Starting phenix.real_space_refine on Sun Aug 9 16:20:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yaw_72740/08_2026/9yaw_72740.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yaw_72740/08_2026/9yaw_72740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yaw_72740/08_2026/9yaw_72740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yaw_72740/08_2026/9yaw_72740.map" model { file = "/net/cci-nas-00/data/ceres_data/9yaw_72740/08_2026/9yaw_72740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yaw_72740/08_2026/9yaw_72740.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 207 5.16 5 C 22154 2.51 5 N 6049 2.21 5 O 6580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 184 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34990 Number of models: 1 Model: "" Number of chains: 22 Chain: "1" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 216} Chain: "2" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1604 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 196} Chain: "A" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3371 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 411} Chain: "B" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3371 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 411} Chain: "C" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3371 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 411} Chain: "D" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3371 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 411} Chain: "P" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1180 Classifications: {'peptide': 153} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 143} Chain: "Q" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1197 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain: "R" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1197 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain: "S" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1188 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "a" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3288 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 385} Chain: "b" Number of atoms: 3296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3296 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 386} Chain: "c" Number of atoms: 3296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3296 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 386} Chain: "d" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3288 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 385} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.18, per 1000 atoms: 0.21 Number of scatterers: 34990 At special positions: 0 Unit cell: (156.94, 162.26, 248.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 207 16.00 O 6580 8.00 N 6049 7.00 C 22154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=64, symmetry=0 Simple disulfide: pdb=" SG CYS 1 22 " - pdb=" SG CYS 1 97 " distance=2.02 Simple disulfide: pdb=" SG CYS 1 105 " - pdb=" SG CYS 1 110 " distance=1.99 Simple disulfide: pdb=" SG CYS 1 156 " - pdb=" SG CYS 1 212 " distance=1.94 Simple disulfide: pdb=" SG CYS 2 22 " - pdb=" SG CYS 2 87 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 136 " - pdb=" SG CYS 2 195 " distance=1.93 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.02 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.02 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 272 " distance=2.02 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 377 " distance=2.03 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 371 " distance=2.03 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.02 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 78 " distance=2.02 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 272 " distance=2.04 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 377 " distance=2.03 Simple disulfide: pdb=" SG CYS B 307 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 329 " - pdb=" SG CYS B 371 " distance=2.02 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 114 " distance=2.02 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.02 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 78 " distance=2.02 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 272 " distance=2.03 Simple disulfide: pdb=" SG CYS C 302 " - pdb=" SG CYS C 377 " distance=2.03 Simple disulfide: pdb=" SG CYS C 307 " - pdb=" SG CYS C 381 " distance=2.03 Simple disulfide: pdb=" SG CYS C 329 " - pdb=" SG CYS C 371 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.01 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.04 Simple disulfide: pdb=" SG CYS D 260 " - pdb=" SG CYS D 272 " distance=2.03 Simple disulfide: pdb=" SG CYS D 302 " - pdb=" SG CYS D 377 " distance=2.03 Simple disulfide: pdb=" SG CYS D 307 " - pdb=" SG CYS D 381 " distance=2.03 Simple disulfide: pdb=" SG CYS D 329 " - pdb=" SG CYS D 371 " distance=2.03 Simple disulfide: pdb=" SG CYS a 19 " - pdb=" SG CYS a 122 " distance=2.02 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 27 " distance=2.03 Simple disulfide: pdb=" SG CYS a 89 " - pdb=" SG CYS a 103 " distance=2.03 Simple disulfide: pdb=" SG CYS a 150 " - pdb=" SG CYS a 263 " distance=2.02 Simple disulfide: pdb=" SG CYS a 199 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 201 " - pdb=" SG CYS a 217 " distance=2.03 Simple disulfide: pdb=" SG CYS a 393 " - pdb=" SG CYS a 413 " distance=2.02 Simple disulfide: pdb=" SG CYS b 19 " - pdb=" SG CYS b 122 " distance=2.03 Simple disulfide: pdb=" SG CYS b 22 " - pdb=" SG CYS b 27 " distance=2.02 Simple disulfide: pdb=" SG CYS b 89 " - pdb=" SG CYS b 103 " distance=2.03 Simple disulfide: pdb=" SG CYS b 150 " - pdb=" SG CYS b 263 " distance=2.02 Simple disulfide: pdb=" SG CYS b 199 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 201 " - pdb=" SG CYS b 217 " distance=2.04 Simple disulfide: pdb=" SG CYS c 19 " - pdb=" SG CYS c 122 " distance=2.02 Simple disulfide: pdb=" SG CYS c 22 " - pdb=" SG CYS c 27 " distance=2.01 Simple disulfide: pdb=" SG CYS c 89 " - pdb=" SG CYS c 103 " distance=2.02 Simple disulfide: pdb=" SG CYS c 150 " - pdb=" SG CYS c 263 " distance=2.02 Simple disulfide: pdb=" SG CYS c 199 " - pdb=" SG CYS c 223 " distance=2.03 Simple disulfide: pdb=" SG CYS c 201 " - pdb=" SG CYS c 217 " distance=2.04 Simple disulfide: pdb=" SG CYS c 393 " - pdb=" SG CYS c 413 " distance=2.03 Simple disulfide: pdb=" SG CYS d 19 " - pdb=" SG CYS d 122 " distance=2.03 Simple disulfide: pdb=" SG CYS d 22 " - pdb=" SG CYS d 27 " distance=2.04 Simple disulfide: pdb=" SG CYS d 89 " - pdb=" SG CYS d 103 " distance=2.02 Simple disulfide: pdb=" SG CYS d 150 " - pdb=" SG CYS d 263 " distance=2.05 Simple disulfide: pdb=" SG CYS d 199 " - pdb=" SG CYS d 223 " distance=2.03 Simple disulfide: pdb=" SG CYS d 201 " - pdb=" SG CYS d 217 " distance=2.04 Simple disulfide: pdb=" SG CYS d 393 " - pdb=" SG CYS d 413 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " NAG-ASN " NAG E 1 " - " ASN A 134 " " NAG F 1 " - " ASN C 134 " " NAG G 1 " - " ASN B 134 " " NAG H 1 " - " ASN D 134 " " NAG a 501 " - " ASN a 315 " " NAG b 501 " - " ASN b 315 " " NAG c 501 " - " ASN c 315 " " NAG d 501 " - " ASN d 315 " Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8322 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 106 sheets defined 14.9% alpha, 38.