F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 430 removed outlier: 3.713A pdb=" N ASN F 428 " --> pdb=" O GLN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 446 removed outlier: 3.686A pdb=" N PHE F 439 " --> pdb=" O GLN F 435 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 9 removed outlier: 4.346A pdb=" N PHE G 8 " --> pdb=" O ASP G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 54 through 66 Processing helix chain 'G' and resid 101 through 112 removed outlier: 3.820A pdb=" N SER G 105 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 139 removed outlier: 3.537A pdb=" N LEU G 135 " --> pdb=" O ASN G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 158 Processing helix chain 'G' and resid 170 through 178 removed outlier: 3.544A pdb=" N SER G 175 " --> pdb=" O PRO G 171 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LYS G 176 " --> pdb=" O GLU G 172 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 186 Processing helix chain 'G' and resid 190 through 199 Processing helix chain 'G' and resid 208 through 213 Processing helix chain 'G' and resid 224 through 233 Processing helix chain 'G' and resid 239 through 246 Processing helix chain 'G' and resid 298 through 311 Processing helix chain 'G' and resid 324 through 332 removed outlier: 3.910A pdb=" N LYS G 328 " --> pdb=" O ALA G 324 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA G 332 " --> pdb=" O LYS G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 360 removed outlier: 3.744A pdb=" N LYS G 351 " --> pdb=" O GLU G 347 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 430 removed outlier: 3.619A pdb=" N ASN G 428 " --> pdb=" O GLN G 425 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 429 " --> pdb=" O ALA G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 436 through 447 removed outlier: 3.577A pdb=" N PHE G 440 " --> pdb=" O THR G 436 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 9 removed outlier: 4.182A pdb=" N PHE H 8 " --> pdb=" O ASP H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 37 removed outlier: 3.585A pdb=" N GLN H 35 " --> pdb=" O GLN H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 67 Processing helix chain 'H' and resid 101 through 112 Processing helix chain 'H' and resid 131 through 139 removed outlier: 3.614A pdb=" N LEU H 135 " --> pdb=" O ASN H 131 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU H 138 " --> pdb=" O GLU H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 158 Processing helix chain 'H' and resid 170 through 178 removed outlier: 4.077A pdb=" N LYS H 176 " --> pdb=" O GLU H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 186 Processing helix chain 'H' and resid 190 through 199 Processing helix chain 'H' and resid 208 through 213 Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 239 through 246 removed outlier: 3.511A pdb=" N VAL H 246 " --> pdb=" O GLU H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 311 Processing helix chain 'H' and resid 324 through 332 removed outlier: 4.253A pdb=" N LYS H 328 " --> pdb=" O ALA H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 360 removed outlier: 3.803A pdb=" N LYS H 351 " --> pdb=" O GLU H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 425 through 430 removed outlier: 3.672A pdb=" N ASN H 428 " --> pdb=" O GLN H 425 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL H 429 " --> pdb=" O ALA H 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 436 through 447 removed outlier: 3.626A pdb=" N PHE H 440 " --> pdb=" O THR H 436 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 removed outlier: 4.283A pdb=" N PHE I 8 " --> pdb=" O ASP I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 37 removed outlier: 3.823A pdb=" N GLN I 35 " --> pdb=" O GLN I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 67 Processing helix chain 'I' and resid 101 through 112 Processing helix chain 'I' and resid 131 through 139 Processing helix chain 'I' and resid 153 through 158 Processing helix chain 'I' and resid 170 through 178 removed outlier: 4.581A pdb=" N LYS I 176 " --> pdb=" O GLU I 172 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN I 177 " --> pdb=" O ALA I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 186 Processing helix chain 'I' and resid 190 through 199 Processing helix chain 'I' and resid 208 through 213 Processing helix chain 'I' and resid 224 through 232 Processing helix chain 'I' and resid 239 through 245 Processing helix chain 'I' and resid 298 through 311 Processing helix chain 'I' and resid 324 through 332 removed outlier: 4.127A pdb=" N LYS I 328 " --> pdb=" O ALA I 324 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA I 332 " --> pdb=" O LYS I 328 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 360 removed outlier: 3.707A pdb=" N LYS I 351 " --> pdb=" O GLU I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 430 removed outlier: 3.563A pdb=" N ASN I 428 " --> pdb=" O GLN I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 436 through 447 Processing helix chain 'J' and resid 4 through 9 removed outlier: 4.050A pdb=" N PHE J 8 " --> pdb=" O ASP J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 37 Processing helix chain 'J' and resid 54 through 66 Processing helix chain 'J' and resid 101 through 112 removed outlier: 3.664A pdb=" N SER J 105 " --> pdb=" O ASP J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 139 Processing helix chain 'J' and resid 153 through 158 Processing helix chain 'J' and resid 170 through 178 removed outlier: 3.594A pdb=" N SER J 175 " --> pdb=" O PRO J 171 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYS J 176 " --> pdb=" O GLU J 172 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN J 177 " --> pdb=" O ALA J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 186 Processing helix chain 'J' and resid 190 through 199 Processing helix chain 'J' and resid 207 through 213 removed outlier: 3.652A pdb=" N THR J 210 " --> pdb=" O GLY J 207 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 232 Processing helix chain 'J' and resid 239 through 245 Processing helix chain 'J' and resid 276 through 281 Processing helix chain 'J' and resid 298 through 311 Processing helix chain 'J' and resid 324 through 332 removed outlier: 4.155A pdb=" N LYS J 328 " --> pdb=" O ALA J 324 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 360 removed outlier: 3.621A pdb=" N LYS J 351 " --> pdb=" O GLU J 347 " (cutoff:3.500A) Processing helix chain 'J' and resid 425 through 430 removed outlier: 3.563A pdb=" N VAL J 429 " --> pdb=" O ALA J 426 " (cutoff:3.500A) Processing helix chain 'J' and resid 436 through 447 removed outlier: 3.663A pdb=" N PHE J 440 " --> pdb=" O THR J 436 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 9 removed outlier: 4.081A pdb=" N PHE K 8 " --> pdb=" O ASP K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 37 removed outlier: 3.577A pdb=" N GLN K 35 " --> pdb=" O GLN K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 67 Processing helix chain 'K' and resid 101 through 112 removed outlier: 3.912A pdb=" N SER K 105 " --> pdb=" O ASP K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 139 removed outlier: 3.677A pdb=" N LEU K 135 " --> pdb=" O ASN K 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 158 Processing helix chain 'K' and resid 170 through 178 removed outlier: 3.597A pdb=" N SER K 175 " --> pdb=" O PRO K 171 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS K 176 " --> pdb=" O GLU K 172 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN K 177 " --> pdb=" O ALA K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 186 Processing helix chain 'K' and resid 190 through 199 Processing helix chain 'K' and resid 207 through 212 removed outlier: 4.091A pdb=" N PHE K 211 " --> pdb=" O GLY K 207 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA K 212 " --> pdb=" O ALA K 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 207 through 212' Processing helix chain 'K' and resid 224 through 233 Processing helix chain 'K' and resid 239 through 246 removed outlier: 3.650A pdb=" N ALA K 245 " --> pdb=" O ASP K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 311 Processing helix chain 'K' and resid 324 through 332 removed outlier: 4.029A pdb=" N LYS K 328 " --> pdb=" O ALA K 324 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA K 332 " --> pdb=" O LYS K 328 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 360 removed outlier: 3.703A pdb=" N LYS K 351 " --> pdb=" O GLU K 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 425 through 430 removed outlier: 3.573A pdb=" N ASN K 428 " --> pdb=" O GLN K 425 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL K 429 " --> pdb=" O ALA K 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 446 Processing helix chain 'L' and resid 4 through 9 removed outlier: 4.103A pdb=" N PHE L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 37 Processing helix chain 'L' and resid 54 through 67 Processing helix chain 'L' and resid 101 through 112 removed outlier: 3.860A pdb=" N SER L 105 " --> pdb=" O ASP L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 139 removed outlier: 3.614A pdb=" N LEU L 135 " --> pdb=" O ASN L 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 153 through 161 removed outlier: 5.331A pdb=" N LEU L 159 " --> pdb=" O THR L 155 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU L 160 " --> pdb=" O PRO L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 178 removed outlier: 4.589A pdb=" N LYS L 176 " --> pdb=" O GLU L 172 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN L 177 " --> pdb=" O ALA L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 186 Processing helix chain 'L' and resid 190 through 199 Processing helix chain 'L' and resid 207 through 213 removed outlier: 3.514A pdb=" N THR L 210 " --> pdb=" O GLY L 207 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 233 Processing helix chain 'L' and resid 239 through 246 removed outlier: 3.628A pdb=" N VAL L 246 " --> pdb=" O GLU L 242 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 281 removed outlier: 3.707A pdb=" N GLN L 281 " --> pdb=" O GLY L 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 311 Processing helix chain 'L' and resid 324 through 332 removed outlier: 4.215A pdb=" N LYS L 328 " --> pdb=" O ALA L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 360 removed outlier: 3.841A pdb=" N LYS L 351 " --> pdb=" O GLU L 347 " (cutoff:3.500A) Processing helix chain 'L' and resid 425 through 430 Processing helix chain 'L' and resid 436 through 447 removed outlier: 3.596A pdb=" N PHE L 440 " --> pdb=" O THR L 436 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 142 through 143 removed outlier: 6.480A pdb=" N ALA C 142 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N GLN C 320 " --> pdb=" O ALA C 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 88 through 89 Processing sheet with id=AA3, first strand: chain 'C' and resid 146 through 150 removed outlier: 4.181A pdb=" N GLY C 206 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA C 149 " --> pdb=" O GLY C 206 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY C 205 " --> pdb=" O GLY C 257 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG C 235 " --> pdb=" O ILE C 256 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 268 through 269 Processing sheet with id=AA5, first strand: chain 'C' and resid 274 through 275 removed outlier: 4.090A pdb=" N ALA C 399 " --> pdb=" O ILE C 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 371 through 372 removed outlier: 3.931A pdb=" N ALA C 371 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR C 413 " --> pdb=" O ALA C 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 255 through 258 removed outlier: 6.977A pdb=" N VAL D 203 " --> pdb=" O GLY D 257 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY D 206 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA D 149 " --> pdb=" O GLY D 206 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA D 142 " --> pdb=" O PHE D 318 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N GLN D 320 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY D 144 " --> pdb=" O GLN D 320 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N GLU D 322 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL D 146 " --> pdb=" O GLU D 322 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 417 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR D 81 " --> pdb=" O GLY D 431 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N THR D 433 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN D 83 " --> pdb=" O THR D 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA9, first strand: chain 'D' and resid 268 through 269 Processing sheet with id=AB1, first strand: chain 'D' and resid 274 through 275 removed outlier: 4.229A pdb=" N ALA D 399 " --> pdb=" O ILE D 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 142 through 143 removed outlier: 6.268A pdb=" N ALA E 142 " --> pdb=" O PHE E 318 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLN E 320 " --> pdb=" O ALA E 142 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY E 206 " --> pdb=" O SER E 147 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA E 149 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL E 203 " --> pdb=" O GLY E 257 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ARG E 235 " --> pdb=" O ILE E 256 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 142 through 143 removed outlier: 6.268A pdb=" N ALA E 142 " --> pdb=" O PHE E 318 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLN E 320 " --> pdb=" O ALA E 142 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASN E 44 " --> pdb=" O LEU E 363 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE E 365 " --> pdb=" O ASN E 44 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE E 46 " --> pdb=" O ILE E 365 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N THR E 367 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU E 48 " --> pdb=" O THR E 367 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU E 80 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY E 431 " --> pdb=" O THR E 81 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 88 through 89 Processing sheet with id=AB5, first strand: chain 'E' and resid 268 through 269 Processing sheet with id=AB6, first strand: chain 'E' and resid 274 through 275 removed outlier: 3.710A pdb=" N ALA E 399 " --> pdb=" O ILE E 377 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 235 through 237 removed outlier: 6.091A pdb=" N ARG F 235 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LEU F 258 " --> pdb=" O ARG F 235 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL F 237 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL F 203 " --> pdb=" O GLY F 257 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 202 " --> pdb=" O THR F 143 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY F 206 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA F 149 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA F 142 " --> pdb=" O PHE F 318 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N GLN F 320 " --> pdb=" O ALA F 142 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY F 144 " --> pdb=" O GLN F 320 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N GLU F 322 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL F 146 " --> pdb=" O GLU F 322 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU F 80 " --> pdb=" O ALA F 421 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY F 431 " --> pdb=" O THR F 81 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 88 through 89 Processing sheet with id=AB9, first strand: chain 'F' and resid 268 through 269 Processing sheet with id=AC1, first strand: chain 'F' and resid 274 through 275 removed outlier: 4.082A pdb=" N ALA F 399 " --> pdb=" O ILE F 377 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 142 through 143 removed outlier: 6.516A pdb=" N ALA G 142 " --> pdb=" O PHE G 318 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N GLN G 320 " --> pdb=" O ALA G 142 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU G 80 " --> pdb=" O ALA G 421 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY G 431 " --> pdb=" O THR G 81 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 88 through 89 Processing sheet with id=AC4, first strand: chain 'G' and resid 146 through 150 removed outlier: 4.328A pdb=" N GLY G 206 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA G 149 " --> pdb=" O GLY G 206 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 235 through 237 Processing sheet with id=AC6, first strand: chain 'G' and resid 268 through 269 Processing sheet with id=AC7, first strand: chain 'G' and resid 274 through 275 removed outlier: 4.118A pdb=" N ALA G 399 " --> pdb=" O ILE G 377 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 235 through 237 removed outlier: 5.873A pdb=" N ARG H 235 " --> pdb=" O ILE H 256 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU H 258 " --> pdb=" O ARG H 235 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL H 237 " --> pdb=" O LEU H 258 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL H 202 " --> pdb=" O THR H 143 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLY H 206 " --> pdb=" O SER H 147 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA H 149 " --> pdb=" O GLY H 206 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA H 142 " --> pdb=" O PHE H 318 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N GLN H 320 " --> pdb=" O ALA H 142 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY H 144 " --> pdb=" O GLN H 320 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N GLU H 322 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL H 146 " --> pdb=" O GLU H 322 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU H 417 " --> pdb=" O TYR H 84 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU H 80 " --> pdb=" O ALA H 421 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR H 81 " --> pdb=" O GLY H 431 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N THR H 433 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN H 83 " --> pdb=" O THR H 433 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AD1, first