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain '1' and resid 75 through 77 No H-bonds generated for 'chain '1' and resid 75 through 77' Processing helix chain '1' and resid 88 through 92 Processing helix chain '1' and resid 143 through 145 No H-bonds generated for 'chain '1' and resid 143 through 145' Processing helix chain '1' and resid 172 through 174 No H-bonds generated for 'chain '1' and resid 172 through 174' Processing helix chain '1' and resid 203 through 205 No H-bonds generated for 'chain '1' and resid 203 through 205' Processing helix chain '1' and resid 217 through 220 Processing helix chain '2' and resid 26 through 30 Processing helix chain '2' and resid 78 through 82 Processing helix chain '2' and resid 123 through 129 Processing helix chain '2' and resid 183 through 190 removed outlier: 3.799A pdb=" N HIS 2 190 " --> pdb=" O GLN 2 186 " (cutoff:3.500A) Processing helix chain '2' and resid 209 through 214 removed outlier: 3.827A pdb=" N CYS 2 213 " --> pdb=" O PRO 2 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 225 through 229 removed outlier: 4.550A pdb=" N GLY A 228 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 247 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 257 through 260 removed outlier: 3.553A pdb=" N CYS A 260 " --> pdb=" O PRO A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 260' Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 398 through 403 removed outlier: 3.501A pdb=" N ALA A 402 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE A 403 " --> pdb=" O THR A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 441 removed outlier: 3.513A pdb=" N HIS A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 239 through 248 Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 284 through 288 Processing helix chain 'B' and resid 404 through 438 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 239 through 248 Processing helix chain 'C' and resid 251 through 256 Processing helix chain 'C' and resid 257 through 260 Processing helix chain 'C' and resid 284 through 288 Processing helix chain 'C' and resid 405 through 441 Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 239 through 247 Processing helix chain 'D' and resid 251 through 255 Processing helix chain 'D' and resid 284 through 288 Processing helix chain 'D' and resid 398 through 403 removed outlier: 4.232A pdb=" N ALA D 402 " --> pdb=" O PHE D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 438 Processing helix chain 'P' and resid 46 through 50 removed outlier: 3.845A pdb=" N ILE P 50 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 70 Processing helix chain 'Q' and resid 6 through 10 Processing helix chain 'Q' and resid 44 through 49 Processing helix chain 'Q' and resid 56 through 58 No H-bonds generated for 'chain 'Q' and resid 56 through 58' Processing helix chain 'Q' and resid 66 through 70 removed outlier: 3.772A pdb=" N MET Q 69 " --> pdb=" O PRO Q 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 10 removed outlier: 4.077A pdb=" N ASP R 10 " --> pdb=" O LEU R 7 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 49 Processing helix chain 'R' and resid 56 through 58 No H-bonds generated for 'chain 'R' and resid 56 through 58' Processing helix chain 'R' and resid 68 through 73 removed outlier: 3.617A pdb=" N THR R 73 " --> pdb=" O LYS R 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 10 removed outlier: 3.583A pdb=" N ASP S 10 " --> pdb=" O LEU S 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 7 through 10' Processing helix chain 'S' and resid 44 through 50 removed outlier: 3.687A pdb=" N ILE S 50 " --> pdb=" O GLN S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 56 through 58 No H-bonds generated for 'chain 'S' and resid 56 through 58' Processing helix chain 'a' and resid 3 through 12 removed outlier: 5.743A pdb=" N GLN a 8 " --> pdb=" O HIS a 5 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR a 9 " --> pdb=" O PHE a 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 348 through 360 removed outlier: 3.844A pdb=" N VAL a 352 " --> pdb=" O TRP a 348 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL a 353 " --> pdb=" O PRO a 349 " (cutoff:3.500A) Processing helix chain 'a' and resid 362 through 400 Proline residue: a 396 - end of helix Processing helix chain 'a' and resid 406 through 413 Processing helix chain 'b' and resid 3 through 8 Processing helix chain 'b' and resid 9 through 12 Processing helix chain 'b' and resid 219 through 221 No H-bonds generated for 'chain 'b' and resid 219 through 221' Processing helix chain 'b' and resid 348 through 360 Processing helix chain 'b' and resid 360 through 395 Processing helix chain 'b' and resid 407 through 412 Processing helix chain 'c' and resid 7 through 12 Processing helix chain 'c' and resid 348 through 360 Processing helix chain 'c' and resid 360 through 399 Proline residue: c 396 - end of helix Processing helix chain 'c' and resid 406 through 413 Processing helix chain 'd' and resid 2 through 7 Processing helix chain 'd' and resid 8 through 12 Processing helix chain 'd' and resid 189 through 193 removed outlier: 4.398A pdb=" N GLY d 192 " --> pdb=" O VAL d 189 " (cutoff:3.500A) Processing helix chain 'd' and resid 348 through 360 Processing helix chain 'd' and resid 360 through 399 Proline residue: d 396 - end of helix Processing helix chain 'd' and resid 406 through 413 Processing sheet with id=AA1, first strand: chain '1' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain '1' and resid 11 through 12 removed outlier: 4.335A pdb=" N ARG 1 35 " --> pdb=" O ILE 1 100 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL 1 36 " --> pdb=" O ARG 1 52 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ARG 1 52 " --> pdb=" O VAL 1 36 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP 1 38 " --> pdb=" O LEU 1 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 11 through 12 removed outlier: 3.709A pdb=" N TYR 1 118 " --> pdb=" O ARG 1 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 136 through 140 removed outlier: 5.318A pdb=" N ALA 1 153 " --> pdb=" O VAL 1 200 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL 1 200 " --> pdb=" O ALA 1 153 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLY 1 155 " --> pdb=" O VAL 1 198 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL 1 198 " --> pdb=" O GLY 1 155 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU 1 157 " --> pdb=" O SER 1 196 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N SER 1 196 " --> pdb=" O LEU 1 157 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LYS 1 159 " --> pdb=" O LEU 1 194 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU 1 194 " --> pdb=" O LYS 1 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 147 through 148 removed outlier: 5.318A pdb=" N ALA 1 153 " --> pdb=" O VAL 1 200 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL 1 200 " --> pdb=" O ALA 1 153 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLY 1 155 " --> pdb=" O VAL 1 198 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL 1 198 " --> pdb=" O GLY 1 155 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU 1 157 " --> pdb=" O SER 1 196 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N SER 1 196 " --> pdb=" O LEU 1 157 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LYS 1 159 " --> pdb=" O LEU 1 194 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU 1 194 " --> pdb=" O