strand: chain 'H' and resid 268 through 269 Processing sheet with id=AD2, first strand: chain 'H' and resid 274 through 275 removed outlier: 4.196A pdb=" N ALA H 399 " --> pdb=" O ILE H 377 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 235 through 237 removed outlier: 6.229A pdb=" N ARG I 235 " --> pdb=" O ILE I 256 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL I 203 " --> pdb=" O GLY I 257 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY I 206 " --> pdb=" O SER I 147 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA I 149 " --> pdb=" O GLY I 206 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA I 142 " --> pdb=" O PHE I 318 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N GLN I 320 " --> pdb=" O ALA I 142 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY I 144 " --> pdb=" O GLN I 320 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N GLU I 322 " --> pdb=" O GLY I 144 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL I 146 " --> pdb=" O GLU I 322 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU I 80 " --> pdb=" O ALA I 421 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY I 431 " --> pdb=" O THR I 81 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN I 83 " --> pdb=" O GLY I 431 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 88 through 89 Processing sheet with id=AD5, first strand: chain 'I' and resid 268 through 269 Processing sheet with id=AD6, first strand: chain 'I' and resid 274 through 275 removed outlier: 4.010A pdb=" N ALA I 399 " --> pdb=" O ILE I 377 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE I 377 " --> pdb=" O ALA I 399 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER I 401 " --> pdb=" O GLN I 375 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 255 through 258 removed outlier: 4.409A pdb=" N GLY J 206 " --> pdb=" O SER J 147 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA J 149 " --> pdb=" O GLY J 206 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA J 142 " --> pdb=" O PHE J 318 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLN J 320 " --> pdb=" O ALA J 142 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY J 144 " --> pdb=" O GLN J 320 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N GLU J 322 " --> pdb=" O GLY J 144 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL J 146 " --> pdb=" O GLU J 322 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASN J 44 " --> pdb=" O LEU J 363 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ILE J 365 " --> pdb=" O ASN J 44 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE J 46 " --> pdb=" O ILE J 365 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N THR J 367 " --> pdb=" O ILE J 46 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU J 48 " --> pdb=" O THR J 367 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU J 80 " --> pdb=" O ALA J 421 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY J 431 " --> pdb=" O THR J 81 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 88 through 89 Processing sheet with id=AD9, first strand: chain 'J' and resid 268 through 269 Processing sheet with id=AE1, first strand: chain 'J' and resid 274 through 275 removed outlier: 3.983A pdb=" N ALA J 399 " --> pdb=" O ILE J 377 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 371 through 372 removed outlier: 3.717A pdb=" N ALA J 371 " --> pdb=" O THR J 413 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 235 through 237 removed outlier: 6.040A pdb=" N ARG K 235 " --> pdb=" O ILE K 256 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL K 203 " --> pdb=" O GLY K 257 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY K 206 " --> pdb=" O SER K 147 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA K 149 " --> pdb=" O GLY K 206 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU K 417 " --> pdb=" O TYR K 84 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU K 80 " --> pdb=" O ALA K 421 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY K 431 " --> pdb=" O THR K 81 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 88 through 89 Processing sheet with id=AE5, first strand: chain 'K' and resid 268 through 269 Processing sheet with id=AE6, first strand: chain 'K' and resid 274 through 275 removed outlier: 4.115A pdb=" N ALA K 399 " --> pdb=" O ILE K 377 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 318 through 322 removed outlier: 3.556A pdb=" N LEU L 80 " --> pdb=" O ALA L 421 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR L 81 " --> pdb=" O GLY L 431 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N THR L 433 " --> pdb=" O THR L 81 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN L 83 " --> pdb=" O THR L 433 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 88 through 89 Processing sheet with id=AE9, first strand: chain 'L' and resid 146 through 150 removed outlier: 4.657A pdb=" N GLY L 206 " --> pdb=" O SER L 147 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA L 149 " --> pdb=" O GLY L 206 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 268 through 269 Processing sheet with id=AF2, first strand: chain 'L' and resid 274 through 275 1332 hydrogen bonds defined for protein. 3630 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: 7.29 Time building geometry restraints manager: 3.62 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: 11740 1.34 - 1.46: 7426 1.46 - 1.58: 15074 1.58 - 1.71: 0 1.71 - 1.83: 100 Bond restraints: 34340 Sorted by residual: bond pdb=" O4 PO4 L 504 " pdb=" P PO4 L 504 " ideal model delta sigma weight residual 1.568 1.497 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" O4 PO4 G 504 " pdb=" P PO4 G 504 " ideal model delta sigma weight residual 1.568 1.501 0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O4 PO4 K 504 " pdb=" P PO4 K 504 " ideal model delta sigma weight residual 1.568 1.502 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" O3 PO4 H 504 " pdb=" P PO4 H 504 " ideal model delta sigma weight residual 1.569 1.504 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" O4 PO4 D 504 " pdb=" P PO4 D 504 " ideal model delta sigma weight residual 1.568 1.504 0.064 2.00e-02 2.50e+03 1.04e+01 ... (remaining 34335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 43680 1.68 - 3.36: 2519 3.36 - 5.04: 360 5.04 - 6.72: 59 6.72 - 8.40: 12 Bond angle restraints: 46630 Sorted by residual: angle pdb=" CA TRP H 195 " pdb=" CB TRP H 195 " pdb=" CG TRP H 195 " ideal model delta sigma weight residual 113.60 122.00 -8.40 1.90e+00 2.77e-01 1.96e+01 angle pdb=" CA TRP L 195 " pdb=" CB TRP L 195 " pdb=" CG TRP L 195 " ideal model delta sigma weight residual 113.60 121.20 -7.60 1.90e+00 2.77e-01 1.60e+01 angle pdb=" CA TRP J 195 " pdb=" CB TRP J 195 " pdb=" CG TRP J 195 " ideal model delta sigma weight residual 113.60 121.05 -7.45 1.90e+00 2.77e-01 1.54e+01 angle pdb=" CA TRP H 109 " pdb=" CB TRP H 109 " pdb=" CG TRP H 109 " ideal model delta sigma weight residual 113.60 120.81 -7.21 1.90e+00 2.77e-01 1.44e+01 angle pdb=" CA TRP K 195 " pdb=" CB TRP K 195 " pdb=" CG TRP K 195 " ideal model delta sigma weight residual 113.60 120.80 -7.20 1.90e+00 2.77e-01 1.44e+01 ... (remaining 46625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 19255 17.72 - 35.44: 1153 35.44 - 53.15: 248 53.15 - 70.87: 103 70.87 - 88.59: 41 Dihedral angle restraints: 20800 sinusoidal: 8040 harmonic: 12760 Sorted by residual: dihedral pdb=" CA SER C 373 " pdb=" C SER C 373 " pdb=" N SER C 374 " pdb=" CA SER C 374 " ideal model delta harmonic sigma weight residual -180.00 -151.44 -28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA LYS H 176 " pdb=" C LYS H 176 " pdb=" N GLN H 177 " pdb=" CA GLN H 177 " ideal model delta harmonic sigma weight residual -180.00 -151.51 -28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA THR H 100 " pdb=" C THR H 100 " pdb=" N ASP H 101 " pdb=" CA ASP H 101 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 20797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3024 0.042 - 0.083: 1533 0.083 - 0.125: 562 0.125 - 0.166: 127 0.166 - 0.208: 14 Chirality restraints: 5260 Sorted by residual: chirality pdb=" CB THR G 415 " pdb=" CA THR G 415 " pdb=" OG1 THR G 415 " pdb=" CG2 THR G 415 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE L 49 " pdb=" CA ILE L 49 " pdb=" CG1 ILE L 49 " pdb=" CG2 ILE L 49 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB THR H 415 " pdb=" CA THR H 415 " pdb=" OG1 THR H 415 " pdb=" CG2 THR H 415 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.12e-01 ... (remaining 5257 not shown) Planarity restraints: 6230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 63 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C ASN C 63 " -0.039 2.00e-02 2.50e+03 pdb=" O ASN C 63 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR C 64 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 63 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" C ASN D 63 " -0.039 2.00e-02 2.50e+03 pdb=" O ASN D 63 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR D 64 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN I 63 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C ASN I 63 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN I 63 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR I 64 " -0.013 2.00e-02 2.50e+03 ... (remaining 6227 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 258 2.49 - 3.09: 26027 3.09 - 3.70: 52647 3.70 - 4.30: 76941 4.30 - 4.90: 131488 Nonbonded interactions: 287361 Sorted by model distance: nonbonded pdb=" OD1 ASP L 51 " pdb="ZN ZN L 501 " model vdw 1.888 2.230 nonbonded pdb=" OD1 ASP C 51 " pdb="ZN ZN C 501 " model vdw 1.899 2.230 nonbonded pdb="ZN ZN L 501 " pdb=" O4 PO4 L 504 " model vdw 1.902 2.230 nonbonded pdb=" OG SER H 102 " pdb="ZN ZN H 501 " model vdw 1.907 2.230 nonbonded pdb=" OD2 ASP I 369 " pdb="ZN ZN I 501 " model vdw 1.913 2.230 ... (remaining 287356 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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=0.72 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 35.340 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 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 : 0.015 0.524 34390 Z= 0.578 Angle : 0.896 8.405 46670 Z= 0.488 Chirality : 0.055 0.208 5260 Planarity : 0.005 0.051 6230 Dihedral : 13.748 88.587 12600 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.11), residues: 4480 helix: -1.44 (0.11), residues: 1450 sheet: -1.43 (0.17), residues: 810 loop : -0.82 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG K 62 TYR 0.036 0.003 TYR I 84 PHE 0.026 0.003 PHE D 259 TRP 0.035 0.004 TRP H 109 HIS 0.017 0.003 HIS E 86 Details of bonding type rmsd/Z covalent geometry : bond 0.01322 / 0.54 (34340) covalent geometry : angle 0.89547 / 0.49 (46630) SS BOND : bond 0.00303 / 0.20 ( 20) SS BOND : angle 1.30600 / 0.82 ( 40) hydrogen bonds : bond 0.19179 / 12.78 ( 1332) hydrogen bonds : angle 7.36807 / 5.23 ( 3630) metal coordination : bond 0.20710 / 13.17 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 443 time to evaluate : 1.295 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: C 76 ASP cc_start: 0.8774 (m-30) cc_final: 0.8541 (m-30) REVERT: C 406 GLU cc_start: 0.7116 (pt0) cc_final: 0.6805 (pt0) REVERT: C 434 ASP cc_start: 0.8689 (t70) cc_final: 0.8304 (t0) REVERT: D 269 LEU cc_start: 0.7873 (tp) cc_final: 0.7558 (tp) REVERT: E 83 GLN cc_start: 0.8492 (mp10) cc_final: 0.8120 (mt0) REVERT: E 168 CYS cc_start: 0.5565 (m) cc_final: 0.4939 (m) REVERT: E 359 ASP cc_start: 0.7372 (t0) cc_final: 0.7150 (t70) REVERT: F 105 SER cc_start: 0.8493 (p) cc_final: 0.8203 (t) REVERT: F 201 ASP cc_start: 0.7987 (m-30) cc_final: 0.7340 (t0) REVERT: G 123 ASP cc_start: 0.8126 (p0) cc_final: 0.7833 (p0) REVERT: G 124 ILE cc_start: 0.8683 (pt) cc_final: 0.8357 (mt) REVERT: G 267 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7614 (mmm160) REVERT: G 437 ASP cc_start: 0.7419 (t70) cc_final: 0.7193 (t0) REVERT: H 110 THR cc_start: 0.8741 (m) cc_final: 0.8516 (p) REVERT: H 437 ASP cc_start: 0.7373 (t70) cc_final: 0.7062 (t70) REVERT: I 83 GLN cc_start: 0.8884 (mp10) cc_final: 0.8564 (mp10) REVERT: J 109 TRP cc_start: 0.9090 (p90) cc_final: 0.8211 (p90) REVERT: J 110 THR cc_start: 0.8623 (m) cc_final: 0.7785 (m) REVERT: K 99 VAL cc_start: 0.9200 (t) cc_final: 0.8967 (m) REVERT: L 31 GLN cc_start: 0.8265 (tp40) cc_final: 0.8036 (tp40) REVERT: L 130 ARG cc_start: 0.8396 (ttm110) cc_final: 0.8106 (mtp85) REVERT: L 372 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.7681 (t-90) outliers start: 1 outliers final: 0 residues processed: 444 average time/residue: 0.2501 time to fit residues: 172.1734 Evaluate side-chains 164 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 372 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [432, 197, 388, 215, 20, 132, 261, 248, 207, 401, 424] chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 2 GLN C 31 GLN D 35 GLN D 410 GLN E 11 GLN E 162 HIS E 181 ASN ** E 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 HIS F 301 GLN G 162 HIS G 280 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 410 GLN H 435 GLN I 228 GLN I 281 GLN I 329 GLN I 447 ASN J 27 GLN J 177 GLN J 181 ASN J 329 GLN J 425 GLN J 447 ASN K 2 GLN K 162 HIS L 177 GLN L 181 ASN L 228 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.097722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.076030 restraints weight = 67826.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.077982 restraints weight = 41510.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.079300 restraints weight = 29696.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.080252 restraints weight = 23460.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.080801 restraints weight = 19952.459| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34390 Z= 0.195 Angle : 0.657 7.734 46670 Z= 0.347 Chirality : 0.046 0.174 5260 Planarity : 0.004 0.057 6230 Dihedral : 5.541 41.477 4842 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.01 % Allowed : 6.82 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.12), residues: 4480 helix: -0.09 (0.13), residues: 1440 sheet: -1.01 (0.17), residues: 850 loop : -0.40 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 166 TYR 0.029 0.002 TYR J 84 PHE 0.022 0.002 PHE F 355 TRP 0.028 0.002 TRP F 109 HIS 0.008 0.001 HIS H 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (34340) covalent geometry : angle 0.65575 / 0.35 (46630) SS BOND : bond 0.00783 / 0.53 ( 20) SS BOND : angle 1.53035 / 1.01 ( 40) hydrogen bonds : bond 0.04371 / 2.87 ( 1332) hydrogen bonds : angle 5.75070 / 4.08 ( 3630) metal coordination : bond 0.01100 / 0.69 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 GLN cc_start: 0.8603 (mp10) cc_final: 0.8025 (mt0) REVERT: C 240 LEU cc_start: 0.8744 (mt) cc_final: 0.8509 (mt) REVERT: C 406 GLU cc_start: 0.7087 (pt0) cc_final: 0.6752 (pt0) REVERT: D 269 LEU cc_start: 0.7783 (tp) cc_final: 0.7528 (tt) REVERT: D 437 ASP cc_start: 0.7400 (t70) cc_final: 0.6889 (t70) REVERT: E 435 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8526 (mt0) REVERT: F 201 ASP cc_start: 0.7401 (m-30) cc_final: 0.7104 (t0) REVERT: G 83 GLN cc_start: 0.8814 (mp10) cc_final: 0.8583 (mt0) REVERT: G 123 ASP cc_start: 0.8136 (p0) cc_final: 0.7836 (p0) REVERT: G 124 ILE cc_start: 0.8775 (pt) cc_final: 0.8488 (mt) REVERT: G 197 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8872 (mttp) REVERT: G 267 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.7708 (mmm-85) REVERT: H 110 THR cc_start: 0.8932 (m) cc_final: 0.8694 (p) REVERT: H 113 VAL cc_start: 0.9258 (t) cc_final: 0.9027 (p) REVERT: H 425 GLN cc_start: 0.7974 (mt0) cc_final: 0.7731 (tt0) REVERT: H 437 ASP cc_start: 0.7459 (t70) cc_final: 0.7147 (t70) REVERT: I 83 GLN cc_start: 0.8646 (mp10) cc_final: 0.8278 (mp10) REVERT: I 402 TYR cc_start: 0.7981 (m-80) cc_final: 0.7752 (m-10) REVERT: J 113 VAL cc_start: 0.9225 (t) cc_final: 0.8997 (p) REVERT: J 127 GLN cc_start: 0.8352 (tp40) cc_final: 0.8084 (tp40) REVERT: J 259 PHE cc_start: 0.8104 (m-10) cc_final: 0.7841 (m-10) REVERT: L 99 VAL cc_start: 0.9404 (t) cc_final: 0.9150 (m) REVERT: L 130 ARG cc_start: 0.8378 (ttm110) cc_final: 0.8098 (mtp85) REVERT: L 372 HIS cc_start: 0.8503 (OUTLIER) cc_final: 0.7954 (t-90) outliers start: 35 outliers final: 13 residues processed: 289 average time/residue: 0.2080 time to fit residues: 100.5629 Evaluate side-chains 180 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 177 GLN Chi-restraints excluded: chain G residue 197 LYS Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain J residue 181 ASN Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 295 ASP Chi-restraints excluded: chain L residue 372 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [383, 178, 312, 431, 57, 423, 340, 143, 93, 65, 329] chunk 383 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 312 optimal weight: 10.0000 chunk 431 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 423 optimal weight: 10.0000 chunk 340 optimal weight: 20.0000 chunk 143 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 329 optimal weight: 9.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 131 ASN C 162 HIS C 435 GLN E 181 ASN ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 181 ASN ** J 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 410 GLN ** L 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.093834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.072479 restraints weight = 68698.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.073965 restraints weight = 42000.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.075264 restraints weight = 30968.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.075617 restraints weight = 24666.