LYS 1 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 167 through 170 removed outlier: 4.460A pdb=" N TYR 1 210 " --> pdb=" O VAL 1 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 9 through 12 removed outlier: 6.462A pdb=" N VAL 2 10 " --> pdb=" O THR 2 106 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA 2 83 " --> pdb=" O VAL 2 105 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLN 2 36 " --> pdb=" O LEU 2 45 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU 2 45 " --> pdb=" O GLN 2 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 9 through 12 removed outlier: 6.462A pdb=" N VAL 2 10 " --> pdb=" O THR 2 106 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA 2 83 " --> pdb=" O VAL 2 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '2' and resid 18 through 23 Processing sheet with id=AB1, first strand: chain '2' and resid 116 through 120 removed outlier: 5.554A pdb=" N TYR 2 174 " --> pdb=" O ASP 2 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '2' and resid 116 through 120 removed outlier: 5.554A pdb=" N TYR 2 174 " --> pdb=" O ASP 2 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '2' and resid 155 through 157 removed outlier: 4.208A pdb=" N TRP 2 150 " --> pdb=" O VAL 2 157 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AB5, first strand: chain 'A' and resid 15 through 19 removed outlier: 5.379A pdb=" N ILE A 31 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N THR A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU A 33 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASN A 134 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN A 35 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TYR A 137 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 15 through 19 Processing sheet with id=AB7, first strand: chain 'A' and resid 42 through 48 removed outlier: 6.853A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA A 119 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.874A pdb=" N THR A 101 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AC1, first strand: chain 'A' and resid 204 through 205 Processing sheet with id=AC2, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AC3, first strand: chain 'A' and resid 297 through 307 removed outlier: 5.337A pdb=" N ASP A 299 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS A 322 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE A 316 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 344 through 347 removed outlier: 3.527A pdb=" N HIS A 332 " --> pdb=" O GLN A 369 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.572A pdb=" N PHE A 366 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N CYS A 377 " --> pdb=" O PHE A 366 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AC7, first strand: chain 'B' and resid 2 through 8 Processing sheet with id=AC8, first strand: chain 'B' and resid 15 through 19 removed outlier: 3.904A pdb=" N ILE B 31 " --> pdb=" O TYR B 15 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 17 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 29 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR B 137 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE B 31 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE B 135 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU B 33 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 133 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN B 35 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA B 131 " --> pdb=" O ASN B 35 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG B 37 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL B 129 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 39 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY B 127 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA B 121 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE B 47 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B 119 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 140 through 148 removed outlier: 5.282A pdb=" N SER B 141 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR B 137 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B 119 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE B 47 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA B 121 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY B 127 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 39 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL B 129 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG B 37 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA B 131 " --> pdb=" O ASN B 35 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN B 35 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 133 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU B 33 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE B 135 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE B 31 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR B 137 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 29 " --> pdb=" O TYR B 137 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 51 through 52 Processing sheet with id=AD2, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AD3, first strand: chain 'B' and resid 77 through 78 Processing sheet with id=AD4, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AD5, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AD6, first strand: chain 'B' and resid 221 through 222 Processing sheet with id=AD7, first strand: chain 'B' and resid 298 through 307 removed outlier: 6.240A pdb=" N LEU B 300 " --> pdb=" O LYS B 322 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LYS B 322 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N CYS B 302 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA B 320 " --> pdb=" O CYS B 302 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE B 304 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR B 318 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 344 through 347 removed outlier: 3.522A pdb=" N CYS B 329 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AE1, first strand: chain 'C' and resid 2 through 8 removed outlier: 4.983A pdb=" N ILE C 164 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N THR C 153 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 14 through 21 removed outlier: 3.659A pdb=" N VAL C 27 " --> pdb=" O VAL C 19 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ARG C 21 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AE4, first strand: chain 'C' and resid 42 through 48 removed outlier: 5.887A pdb=" N LEU C 44 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS C 123 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR C 46 " --> pdb=" O ALA C 121 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 51 through 54 Processing sheet with id=AE6, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AE7, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AE8, first strand: chain 'C' and resid 204 through 206 Processing sheet with id=AE9, first strand: chain 'C' and resid 297 through 307 removed outlier: 4.893A pdb=" N ASP C 299 " --> pdb=" O LYS C 322 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS C 322 " --> pdb=" O ASP C 299 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE C 316 " --> pdb=" O THR C 305 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 344 through 347 Processing sheet with id=AF2, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AF3, first strand: chain 'D' and resid 15 through 21 removed outlier: 7.225A pdb=" N TYR D 15 " --> pdb=" O GLN D 30 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLN D 30 " --> pdb=" O TYR D 15 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ALA D 17 " --> pdb=" O HIS D 28 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N HIS D 28 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL D 19 " --> pdb=" O PRO D 26 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG D 21 " --> pdb=" O TYR D 24 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N MET D 132 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N THR D 36 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN D 130 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE D 38 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR D 128 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR D 126 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR D 42 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL D 124 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU D 44 " --> pdb=" O TYR D 122 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TYR D 122 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR D 46 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS D 120 " --> pdb=" O TYR D 46 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 140 through 148 removed outlier: 5.166A pdb=" N SER D 141 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N TYR D 137 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS D 120 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR D 46 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TYR D 122 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU D 44 " --> pdb=" O TYR D 122 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL D 124 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR D 42 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR D 126 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR D 128 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE D 38 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN D 130 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N THR D 36 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N MET D 132 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 51 through 54 Processing sheet with id=AF6, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AF7, first strand: chain 'D' and resid 204 through 205 Processing sheet with id=AF8, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AF9, first strand: chain 'D' and resid 298 through 306 removed outlier: 4.969A pdb=" N ASP D 299 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS D 322 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE D 316 " --> pdb=" O THR D 305 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 344 through 347 Processing sheet with id=AG2, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AG3, first strand: chain 'P' and resid 41 through 42 removed outlier: 3.552A pdb=" N ARG P 41 " --> pdb=" O MET P 16 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY P 23 " --> pdb=" O ILE P 15 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU P 17 " --> pdb=" O VAL P 21 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VAL P 21 " --> pdb=" O LEU P 17 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N TYR P 24 " --> pdb=" O PRO P 35 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 83 through 85 removed outlier: 5.476A pdb=" N PHE P 99 " --> pdb=" O LEU P 138 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA P 137 " --> pdb=" O GLY P 129 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY P 129 " --> pdb=" O ALA P 137 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER P 139 " --> pdb=" O LEU P 127 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TRP P 143 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N VAL P 123 " --> pdb=" O TRP P 143 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE P 115 " --> pdb=" O VAL P 123 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 83 through 85 removed outlier: 5.476A pdb=" N PHE P 99 " --> pdb=" O LEU P 138 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 41 through 42 removed outlier: 7.747A pdb=" N TYR Q 24 " --> pdb=" O PRO Q 35 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 83 through 87 removed outlier: 9.797A pdb=" N ALA Q 91 " --> pdb=" O PRO Q 102 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE Q 99 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL Q 141 " --> pdb=" O VAL Q 126 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL Q 126 " --> pdb=" O VAL Q 141 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N TRP Q 143 " --> pdb=" O ALA Q 124 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA Q 124 " --> pdb=" O TRP Q 143 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 114 through 116 removed outlier: 6.837A pdb=" N ILE Q 115 " --> pdb=" O VAL Q 123 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA Q 124 " --> pdb=" O TRP Q 143 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N TRP Q 143 " --> pdb=" O ALA Q 124 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL Q 126 " --> pdb=" O VAL Q 141 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL Q 141 " --> pdb=" O VAL Q 126 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'R' and resid 41 through 42 removed outlier: 5.613A pdb=" N LEU R 17 " --> pdb=" O VAL R 21 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N VAL R 21 " --> pdb=" O LEU R 17 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N TYR R 24 " --> pdb=" O PRO R 35 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'R' and resid 149 through 152 removed outlier: 5.795A pdb=" N PHE R 99 " --> pdb=" O LEU R 138 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N ALA R 91 " --> pdb=" O PRO R 102 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE R 115 " --> pdb=" O VAL R 123 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'R' and resid 149 through 152 removed outlier: 7.322A pdb=" N ARG R 135 " --> pdb=" O ASN R 131 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN R 131 " --> pdb=" O ARG R 135 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA R 137 " --> pdb=" O GLY R 129 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY R 129 " --> pdb=" O ALA R 137 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER R 139 " --> pdb=" O LEU R 127 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TRP R 143 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N VAL R 123 " --> pdb=" O TRP R 143 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'S' and resid 41 through 42 removed outlier: 6.347A pdb=" N PHE S 13 " --> pdb=" O TYR S 24 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR S 24 " --> pdb=" O PHE S 13 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE S 15 " --> pdb=" O ASN S 22 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N TYR S 24 " --> pdb=" O PRO S 35 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'S' and resid 149 through 152 removed outlier: 6.014A pdb=" N PHE S 99 " --> pdb=" O LEU S 138 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N ALA S 91 " --> pdb=" O PRO S 102 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY S 83 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE S 115 " --> pdb=" O