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.075795 restraints weight = 23280.485| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 34390 Z= 0.265 Angle : 0.673 7.567 46670 Z= 0.352 Chirality : 0.047 0.191 5260 Planarity : 0.004 0.057 6230 Dihedral : 5.410 39.895 4842 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.02 % Allowed : 9.48 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.12), residues: 4480 helix: 0.24 (0.14), residues: 1410 sheet: -1.06 (0.18), residues: 790 loop : -0.15 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 166 TYR 0.032 0.002 TYR L 84 PHE 0.027 0.002 PHE F 355 TRP 0.017 0.002 TRP J 109 HIS 0.007 0.001 HIS E 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.26 (34340) covalent geometry : angle 0.67193 / 0.35 (46630) SS BOND : bond 0.00437 / 0.29 ( 20) SS BOND : angle 1.45704 / 0.88 ( 40) hydrogen bonds : bond 0.04407 / 2.90 ( 1332) hydrogen bonds : angle 5.69279 / 4.02 ( 3630) metal coordination : bond 0.00661 / 0.40 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 175 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: C 244 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8032 (mptt) REVERT: C 406 GLU cc_start: 0.7238 (pt0) cc_final: 0.6975 (pt0) REVERT: D 269 LEU cc_start: 0.7967 (tp) cc_final: 0.7654 (tt) REVERT: D 437 ASP cc_start: 0.7554 (t70) cc_final: 0.7033 (t70) REVERT: E 255 LEU cc_start: 0.7932 (tp) cc_final: 0.7649 (tt) REVERT: E 372 HIS cc_start: 0.6859 (OUTLIER) cc_final: 0.6060 (t-90) REVERT: E 435 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8527 (mt0) REVERT: F 49 ILE cc_start: 0.9371 (mm) cc_final: 0.9110 (mt) REVERT: G 197 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8914 (mttp) REVERT: G 213 GLU cc_start: 0.7129 (tt0) cc_final: 0.6587 (tt0) REVERT: H 113 VAL cc_start: 0.9332 (t) cc_final: 0.9125 (p) REVERT: H 437 ASP cc_start: 0.7708 (t70) cc_final: 0.7409 (t70) REVERT: I 83 GLN cc_start: 0.8736 (mp10) cc_final: 0.8361 (mp10) REVERT: J 113 VAL cc_start: 0.9313 (t) cc_final: 0.9070 (p) REVERT: K 28 ASP cc_start: 0.7995 (t0) cc_final: 0.7651 (t0) REVERT: L 53 MET cc_start: 0.9146 (ttm) cc_final: 0.8705 (ttp) REVERT: L 130 ARG cc_start: 0.8429 (ttm110) cc_final: 0.8120 (mtp85) REVERT: L 361 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7744 (mt-10) REVERT: L 372 HIS cc_start: 0.8710 (OUTLIER) cc_final: 0.8309 (t-90) outliers start: 70 outliers final: 40 residues processed: 234 average time/residue: 0.1931 time to fit residues: 78.1040 Evaluate side-chains 191 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 372 HIS Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 84 TYR Chi-restraints excluded: chain G residue 177 GLN Chi-restraints excluded: chain G residue 197 LYS Chi-restraints excluded: chain G residue 344 ASP Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain H residue 415 THR Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain J residue 276 HIS Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain K residue 415 THR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 325 SER Chi-restraints excluded: chain L residue 372 HIS Chi-restraints excluded: chain L residue 415 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [200, 1, 417, 226, 69, 293, 7, 16, 348, 430, 370] chunk 200 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 417 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 293 optimal weight: 20.0000 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 348 optimal weight: 4.9990 chunk 430 optimal weight: 10.0000 chunk 370 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 131 ASN ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN E 425 GLN ** E 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 281 GLN J 181 ASN J 228 GLN J 281 GLN J 388 GLN ** L 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 HIS L 251 GLN L 375 GLN ** L 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.095597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.074017 restraints weight = 67194.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.075722 restraints weight = 40894.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.077139 restraints weight = 29347.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.077349 restraints weight = 22883.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.077521 restraints weight = 22263.750| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34390 Z= 0.192 Angle : 0.599 11.731 46670 Z= 0.313 Chirality : 0.045 0.220 5260 Planarity : 0.004 0.051 6230 Dihedral : 5.097 40.932 4842 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.05 % Allowed : 11.13 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.12), residues: 4480 helix: 0.48 (0.14), residues: 1410 sheet: -0.93 (0.18), residues: 790 loop : -0.08 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 23 TYR 0.025 0.002 TYR L 84 PHE 0.028 0.001 PHE F 355 TRP 0.036 0.002 TRP L 109 HIS 0.006 0.001 HIS L 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (34340) covalent geometry : angle 0.59779 / 0.31 (46630) SS BOND : bond 0.00377 / 0.25 ( 20) SS BOND : angle 1.31248 / 0.83 ( 40) hydrogen bonds : bond 0.03802 / 2.50 ( 1332) hydrogen bonds : angle 5.50221 / 3.90 ( 3630) metal coordination : bond 0.00449 / 0.27 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 183 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 244 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7661 (mppt) REVERT: C 406 GLU cc_start: 0.7259 (pt0) cc_final: 0.7034 (pt0) REVERT: D 437 ASP cc_start: 0.7573 (t70) cc_final: 0.7061 (t70) REVERT: E 372 HIS cc_start: 0.6918 (OUTLIER) cc_final: 0.6498 (t-90) REVERT: E 435 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8550 (mt0) REVERT: F 49 ILE cc_start: 0.9318 (mm) cc_final: 0.9093 (mt) REVERT: F 113 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8608 (m) REVERT: G 197 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.9047 (mttp) REVERT: H 110 THR cc_start: 0.9061 (m) cc_final: 0.8812 (p) REVERT: H 113 VAL cc_start: 0.9342 (t) cc_final: 0.9109 (p) REVERT: H 437 ASP cc_start: 0.7750 (t70) cc_final: 0.7502 (t70) REVERT: I 83 GLN cc_start: 0.8644 (mp10) cc_final: 0.8291 (mp10) REVERT: I 402 TYR cc_start: 0.8366 (m-80) cc_final: 0.7783 (m-10) REVERT: J 113 VAL cc_start: 0.9317 (t) cc_final: 0.9104 (p) REVERT: L 53 MET cc_start: 0.9161 (ttm) cc_final: 0.8758 (ttp) REVERT: L 130 ARG cc_start: 0.8436 (ttm110) cc_final: 0.8164 (mtp85) REVERT: L 372 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.8191 (t-90) outliers start: 71 outliers final: 46 residues processed: 245 average time/residue: 0.1962 time to fit residues: 82.8943 Evaluate side-chains 200 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 TRP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 109 TRP Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 84 TYR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 372 HIS Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain F residue 109 TRP Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 177 GLN Chi-restraints excluded: chain G residue 197 LYS Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 344 ASP Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain J residue 181 ASN Chi-restraints excluded: chain J residue 276 HIS Chi-restraints excluded: chain J residue 419 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 168 CYS Chi-restraints excluded: chain L residue 325 SER Chi-restraints excluded: chain L residue 372 HIS Chi-restraints excluded: chain L residue 415 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [373, 16, 51, 414, 125, 408, 446, 188, 449, 57, 225] chunk 373 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 414 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 408 optimal weight: 6.9990 chunk 446 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 449 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 338 GLN ** E 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 HIS F 425 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN J 181 ASN ** L 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.096955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.075401 restraints weight = 67227.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.077072 restraints weight = 40880.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.078393 restraints weight = 29512.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.078631 restraints weight = 23368.