VAL S 123 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'S' and resid 149 through 152 removed outlier: 6.638A pdb=" N ARG S 135 " --> pdb=" O ASN S 131 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASN S 131 " --> pdb=" O ARG S 135 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA S 137 " --> pdb=" O GLY S 129 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY S 129 " --> pdb=" O ALA S 137 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER S 139 " --> pdb=" O LEU S 127 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N TRP S 143 " --> pdb=" O VAL S 123 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N VAL S 123 " --> pdb=" O TRP S 143 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'a' and resid 17 through 19 Processing sheet with id=AH7, first strand: chain 'a' and resid 33 through 37 removed outlier: 5.197A pdb=" N GLU a 35 " --> pdb=" O GLN a 48 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN a 48 " --> pdb=" O GLU a 35 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG a 46 " --> pdb=" O ARG a 37 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLN a 102 " --> pdb=" O LEU a 91 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU a 91 " --> pdb=" O GLN a 102 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'a' and resid 65 through 69 removed outlier: 3.718A pdb=" N PHE a 67 " --> pdb=" O LYS a 74 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'a' and resid 82 through 84 removed outlier: 3.520A pdb=" N THR a 108 " --> pdb=" O HIS a 126 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N HIS a 126 " --> pdb=" O THR a 108 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N THR a 110 " --> pdb=" O VAL a 124 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL a 124 " --> pdb=" O THR a 110 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLY a 112 " --> pdb=" O CYS a 122 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N CYS a 122 " --> pdb=" O GLY a 112 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'a' and resid 146 through 153 Processing sheet with id=AI2, first strand: chain 'a' and resid 234 through 235 Processing sheet with id=AI3, first strand: chain 'a' and resid 172 through 173 removed outlier: 3.618A pdb=" N ARG a 224 " --> pdb=" O TYR a 198 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR a 198 " --> pdb=" O ARG a 224 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY a 207 " --> pdb=" O TYR a 197 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'a' and resid 178 through 181 Processing sheet with id=AI5, first strand: chain 'a' and resid 272 through 276 removed outlier: 3.688A pdb=" N GLU a 274 " --> pdb=" O ILE a 281 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE a 281 " --> pdb=" O GLU a 274 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'b' and resid 17 through 19 Processing sheet with id=AI7, first strand: chain 'b' and resid 33 through 37 removed outlier: 5.016A pdb=" N GLU b 35 " --> pdb=" O GLN b 48 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN b 48 " --> pdb=" O GLU b 35 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLN b 102 " --> pdb=" O LEU b 91 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU b 91 " --> pdb=" O GLN b 102 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'b' and resid 52 through 55 removed outlier: 5.740A pdb=" N TYR b 64 " --> pdb=" O GLY b 54 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'b' and resid 82 through 84 removed outlier: 5.680A pdb=" N HIS b 126 " --> pdb=" O THR b 108 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N THR b 110 " --> pdb=" O VAL b 124 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL b 124 " --> pdb=" O THR b 110 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY b 112 " --> pdb=" O CYS b 122 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N CYS b 122 " --> pdb=" O GLY b 112 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'b' and resid 146 through 153 Processing sheet with id=AJ2, first strand: chain 'b' and resid 163 through 164 Processing sheet with id=AJ3, first strand: chain 'b' and resid 166 through 167 Processing sheet with id=AJ4, first strand: chain 'b' and resid 172 through 174 removed outlier: 4.067A pdb=" N ALA b 225 " --> pdb=" O ASP b 174 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'b' and resid 178 through 181 removed outlier: 3.668A pdb=" N HIS b 213 " --> pdb=" O ILE b 187 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'b' and resid 272 through 276 Processing sheet with id=AJ7, first strand: chain 'b' and resid 272 through 276 Processing sheet with id=AJ8, first strand: chain 'c' and resid 33 through 37 removed outlier: 8.307A pdb=" N ILE c 33 " --> pdb=" O SER c 50 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER c 50 " --> pdb=" O ILE c 33 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLU c 35 " --> pdb=" O GLN c 48 " (cutoff:3.500A) removed outlier: 27.856A pdb=" N ARG c 46 " --> pdb=" O ASN c 69 " (cutoff:3.500A) removed outlier: 23.366A pdb=" N ASN c 69 " --> pdb=" O ARG c 46 " (cutoff:3.500A) removed outlier: 17.181A pdb=" N GLN c 48 " --> pdb=" O PHE c 67 " (cutoff:3.500A) removed outlier: 13.531A pdb=" N PHE c 67 " --> pdb=" O GLN c 48 " (cutoff:3.500A) removed outlier: 12.238A pdb=" N SER c 50 " --> pdb=" O MET c 65 " (cutoff:3.500A) removed outlier: 10.614A pdb=" N MET c 65 " --> pdb=" O SER c 50 " (cutoff:3.500A) removed outlier: 11.613A pdb=" N MET c 52 " --> pdb=" O ALA c 63 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ALA c 63 " --> pdb=" O MET c 52 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY c 54 " --> pdb=" O ASP c 61 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'c' and resid 33 through 37 removed outlier: 8.307A pdb=" N ILE c 33 " --> pdb=" O SER c 50 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER c 50 " --> pdb=" O ILE c 33 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLU c 35 " --> pdb=" O GLN c 48 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TYR c 97 " --> pdb=" O THR c 49 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N ALA c 51 " --> pdb=" O HIS c 95 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N HIS c 95 " --> pdb=" O ALA c 51 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N PHE c 53 " --> pdb=" O SER c 93 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N SER c 93 " --> pdb=" O PHE c 53 " (cutoff:3.500A) removed outlier: 15.466A pdb=" N LEU c 55 " --> pdb=" O LEU c 91 " (cutoff:3.500A) removed outlier: 18.124A pdb=" N LEU c 91 " --> pdb=" O LEU c 55 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'c' and resid 81 through 84 removed outlier: 4.490A pdb=" N ASP c 107 " --> pdb=" O HIS c 126 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'c' and resid 146 through 153 Processing sheet with id=AK3, first strand: chain 'c' and resid 234 through 235 Processing sheet with id=AK4, first strand: chain 'c' and resid 172 through 173 Processing sheet with id=AK5, first strand: chain 'c' and resid 178 through 180 Processing sheet with id=AK6, first strand: chain 'c' and resid 272 through 276 Processing sheet with id=AK7, first strand: chain 'c' and resid 304 through 308 Processing sheet with id=AK8, first strand: chain 'd' and resid 25 through 29 removed outlier: 5.566A pdb=" N SER d 25 " --> pdb=" O ASN d 21 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASN d 21 " --> pdb=" O SER d 25 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN d 21 " --> pdb=" O THR d 123 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'd' and resid 33 through 37 removed outlier: 8.391A pdb=" N ILE d 33 " --> pdb=" O SER d 50 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N SER d 50 " --> pdb=" O ILE d 33 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLU d 35 " --> pdb=" O GLN d 48 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLN d 48 " --> pdb=" O GLU d 35 " (cutoff:3.500A) removed outlier: 26.838A pdb=" N ARG d 46 " --> pdb=" O ASN d 69 " (cutoff:3.500A) removed outlier: 22.353A pdb=" N ASN d 69 " --> pdb=" O ARG d 46 " (cutoff:3.500A) removed outlier: 16.968A pdb=" N GLN d 48 " --> pdb=" O PHE d 67 " (cutoff:3.500A) removed outlier: 13.831A pdb=" N PHE d 67 " --> pdb=" O GLN d 48 " (cutoff:3.500A) removed outlier: 12.100A pdb=" N SER d 50 " --> pdb=" O MET d 65 " (cutoff:3.500A) removed outlier: 11.103A pdb=" N MET d 65 " --> pdb=" O SER d 50 " (cutoff:3.500A) removed outlier: 11.178A pdb=" N MET d 52 " --> pdb=" O ALA d 63 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ALA d 63 " --> pdb=" O MET d 52 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY d 54 " --> pdb=" O ASP d 61 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'd' and resid 33 through 37 removed outlier: 8.391A pdb=" N ILE d 33 " --> pdb=" O SER d 50 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N SER d 50 " --> pdb=" O ILE d 33 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLU d 35 " --> pdb=" O GLN d 48 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLN d 48 " --> pdb=" O GLU d 35 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N TYR d 97 " --> pdb=" O THR d 49 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ALA d 51 " --> pdb=" O HIS d 95 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N HIS d 95 " --> pdb=" O ALA d 51 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N PHE d 53 " --> pdb=" O SER d 93 " (cutoff:3.500A) removed outlier: 10.662A pdb=" N SER d 93 " --> pdb=" O PHE d 53 " (cutoff:3.500A) removed outlier: 16.214A pdb=" N LEU d 55 " --> pdb=" O LEU d 91 " (cutoff:3.500A) removed outlier: 18.326A pdb=" N LEU d 91 " --> pdb=" O LEU d 55 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'd' and resid 146 through 153 Processing sheet with id=AL3, first strand: chain 'd' and resid 163 through 164 Processing sheet with id=AL4, first strand: chain 'd' and resid 166 through 167 Processing sheet with id=AL5, first strand: chain 'd' and resid 172 through 174 removed outlier: 3.962A pdb=" N ALA d 225 " --> pdb=" O ASP d 174 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'd' and resid 178 through 181 removed outlier: 3.812A pdb=" N VAL d 185 " --> pdb=" O THR d 215 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'd' and resid 272 through 276 1404 hydrogen bonds defined for protein. 3423 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.54 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 6028 1.32 - 1.45: 9807 1.45 - 1.59: 19848 1.59 - 1.72: 0 1.72 - 1.85: 254 Bond restraints: 35937 Sorted by residual: bond pdb=" CZ ARG D 37 " pdb=" NH2 ARG D 37 " ideal model delta sigma weight residual 1.330 1.273 0.057 1.30e-02 5.92e+03 1.91e+01 bond pdb=" CZ ARG b 305 " pdb=" NH2 ARG b 305 " ideal model delta sigma weight residual 1.330 1.278 0.052 1.30e-02 5.92e+03 1.61e+01 bond pdb=" N ILE C 135 " pdb=" CA ILE C 135 " ideal model delta sigma weight residual 1.459 1.508 -0.049 1.25e-02 6.40e+03 1.52e+01 bond pdb=" CB THR P 142 " pdb=" OG1 THR P 142 " ideal model delta sigma weight residual 1.433 1.371 0.062 1.60e-02 3.91e+03 1.51e+01 bond pdb=" N ILE A 135 " pdb=" CA ILE A 135 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.14e-02 7.69e+03 1.47e+01 ... (remaining 35932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 43074 2.33 - 4.66: 5452 4.66 - 6.99: 452 6.99 - 9.33: 27 9.33 - 11.66: 6 Bond angle restraints: 49011 Sorted by residual: angle pdb=" C CYS d 201 " pdb=" CA CYS d 201 " pdb=" CB CYS d 201 " ideal model delta sigma weight residual 109.52 119.42 -9.90 1.58e+00 4.01e-01 3.93e+01 angle pdb=" CB HIS 2 33 " pdb=" CG HIS 2 33 " pdb=" CD2 HIS 2 33 " ideal model delta sigma weight residual 131.20 123.25 7.95 1.30e+00 5.92e-01 3.74e+01 angle pdb=" N TYR 1 111 " pdb=" CA TYR 1 111 " pdb=" C TYR 1 111 " ideal model delta sigma weight residual 111.02 117.88 -6.86 1.25e+00 6.40e-01 3.01e+01 angle pdb=" CA PHE a 53 " pdb=" CB PHE a 53 " pdb=" CG PHE a 53 " ideal model delta sigma weight residual 113.80 108.38 5.42 1.00e+00 1.00e+00 2.94e+01 angle pdb=" CA PHE P 33 " pdb=" CB PHE P 33 " pdb=" CG PHE P 33 " ideal model delta sigma weight residual 113.80 119.17 -5.37 1.00e+00 1.00e+00 2.88e+01 ... (remaining 49006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.08: 20131 23.08 - 46.16: 1290 46.16 - 69.23: 215 69.23 - 92.31: 73 92.31 - 115.39: 34 Dihedral angle restraints: 21743 sinusoidal: 8737 harmonic: 13006 Sorted by residual: dihedral pdb=" CB CYS b 22 " pdb=" SG CYS b 22 " pdb=" SG CYS b 27 " pdb=" CB CYS b 27 " ideal model delta sinusoidal sigma weight residual -86.00 -148.21 62.21 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS b 201 " pdb=" SG CYS b 201 " pdb=" SG CYS b 217 " pdb=" CB CYS b 217 " ideal model delta sinusoidal sigma weight residual 93.00 148.92 -55.92 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CA ASP B 203 " pdb=" C ASP B 203 " pdb=" N LEU B 204 " pdb=" CA LEU B 204 " ideal model delta harmonic sigma weight residual 180.00 150.23 29.77 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 21740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.401: 5512 0.401 - 0.801: 5 0.801 - 1.202: 0 1.202 - 1.602: 0 1.602 - 2.003: 2 Chirality restraints: 5519 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-02 2.50e+03 8.83e+02 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-02 2.50e+03 7.42e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-02 2.50e+03 3.96e+02 ... (remaining 5516 not shown) Planarity restraints: 6297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 134 " -0.207 2.00e-02 2.50e+03 6.71e-01 5.62e+03 pdb=" CG ASN C 134 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN C 134 " -0.761 2.00e-02 2.50e+03 pdb=" ND2 ASN C 134 " 1.230 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.331 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 134 " 0.006 2.00e-02 2.50e+03 3.21e-01 1.29e+03 pdb=" CG ASN A 134 " -0.092 2.00e-02 2.50e+03 pdb=" OD1 ASN A 134 " 0.256 2.00e-02 2.50e+03 pdb=" ND2 ASN A 134 " -0.547 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.377 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 134 " 0.186 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" CG ASN B 134 " -0.096 2.00e-02 2.50e+03 pdb=" OD1 ASN B 134 " 0.066 2.00e-02 2.50e+03 pdb=" ND2 ASN B 134 " -0.535 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.378 2.00e-02 2.50e+03 ... (remaining 6294 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.90: 3 1.90 - 2.65: 403 2.65 - 3.40: 50021 3.40 - 4.15: 90345 4.15 - 4.90: 151740 Nonbonded interactions: 292512 Sorted by model distance: nonbonded pdb=" ND2 ASN C 134 " pdb=" C7 NAG F 1 " model vdw 1.156 3.350 nonbonded pdb=" ND2 ASN C 134 " pdb=" C8 NAG F 1 " model vdw 1.621 3.540 nonbonded pdb=" ND2 ASN C 134 " pdb=" O7 NAG F 1 " model vdw 1.730 3.120 nonbonded pdb=" ND2 ASN C 134 " pdb=" N2 