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.078891 restraints weight = 22577.752| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34390 Z= 0.126 Angle : 0.548 9.303 46670 Z= 0.287 Chirality : 0.043 0.274 5260 Planarity : 0.004 0.045 6230 Dihedral : 4.791 42.468 4842 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.23 % Allowed : 11.53 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.13), residues: 4480 helix: 0.69 (0.14), residues: 1410 sheet: -0.77 (0.18), residues: 790 loop : -0.00 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 23 TYR 0.020 0.001 TYR G 84 PHE 0.018 0.001 PHE F 355 TRP 0.041 0.002 TRP L 109 HIS 0.006 0.001 HIS F 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (34340) covalent geometry : angle 0.54687 / 0.29 (46630) SS BOND : bond 0.00312 / 0.21 ( 20) SS BOND : angle 1.35625 / 0.84 ( 40) hydrogen bonds : bond 0.03435 / 2.25 ( 1332) hydrogen bonds : angle 5.35237 / 3.80 ( 3630) metal coordination : bond 0.00325 / 0.20 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 192 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 244 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7673 (mppt) REVERT: D 437 ASP cc_start: 0.7526 (t70) cc_final: 0.7031 (t70) REVERT: E 330 ASP cc_start: 0.8581 (t0) cc_final: 0.8233 (t0) REVERT: E 372 HIS cc_start: 0.7151 (OUTLIER) cc_final: 0.6253 (t-90) REVERT: E 435 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8560 (mt0) REVERT: F 49 ILE cc_start: 0.9302 (mm) cc_final: 0.9102 (mt) REVERT: G 109 TRP cc_start: 0.9385 (OUTLIER) cc_final: 0.8747 (p90) REVERT: G 197 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9042 (mttp) REVERT: H 110 THR cc_start: 0.9093 (m) cc_final: 0.8818 (p) REVERT: H 437 ASP cc_start: 0.7788 (t70) cc_final: 0.7501 (t70) REVERT: I 83 GLN cc_start: 0.8522 (mp10) cc_final: 0.8224 (mp10) REVERT: I 372 HIS cc_start: 0.8304 (OUTLIER) cc_final: 0.6812 (t-170) REVERT: I 402 TYR cc_start: 0.8259 (m-80) cc_final: 0.8058 (m-80) REVERT: J 87 TYR cc_start: 0.8714 (p90) cc_final: 0.8032 (p90) REVERT: J 113 VAL cc_start: 0.9316 (t) cc_final: 0.9101 (p) REVERT: K 258 LEU cc_start: 0.8027 (tp) cc_final: 0.7822 (tp) REVERT: L 53 MET cc_start: 0.9127 (ttm) cc_final: 0.8734 (ttp) REVERT: L 130 ARG cc_start: 0.8441 (ttm110) cc_final: 0.8187 (mtp85) REVERT: L 372 HIS cc_start: 0.8434 (OUTLIER) cc_final: 0.8048 (t-90) outliers start: 77 outliers final: 46 residues processed: 258 average time/residue: 0.1930 time to fit residues: 85.7652 Evaluate side-chains 206 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 153 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 TRP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 109 TRP Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 372 HIS Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain F residue 109 TRP Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 84 TYR Chi-restraints excluded: chain G residue 109 TRP Chi-restraints excluded: chain G residue 177 GLN Chi-restraints excluded: chain G residue 197 LYS Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 344 ASP Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain H residue 415 THR Chi-restraints excluded: chain H residue 436 THR Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain K residue 415 THR Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 168 CYS Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 325 SER Chi-restraints excluded: chain L residue 372 HIS Chi-restraints excluded: chain L residue 415 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [129, 59, 167, 151, 39, 257, 169, 431, 362, 67, 161] chunk 129 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 257 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 431 optimal weight: 0.0030 chunk 362 optimal weight: 0.0040 chunk 67 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 overall best weight: 3.6008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 181 ASN ** E 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN G 181 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 ASN I 2 GLN I 31 GLN I 301 GLN I 338 GLN J 181 ASN K 239 ASN K 281 GLN ** L 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 410 GLN ** L 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.095487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.073406 restraints weight = 67332.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.075267 restraints weight = 42062.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.076497 restraints weight = 30618.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.077430 restraints weight = 24549.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.077898 restraints weight = 20996.889| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 34390 Z= 0.185 Angle : 0.584 7.293 46670 Z= 0.304 Chirality : 0.044 0.189 5260 Planarity : 0.004 0.046 6230 Dihedral : 4.810 42.264 4842 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.63 % Allowed : 12.31 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.13), residues: 4480 helix: 0.70 (0.14), residues: 1410 sheet: -0.80 (0.18), residues: 790 loop : 0.00 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 23 TYR 0.023 0.002 TYR L 84 PHE 0.030 0.001 PHE F 355 TRP 0.044 0.002 TRP L 109 HIS 0.006 0.001 HIS L 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (34340) covalent geometry : angle 0.58312 / 0.30 (46630) SS BOND : bond 0.00332 / 0.21 ( 20) SS BOND : angle 1.22510 / 0.77 ( 40) hydrogen bonds : bond 0.03598 / 2.36 ( 1332) hydrogen bonds : angle 5.39901 / 3.84 ( 3630) metal coordination : bond 0.00410 / 0.26 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 153 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 124 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8853 (tt) REVERT: C 244 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7628 (mppt) REVERT: D 437 ASP cc_start: 0.7612 (t70) cc_final: 0.7122 (t70) REVERT: E 372 HIS cc_start: 0.7282 (OUTLIER) cc_final: 0.6594 (t-90) REVERT: E 435 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8571 (mt0) REVERT: F 49 ILE cc_start: 0.9323 (mm) cc_final: 0.9115 (mt) REVERT: G 109 TRP cc_start: 0.9423 (OUTLIER) cc_final: 0.8935 (p90) REVERT: G 197 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.9090 (mttp) REVERT: H 110 THR cc_start: 0.9135 (m) cc_final: 0.8809 (p) REVERT: H 437 ASP cc_start: 0.7846 (t70) cc_final: 0.7528 (t70) REVERT: I 45 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8844 (m) REVERT: I 83 GLN cc_start: 0.8564 (mp10) cc_final: 0.8250 (mp10) REVERT: I 372 HIS cc_start: 0.8452 (OUTLIER) cc_final: 0.7079 (t-170) REVERT: I 402 TYR cc_start: 0.8304 (m-80) cc_final: 0.8047 (m-80) REVERT: J 113 VAL cc_start: 0.9344 (t) cc_final: 0.9117 (p) REVERT: J 372 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.6872 (t-90) REVERT: L 53 MET cc_start: 0.9143 (ttm) cc_final: 0.8808 (ttp) REVERT: L 130 ARG cc_start: 0.8434 (ttm110) cc_final: 0.8164 (mtp85) REVERT: L 372 HIS cc_start: 0.8432 (OUTLIER) cc_final: 0.8078 (t-90) outliers start: 91 outliers final: 59 residues processed: 234 average time/residue: 0.1934 time to fit residues: 78.0584 Evaluate side-chains 215 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 146 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 TRP Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 109 TRP Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 84 TYR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 372 HIS Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain F residue 109 TRP Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 84 TYR Chi-restraints excluded: chain G residue 109 TRP Chi-restraints excluded: chain G residue 177 GLN Chi-restraints excluded: chain G residue 197 LYS Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 344 ASP Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain H residue 415 THR Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 301 GLN Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 377 ILE Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 109 TRP Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain J residue 181 ASN Chi-restraints excluded: chain J residue 276 HIS Chi-restraints excluded: chain J residue 372 HIS Chi-restraints excluded: chain J residue 419 ILE Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain K residue 415 THR Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 168 CYS Chi-restraints excluded: chain L residue 325 SER Chi-restraints excluded: chain L residue 372 HIS Chi-restraints excluded: chain L residue 415 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [365, 298, 212, 240, 372, 215, 167, 350, 403, 370, 401] chunk 365 optimal weight: 0.9990 chunk 298 optimal weight: 0.0470 chunk 212 optimal weight: 6.9990 chunk 240 optimal weight: 0.7980 chunk 372 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 350 optimal weight: 10.0000 chunk 403 optimal weight: 3.9990 chunk 370 optimal weight: 4.9990 chunk 401 optimal weight: 1.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 HIS J 181 ASN J 447 ASN ** L 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 185 ASN ** L 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.097311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.075359 restraints weight = 66876.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.077289 restraints weight = 41236.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.078607 restraints weight = 29661.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.079391 restraints weight = 23663.