NAG F 1 " model vdw 1.956 2.560 nonbonded pdb=" CG ASN C 134 " pdb=" C8 NAG F 1 " model vdw 2.076 3.690 ... (remaining 292507 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'P' selection = (chain 'Q' and resid 8 through 160) selection = (chain 'R' and resid 8 through 160) selection = (chain 'S' and resid 8 through 160) } ncs_group { reference = chain 'a' selection = (chain 'b' and resid 2 through 501) selection = (chain 'c' and resid 2 through 501) selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.210 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.110 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 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 : 0.016 1.437 36017 Z= 0.867 Angle : 1.592 57.022 49187 Z= 0.972 Chirality : 0.116 2.003 5519 Planarity : 0.018 0.344 6289 Dihedral : 16.642 115.391 13229 Min Nonbonded Distance : 1.156 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.57 % Favored : 93.09 % Rotamer: Outliers : 5.10 % Allowed : 14.88 % Favored : 80.03 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.92 % 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: -1.78 (0.11), residues: 4473 helix: -1.07 (0.21), residues: 464 sheet: -0.66 (0.14), residues: 1182 loop : -1.47 (0.11), residues: 2827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.002 ARG C 21 TYR 0.266 0.016 TYR 1 112 PHE 0.122 0.009 PHE a 53 TRP 0.133 0.015 TRP R 87 HIS 0.017 0.004 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.01337 / 0.77 (35937) covalent geometry : angle 1.52262 / 0.96 (49011) SS BOND : bond 0.01874 / 0.99 ( 64) SS BOND : angle 2.41803 / 1.48 ( 128) hydrogen bonds : bond 0.17035 / 11.13 ( 1319) hydrogen bonds : angle 8.95904 / 6.23 ( 3423) link_BETA1-4 : bond 0.04545 / 2.17 ( 8) link_BETA1-4 : angle 7.03401 / 4.59 ( 24) link_NAG-ASN : bond 0.53346 / 26.67 ( 8) link_NAG-ASN : angle 19.55181 / 10.84 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 958 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 58 ASP cc_start: 0.9762 (m-30) cc_final: 0.9560 (t70) REVERT: 1 71 ILE cc_start: 0.8423 (tt) cc_final: 0.7958 (tt) REVERT: 1 116 PHE cc_start: 0.8645 (m-80) cc_final: 0.8296 (m-80) REVERT: 1 192 TYR cc_start: 0.9418 (m-80) cc_final: 0.9180 (m-80) REVERT: 2 11 SER cc_start: 0.9558 (m) cc_final: 0.9292 (t) REVERT: 2 26 ASN cc_start: 0.9479 (t0) cc_final: 0.8908 (t0) REVERT: A 15 TYR cc_start: 0.8023 (t80) cc_final: 0.7496 (t80) REVERT: A 24 TYR cc_start: 0.9553 (m-80) cc_final: 0.8898 (m-80) REVERT: A 45 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8838 (tp30) REVERT: A 100 ASN cc_start: 0.6727 (OUTLIER) cc_final: 0.5893 (m-40) REVERT: A 118 HIS cc_start: 0.8550 (p-80) cc_final: 0.8115 (p-80) REVERT: A 132 MET cc_start: 0.9793 (tpp) cc_final: 0.9417 (tpp) REVERT: A 143 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8422 (ttp-170) REVERT: A 146 ASP cc_start: 0.9391 (m-30) cc_final: 0.8945 (t0) REVERT: A 156 LYS cc_start: 0.9713 (mttt) cc_final: 0.9406 (ttpp) REVERT: A 159 ASP cc_start: 0.9677 (OUTLIER) cc_final: 0.9425 (p0) REVERT: A 220 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8476 (tp) REVERT: A 343 ASN cc_start: 0.8143 (m-40) cc_final: 0.7766 (t0) REVERT: A 359 THR cc_start: 0.5239 (OUTLIER) cc_final: 0.5037 (t) REVERT: A 361 ASN cc_start: 0.8979 (m-40) cc_final: 0.8290 (m110) REVERT: B 10 LYS cc_start: 0.9021 (ptpp) cc_final: 0.8691 (mtmm) REVERT: B 100 ASN cc_start: 0.6699 (OUTLIER) cc_final: 0.6032 (m110) REVERT: B 102 GLN cc_start: 0.8432 (tt0) cc_final: 0.7648 (tm-30) REVERT: B 103 MET cc_start: 0.8087 (tpp) cc_final: 0.7448 (tpp) REVERT: B 104 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.7300 (p) REVERT: B 129 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8404 (p) REVERT: B 135 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7641 (mm) REVERT: B 175 ASP cc_start: 0.8912 (p0) cc_final: 0.7997 (p0) REVERT: B 242 GLU cc_start: 0.9570 (mp0) cc_final: 0.9281 (mp0) REVERT: B 243 ARG cc_start: 0.9710 (tmm-80) cc_final: 0.9411 (ttt180) REVERT: B 246 ARG cc_start: 0.9571 (mtm110) cc_final: 0.9339 (mmt-90) REVERT: B 254 ASP cc_start: 0.9566 (m-30) cc_final: 0.8726 (t0) REVERT: B 277 ILE cc_start: 0.9217 (mm) cc_final: 0.8629 (mm) REVERT: B 339 VAL cc_start: 0.8565 (t) cc_final: 0.7797 (m) REVERT: B 362 ILE cc_start: 0.9545 (mm) cc_final: 0.9271 (tp) REVERT: B 366 PHE cc_start: 0.8207 (p90) cc_final: 0.7863 (p90) REVERT: B 386 ASP cc_start: 0.9639 (m-30) cc_final: 0.9389 (p0) REVERT: B 432 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8299 (p) REVERT: B 438 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8358 (m-10) REVERT: C 33 LEU cc_start: 0.8727 (mp) cc_final: 0.7753 (tp) REVERT: C 38 ILE cc_start: 0.9070 (mt) cc_final: 0.8657 (tt) REVERT: C 53 THR cc_start: 0.9229 (p) cc_final: 0.9015 (m) REVERT: C 103 MET cc_start: 0.3970 (tpp) cc_final: 0.3511 (tpp) REVERT: C 118 HIS cc_start: 0.4009 (OUTLIER) cc_final: 0.2971 (p-80) REVERT: C 144 SER cc_start: 0.6607 (t) cc_final: 0.5910 (p) REVERT: C 181 TYR cc_start: 0.8585 (t80) cc_final: 0.8291 (t80) REVERT: C 188 TYR cc_start: 0.9356 (t80) cc_final: 0.9103 (t80) REVERT: C 234 PHE cc_start: 0.9021 (p90) cc_final: 0.8639 (p90) REVERT: C 242 GLU cc_start: 0.9427 (mm-30) cc_final: 0.9203 (mm-30) REVERT: C 243 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8221 (ttp80) REVERT: C 270 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8814 (pm20) REVERT: C 279 ILE cc_start: 0.8566 (mm) cc_final: 0.8056 (mm) REVERT: C 339 VAL cc_start: 0.7383 (p) cc_final: 0.6964 (m) REVERT: C 375 VAL cc_start: 0.5654 (p) cc_final: 0.5426 (p) REVERT: C 439 HIS cc_start: 0.8857 (m170) cc_final: 0.8518 (m90) REVERT: D 33 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9328 (tt) REVERT: D 55 VAL cc_start: 0.9330 (m) cc_final: 0.9082 (t) REVERT: D 100 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8360 (m-40) REVERT: D 105 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8606 (pm20) REVERT: D 175 ASP cc_start: 0.8903 (m-30) cc_final: 0.8627 (p0) REVERT: D 188 TYR cc_start: 0.9127 (t80) cc_final: 0.8614 (t80) REVERT: D 191 PRO cc_start: 0.9695 (Cg_exo) cc_final: 0.9438 (Cg_endo) REVERT: D 243 ARG cc_start: 0.9567 (ttt180) cc_final: 0.9136 (ttt90) REVERT: D 247 ASP cc_start: 0.8801 (p0) cc_final: 0.8504 (p0) REVERT: D 252 LEU cc_start: 0.9498 (tp) cc_final: 0.9236 (mt) REVERT: D 254 ASP cc_start: 0.9270 (m-30) cc_final: 0.8231 (p0) REVERT: D 277 ILE cc_start: 0.9608 (mm) cc_final: 0.9095 (tp) REVERT: D 281 ILE cc_start: 0.9578 (tt) cc_final: 0.9288 (tt) REVERT: P 89 HIS cc_start: 0.9139 (m90) cc_final: 0.8872 (m-70) REVERT: Q 33 PHE cc_start: 0.8236 (m-10) cc_final: 0.7831 (m-10) REVERT: Q 77 THR cc_start: 0.5998 (OUTLIER) cc_final: 0.4842 (p) REVERT: Q 82 PRO cc_start: 0.3724 (Cg_exo) cc_final: 0.2724 (Cg_endo) REVERT: R 16 MET cc_start: 0.8371 (mmm) cc_final: 0.8170 (mmm) REVERT: R 33 PHE cc_start: 0.7590 (m-10) cc_final: 0.7363 (m-80) REVERT: R 72 ASP cc_start: 0.7856 (t0) cc_final: 0.7634 (p0) REVERT: R 117 ASP cc_start: 0.8921 (p0) cc_final: 0.7983 (p0) REVERT: R 132 GLU cc_start: 0.4267 (OUTLIER) cc_final: 0.3972 (pp20) REVERT: S 15 ILE cc_start: 0.8507 (tp) cc_final: 0.8213 (pt) REVERT: S 26 CYS cc_start: 0.8282 (t) cc_final: 0.8000 (p) REVERT: S 115 ILE cc_start: 0.7166 (mp) cc_final: 0.6765 (tp) REVERT: S 125 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.6921 (tp) REVERT: a 8 GLN cc_start: 0.8048 (tp40) cc_final: 