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.080122 restraints weight = 20344.000| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34390 Z= 0.114 Angle : 0.541 10.602 46670 Z= 0.281 Chirality : 0.043 0.497 5260 Planarity : 0.003 0.042 6230 Dihedral : 4.618 43.243 4842 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.17 % Allowed : 12.98 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.13), residues: 4480 helix: 1.08 (0.14), residues: 1350 sheet: -0.65 (0.19), residues: 790 loop : 0.03 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 267 TYR 0.018 0.001 TYR E 402 PHE 0.047 0.001 PHE F 355 TRP 0.042 0.002 TRP E 109 HIS 0.004 0.001 HIS L 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (34340) covalent geometry : angle 0.53936 / 0.28 (46630) SS BOND : bond 0.00298 / 0.20 ( 20) SS BOND : angle 1.46323 / 0.89 ( 40) hydrogen bonds : bond 0.03290 / 2.15 ( 1332) hydrogen bonds : angle 5.30292 / 3.77 ( 3630) metal coordination : bond 0.00286 / 0.18 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 188 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 MET cc_start: 0.8953 (ttp) cc_final: 0.8668 (ttp) REVERT: C 244 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7644 (mppt) REVERT: D 437 ASP cc_start: 0.7493 (t70) cc_final: 0.7009 (t70) REVERT: E 372 HIS cc_start: 0.7222 (OUTLIER) cc_final: 0.6643 (t-90) REVERT: E 435 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8526 (mt0) REVERT: G 53 MET cc_start: 0.9262 (ttp) cc_final: 0.9030 (ttm) REVERT: G 109 TRP cc_start: 0.9396 (OUTLIER) cc_final: 0.8996 (p90) REVERT: H 437 ASP cc_start: 0.7802 (t70) cc_final: 0.7513 (t70) REVERT: I 83 GLN cc_start: 0.8475 (mp10) cc_final: 0.8126 (mp10) REVERT: I 372 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.7301 (t-170) REVERT: I 402 TYR cc_start: 0.8265 (m-80) cc_final: 0.8055 (m-80) REVERT: J 87 TYR cc_start: 0.8695 (p90) cc_final: 0.8017 (p90) REVERT: J 113 VAL cc_start: 0.9351 (t) cc_final: 0.9109 (p) REVERT: L 53 MET cc_start: 0.9106 (ttm) cc_final: 0.8826 (ttp) REVERT: L 130 ARG cc_start: 0.8422 (ttm110) cc_final: 0.8172 (mtp85) outliers start: 75 outliers final: 50 residues processed: 253 average time/residue: 0.1838 time to fit residues: 80.9878 Evaluate side-chains 218 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 TRP Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 109 TRP Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 372 HIS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain F residue 109 TRP Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 109 TRP Chi-restraints excluded: chain G residue 177 GLN Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 344 ASP Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain H residue 415 THR Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 377 ILE Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 109 TRP Chi-restraints excluded: chain J residue 276 HIS Chi-restraints excluded: chain J residue 419 ILE Chi-restraints excluded: chain K residue 9 ASN Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain K residue 415 THR Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 168 CYS Chi-restraints excluded: chain L residue 325 SER Chi-restraints excluded: chain L residue 415 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [126, 400, 311, 98, 420, 132, 167, 410, 370, 51, 230] chunk 126 optimal weight: 0.9990 chunk 400 optimal weight: 9.9990 chunk 311 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 420 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 410 optimal weight: 9.9990 chunk 370 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 230 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 281 GLN I 301 GLN J 447 ASN K 239 ASN ** L 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.095546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.073479 restraints weight = 67386.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.075343 restraints weight = 42140.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.076615 restraints weight = 30675.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.077423 restraints weight = 24570.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.078066 restraints weight = 21083.725| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34390 Z= 0.181 Angle : 0.588 16.330 46670 Z= 0.304 Chirality : 0.044 0.468 5260 Planarity : 0.004 0.043 6230 Dihedral : 4.645 23.367 4840 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.37 % Allowed : 13.32 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.13), residues: 4480 helix: 1.09 (0.14), residues: 1350 sheet: -0.74 (0.19), residues: 790 loop : 0.00 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 10 TYR 0.023 0.002 TYR G 84 PHE 0.044 0.001 PHE F 355 TRP 0.044 0.002 TRP E 109 HIS 0.006 0.001 HIS L 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (34340) covalent geometry : angle 0.58226 / 0.30 (46630) SS BOND : bond 0.00463 / 0.32 ( 20) SS BOND : angle 2.75845 / 1.83 ( 40) hydrogen bonds : bond 0.03479 / 2.28 ( 1332) hydrogen bonds : angle 5.36221 / 3.81 ( 3630) metal coordination : bond 0.00391 / 0.25 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 169 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 MET cc_start: 0.8984 (ttp) cc_final: 0.8696 (ttp) REVERT: D 57 GLU cc_start: 0.7919 (mp0) cc_final: 0.7249 (mp0) REVERT: D 437 ASP cc_start: 0.7621 (t70) cc_final: 0.7116 (t70) REVERT: E 372 HIS cc_start: 0.7296 (OUTLIER) cc_final: 0.6742 (t-90) REVERT: E 435 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8443 (mt0) REVERT: G 109 TRP cc_start: 0.9437 (OUTLIER) cc_final: 0.8970 (p90) REVERT: G 213 GLU cc_start: 0.6927 (tt0) cc_final: 0.6681 (tt0) REVERT: H 437 ASP cc_start: 0.7872 (t70) cc_final: 0.7564 (t70) REVERT: I 45 VAL cc_start: 0.9144 (OUTLIER) cc_final: 0.8852 (m) REVERT: I 83 GLN cc_start: 0.8496 (mp10) cc_final: 0.8187 (mp10) REVERT: I 372 HIS cc_start: 0.8522 (OUTLIER) cc_final: 0.7346 (t-170) REVERT: I 402 TYR cc_start: 0.8284 (m-80) cc_final: 0.8064 (m-80) REVERT: J 87 TYR cc_start: 0.8783 (p90) cc_final: 0.8112 (p90) REVERT: J 113 VAL cc_start: 0.9354 (t) cc_final: 0.9103 (p) REVERT: J 372 HIS cc_start: 0.7298 (OUTLIER) cc_final: 0.6593 (t-90) REVERT: K 133 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8481 (tt) REVERT: L 53 MET cc_start: 0.9130 (ttm) cc_final: 0.8857 (ttp) REVERT: L 372 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.8048 (t-90) outliers start: 82 outliers final: 58 residues processed: 242 average time/residue: 0.1867 time to fit residues: 79.1908 Evaluate side-chains 226 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 160 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 TRP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 109 TRP Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 372 HIS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 109 TRP Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 177 GLN Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 344 ASP Chi-restraints excluded: chain G residue 346 ASP Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain H residue 415 THR Chi-restraints excluded: chain H residue 436 THR Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 377 ILE Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 109 TRP Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain J residue 276 HIS Chi-restraints excluded: chain J residue 372 HIS Chi-restraints excluded: chain J residue 419 ILE Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain K residue 387 THR Chi-restraints excluded: chain K residue 415 THR Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 168 CYS Chi-restraints excluded: chain L residue 325 SER Chi-restraints excluded: chain L residue 372 HIS Chi-restraints excluded: chain L residue 415 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [216, 375, 331, 124, 217, 139, 117, 1, 415, 354, 157] chunk 216 optimal weight: 0.9990 chunk 375 optimal weight: 1.9990 chunk 331 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 217 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 117 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 415 optimal weight: 9.9990 chunk 354 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.096228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.074200 restraints weight = 66939.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.076104 restraints weight = 41667.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.077294 restraints weight = 30164.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.078235 restraints weight = 24341.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.078785 restraints weight = 20773.511| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (19 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34390 Z= 0.145 Angle : 0.561 13.051 46670 Z= 0.291 Chirality : 0.043 0.375 5260 Planarity : 0.004 0.053 6230 Dihedral : 4.564 23.724 4840 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.17 % Allowed : 13.76 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.13), residues: 4480 helix: 1.11 (0.14), residues: 1350 sheet: -0.68 (0.19), residues: 790 loop : 0.01 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 62 TYR 0.020 0.001 TYR J 84 PHE 0.033 0.001 PHE F 355 TRP 0.048 0.002 TRP E 109 HIS 0.005 0.001 HIS L 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (34340) covalent geometry : angle 0.55582 / 0.29 (46630) SS BOND : bond 0.00312 / 0.21 ( 20) SS BOND : angle 2.69848 / 1.87 ( 40) hydrogen bonds : bond 0.03340 / 2.18 ( 1332) hydrogen bonds : angle 5.31421 / 3.78 ( 3630) metal coordination : bond 0.00324 / 0.20 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 176 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 MET cc_start: 0.8983 (ttp) cc_final: 0.8689 (ttp) REVERT: C 244 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7809 (mppt) REVERT: D 57 GLU cc_start: 0.7909 (mp0) cc_final: 0.7402 (mp0) REVERT: D 437 ASP cc_start: 0.7581 (t70) cc_final: 0.7092 (t70) REVERT: E 372 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6768 (t-90) REVERT: E 435 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8527 (mt0) REVERT: F 307 ILE cc_start: 0.8875 (mm) cc_final: 0.8593 (mm) REVERT: G 109 TRP cc_start: 0.9418 (OUTLIER) cc_final: 0.9004 (p90) REVERT: G 213 GLU cc_start: 0.6877 (tt0) cc_final: 0.6589 (tt0) REVERT: H 437 ASP cc_start: 0.7808 (t70) cc_final: 0.7507 (t70) REVERT: I 45 VAL cc_start: 0.9129 (OUTLIER) cc_final: 0.8841 (m) REVERT: I 83 GLN cc_start: 0.8470 (mp10) cc_final: 0.8168 (mp10) REVERT: I 372 HIS cc_start: 0.8614 (OUTLIER) cc_final: 0.7664 (t-170) REVERT: I 402 TYR cc_start: 0.8264 (m-80) cc_final: 0.8057 (m-10) REVERT: J 87 TYR cc_start: 0.8737 (p90) cc_final: 0.8114 (p90) REVERT: J 113 VAL cc_start: 0.9354 (t) cc_final: 0.9111 (p) REVERT: J 372 HIS cc_start: 0.7071 (OUTLIER) cc_final: 0.6234 (t-90) REVERT: K 133 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8481 (tt) REVERT: L 53 MET cc_start: 0.9113 (ttm) cc_final: 0.8871 (ttp) outliers start: 75 outliers final: 55 residues processed: 242 average time/residue: 0.1882 time to fit residues: 79.4357 Evaluate side-chains 223 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 160 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 TRP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 109 TRP Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain E residue 372 HIS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 109 TRP Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 177 GLN Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 344 ASP Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 415 THR Chi-restraints excluded: chain H residue 436 THR Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 377 ILE Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 109 TRP Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain J residue 276 HIS Chi-restraints excluded: chain J residue 372 HIS Chi-restraints excluded: chain J residue 419 ILE Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain K residue 387 THR Chi-restraints excluded: chain K residue 415 THR Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 168 CYS Chi-restraints excluded: chain L residue 325 SER Chi-restraints excluded: chain L residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [168, 58, 323, 83, 182, 173, 274, 381, 149, 19, 82] chunk 168 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 323 optimal weight: 10.0000 chunk 83 optimal weight: 0.5980 chunk 182 optimal weight: 0.0570 chunk 173 optimal weight: 4.9990 chunk 274 optimal weight: 5.9990 chunk 381 optimal weight: 0.8980 chunk 149 optimal weight: 30.0000 chunk 19 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 HIS G 181 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 HIS H 329 GLN J 44 ASN J 63 ASN K 239 ASN ** L 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 425 GLN ** 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 = 0.3342 r_free = 0.3342 target = 0.096513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.074499 restraints weight = 67245.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.076398 restraints weight = 41681.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.077702 restraints weight = 30200.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.078577 restraints weight = 24110.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.079114 restraints weight = 20589.411| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34390 Z= 0.138 Angle : 0.557 12.184 46670 Z= 0.288 Chirality : 0.043 0.320 5260 Planarity : 0.004 0.058 6230 Dihedral : 4.499 22.600 4840 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.91 % Allowed : 14.25 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.13), residues: 4480 helix: 1.17 (0.14), residues: 1350 sheet: -0.65 (0.19), residues: 790 loop : 0.03 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 62 TYR 0.020 0.001 TYR J 84 PHE 0.030 0.001 PHE F 355 TRP 0.055 0.003 TRP L 109 HIS 0.005 0.001 HIS L 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (34340) covalent geometry : angle 0.55220 / 0.29 (46630) SS BOND : bond 0.00339 / 0.22 ( 20) SS BOND : angle 2.55513 / 1.83 ( 40) hydrogen bonds : bond 0.03286 / 2.15 ( 1332) hydrogen bonds : angle 5.29407 / 3.76 ( 3630) metal coordination : bond 0.00310 / 0.20 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 173 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 MET cc_start: 0.8978 (ttp) cc_final: 0.8688 (ttp) REVERT: C 244 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7810 (mppt) REVERT: D 57 GLU cc_start: 0.7852 (mp0) cc_final: 0.7366 (mp0) REVERT: E 372 HIS cc_start: 0.7272 (OUTLIER) cc_final: 0.6963 (t-90) REVERT: E 435 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8420 (mt0) REVERT: F 109 TRP cc_start: 0.8116 (p90) cc_final: 0.7226 (p90) REVERT: F 307 ILE cc_start: 0.8852 (mm) cc_final: 0.8350 (mm) REVERT: G 109 TRP cc_start: 0.9434 (OUTLIER) cc_final: 0.8996 (p90) REVERT: G 213 GLU cc_start: 0.6964 (tt0) cc_final: 0.6686 (tt0) REVERT: H 437 ASP cc_start: 0.7816 (t70) cc_final: 0.7542 (t70) REVERT: I 45 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8843 (m) REVERT: I 372 HIS cc_start: 0.8610 (OUTLIER) cc_final: 0.7663 (t-170) REVERT: J 87 TYR cc_start: 0.8723 (p90) cc_final: 0.8094 (p90) REVERT: J 113 VAL cc_start: 0.9360 (t) cc_final: 0.9119 (p) REVERT: J 372 HIS cc_start: 0.6993 (OUTLIER) cc_final: 0.6378 (t-90) REVERT: K 133 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8475 (tt) REVERT: L 53 MET cc_start: 0.9116 (ttm) cc_final: 0.8865 (ttp) outliers start: 66 outliers final: 52 residues processed: 231 average time/residue: 0.1837 time to fit residues: 74.1379 Evaluate side-chains 219 residues out of total 3460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 159 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 TRP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 109 TRP Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain E residue 372 HIS Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 109 TRP Chi-restraints excluded: chain G residue 177 GLN Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 344 ASP Chi-restraints excluded: chain G residue 346 ASP Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain H residue 415 THR Chi-restraints excluded: chain H residue 436 THR Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 372 HIS Chi-restraints excluded: chain I residue 377 ILE Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 44 ASN Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 109 TRP Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain J residue 276 HIS Chi-restraints excluded: chain J residue 372 HIS Chi-restraints excluded: chain J residue 419 ILE Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain K residue 387 THR Chi-restraints excluded: chain K residue 415 THR Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 168 CYS Chi-restraints excluded: chain L residue 325 SER Chi-restraints excluded: chain L residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: [372, 166, 229, 156, 159, 52, 235, 26, 267, 191, 106] chunk 372 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 229 optimal weight: 4.9990 chunk 156 optimal weight: 20.0000 chunk 159 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 267 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 338 GLN ** E 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 HIS G 181 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 ASN J 63 ASN ** L 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.096041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.073998 restraints weight = 67083.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.075827 restraints weight = 41873.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.077141 restraints weight = 30510.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.077939 restraints weight = 24419.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.078666 restraints weight = 20946.819| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34390 Z= 0.161 Angle : 0.574 11.440 46670 Z= 0.297 Chirality : 0.044 0.334 5260 Planarity : 0.004 0.057 6230 Dihedral : 4.528 21.498 4840 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.91 % Allowed : 14.45 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.13), residues: 4480 helix: 1.16 (0.14), residues: 1350 sheet: -0.68 (0.19), residues: 790 loop : 0.03 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 62 TYR 0.021 0.002 TYR I 402 PHE 0.037 0.001 PHE F 355 TRP 0.053 0.003 TRP E 109 HIS 0.005 0.001 HIS L 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (34340) covalent geometry : angle 0.56989 / 0.30 (46630) SS BOND : bond 0.00315 / 0.20 ( 20) SS BOND : angle 2.50221 / 1.78 ( 40) hydrogen bonds : bond 0.03344 / 2.19 ( 1332) hydrogen bonds : angle 5.30868 / 3.77 ( 3630) metal coordination : bond 0.00341 / 0.22 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4955.39 seconds wall clock time: 86 minutes 54.61 seconds (5214.61 seconds total)