0.7817 (pm20) REVERT: a 11 LEU cc_start: 0.9127 (mt) cc_final: 0.8894 (tp) REVERT: a 34 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5603 (pm20) REVERT: a 126 HIS cc_start: 0.7891 (t-90) cc_final: 0.7467 (t-170) REVERT: a 135 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.8312 (ttm-80) REVERT: a 187 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.6815 (tt) REVERT: a 308 ILE cc_start: 0.9045 (mm) cc_final: 0.8706 (tp) REVERT: a 316 PHE cc_start: 0.7849 (m-10) cc_final: 0.7370 (m-80) REVERT: a 334 ARG cc_start: 0.9173 (mmt90) cc_final: 0.8854 (tpp80) REVERT: a 356 TYR cc_start: 0.8749 (m-80) cc_final: 0.8533 (m-80) REVERT: a 415 ILE cc_start: 0.9261 (pt) cc_final: 0.9055 (mm) REVERT: b 8 GLN cc_start: 0.9280 (tp40) cc_final: 0.8874 (tt0) REVERT: b 36 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8671 (p) REVERT: b 45 ILE cc_start: 0.9836 (pt) cc_final: 0.9479 (mm) REVERT: b 52 MET cc_start: 0.8066 (mtp) cc_final: 0.7791 (mmm) REVERT: b 53 PHE cc_start: 0.8669 (m-80) cc_final: 0.8159 (m-80) REVERT: b 65 MET cc_start: 0.9635 (ptm) cc_final: 0.9272 (ppp) REVERT: b 68 MET cc_start: 0.8993 (mmm) cc_final: 0.8420 (mmt) REVERT: b 102 GLN cc_start: 0.9769 (tt0) cc_final: 0.9431 (mm-40) REVERT: b 139 ARG cc_start: 0.9658 (ttm-80) cc_final: 0.9266 (ttm-80) REVERT: b 148 LEU cc_start: 0.9339 (mp) cc_final: 0.8999 (mp) REVERT: b 270 GLU cc_start: 0.9560 (mm-30) cc_final: 0.8939 (tm-30) REVERT: b 274 GLU cc_start: 0.9436 (mm-30) cc_final: 0.8991 (mm-30) REVERT: b 279 THR cc_start: 0.9185 (p) cc_final: 0.8961 (t) REVERT: b 288 HIS cc_start: 0.9708 (m-70) cc_final: 0.9437 (m-70) REVERT: b 306 GLN cc_start: 0.9528 (pt0) cc_final: 0.9304 (pm20) REVERT: b 309 GLU cc_start: 0.9536 (mp0) cc_final: 0.9114 (mp0) REVERT: b 386 LEU cc_start: 0.9793 (mm) cc_final: 0.9564 (mm) REVERT: c 52 MET cc_start: 0.8508 (mmm) cc_final: 0.7870 (mmm) REVERT: c 53 PHE cc_start: 0.9205 (m-80) cc_final: 0.8736 (m-80) REVERT: c 248 PHE cc_start: 0.9293 (m-80) cc_final: 0.9090 (m-80) REVERT: c 289 PRO cc_start: 0.9800 (Cg_exo) cc_final: 0.9592 (Cg_endo) REVERT: c 300 ASP cc_start: 0.9659 (t0) cc_final: 0.9364 (t0) REVERT: c 304 THR cc_start: 0.9481 (t) cc_final: 0.9221 (p) REVERT: c 327 TRP cc_start: 0.6475 (t-100) cc_final: 0.6260 (t-100) REVERT: c 386 LEU cc_start: 0.9553 (mm) cc_final: 0.9191 (mm) REVERT: d 9 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.8741 (m-80) REVERT: d 41 HIS cc_start: 0.9245 (m90) cc_final: 0.8574 (m90) REVERT: d 45 ILE cc_start: 0.9833 (pt) cc_final: 0.9626 (mm) REVERT: d 53 PHE cc_start: 0.8801 (m-80) cc_final: 0.8336 (m-80) REVERT: d 68 MET cc_start: 0.9422 (mmm) cc_final: 0.8693 (mmm) REVERT: d 148 LEU cc_start: 0.9190 (mp) cc_final: 0.8921 (mm) REVERT: d 151 ASN cc_start: 0.8491 (p0) cc_final: 0.8029 (p0) REVERT: d 166 MET cc_start: 0.9441 (ptp) cc_final: 0.8966 (ptm) REVERT: d 175 HIS cc_start: 0.9661 (OUTLIER) cc_final: 0.9446 (p-80) REVERT: d 200 LYS cc_start: 0.9582 (OUTLIER) cc_final: 0.9325 (tppt) REVERT: d 287 ASP cc_start: 0.9476 (p0) cc_final: 0.8783 (p0) REVERT: d 292 LEU cc_start: 0.9424 (tp) cc_final: 0.9203 (tp) REVERT: d 306 GLN cc_start: 0.9615 (pt0) cc_final: 0.9398 (pm20) REVERT: d 314 VAL cc_start: 0.9582 (OUTLIER) cc_final: 0.9318 (p) REVERT: d 358 ASN cc_start: 0.9333 (OUTLIER) cc_final: 0.9058 (p0) REVERT: d 376 MET cc_start: 0.9057 (mmm) cc_final: 0.8813 (mmm) REVERT: d 397 TYR cc_start: 0.8960 (m-80) cc_final: 0.8390 (m-80) REVERT: d 409 LEU cc_start: 0.9266 (mm) cc_final: 0.9017 (tt) outliers start: 196 outliers final: 41 residues processed: 1091 average time/residue: 0.2202 time to fit residues: 383.9036 Evaluate side-chains 660 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 591 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 0.0050 chunk 215 optimal weight: 0.0970 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 5.9990 overall best weight: 3.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN C 394 GLN D 100 ASN D 236 GLN D 395 HIS P 97 ASN Q 89 HIS ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 167 HIS ** a 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 222 GLN a 277 HIS ** a 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 94 HIS c 160 GLN c 213 HIS d 80 ASN ** d 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 168 GLN d 175 HIS d 277 HIS ** d 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.094268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.075082 restraints weight = 169130.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.076429 restraints weight = 131121.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.077404 restraints weight = 108051.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.078019 restraints weight = 92805.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.078642 restraints weight = 83140.843| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 36017 Z= 0.196 Angle : 0.853 17.130 49187 Z= 0.441 Chirality : 0.053 0.331 5519 Planarity : 0.007 0.101 6289 Dihedral : 11.125 107.538 5204 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.72 % Favored : 95.26 % Rotamer: Outliers : 0.21 % Allowed : 5.20 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.07 % 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: -1.31 (0.12), residues: 4473 helix: -0.19 (0.23), residues: 471 sheet: -0.59 (0.14), residues: 1325 loop : -1.14 (0.12), residues: 2677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 268 TYR 0.024 0.002 TYR A 24 PHE 0.031 0.002 PHE a 53 TRP 0.031 0.002 TRP Q 87 HIS 0.018 0.002 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (35937) covalent geometry : angle 0.82546 / 0.43 (49011) SS BOND : bond 0.00542 / 0.35 ( 64) SS BOND : angle 1.91659 / 1.26 ( 128) hydrogen bonds : bond 0.05118 / 3.32 ( 1319) hydrogen bonds : angle 7.05845 / 4.89 ( 3423) link_BETA1-4 : bond 0.01528 / 0.73 ( 8) link_BETA1-4 : angle 4.10106 / 2.56 ( 24) link_NAG-ASN : bond 0.00957 / 0.48 ( 8) link_NAG-ASN : angle 7.91770 / 5.60 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 728 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 84 MET cc_start: 0.9395 (ttt) cc_final: 0.8960 (tpp) REVERT: 1 192 TYR cc_start: 0.9421 (m-80) cc_final: 0.9061 (m-80) REVERT: 2 16 GLN cc_start: 0.9693 (mm-40) cc_final: 0.9491 (mp10) REVERT: 2 25 ASN cc_start: 0.8945 (m-40) cc_final: 0.8448 (m-40) REVERT: 2 26 ASN cc_start: 0.9421 (t0) cc_final: 0.8855 (t0) REVERT: 2 27 ILE cc_start: 0.9807 (tp) cc_final: 0.9312 (tp) REVERT: 2 30 LYS cc_start: 0.9572 (mttm) cc_final: 0.9129 (mtmm) REVERT: A 24 TYR cc_start: 0.9253 (m-80) cc_final: 0.8966 (m-80) REVERT: A 45 GLU cc_start: 0.9264 (mm-30) cc_final: 0.9025 (mp0) REVERT: A 130 GLN cc_start: 0.9632 (pt0) cc_final: 0.9270 (tt0) REVERT: A 244 TRP cc_start: 0.8862 (t60) cc_final: 0.8417 (t60) REVERT: A 285 ASP cc_start: 0.9839 (m-30) cc_final: 0.9636 (m-30) REVERT: A 343 ASN cc_start: 0.8530 (m-40) cc_final: 0.7904 (t0) REVERT: A 411 LEU cc_start: 0.9485 (mt) cc_final: 0.9207 (pp) REVERT: B 10 LYS cc_start: 0.9161 (mtmm) cc_final: 0.8941 (mmtm) REVERT: B 50 LYS cc_start: 0.9246 (ttpp) cc_final: 0.8771 (tmmt) REVERT: B 79 GLN cc_start: 0.8289 (tp-100) cc_final: 0.7459 (tm-30) REVERT: B 102 GLN cc_start: 0.8729 (tt0) cc_final: 0.8387 (tp-100) REVERT: B 124 VAL cc_start: 0.9089 (t) cc_final: 0.8801 (t) REVERT: B 175 ASP cc_start: 0.8312 (p0) cc_final: 0.7713 (p0) REVERT: B 184 GLU cc_start: 0.8698 (pm20) cc_final: 0.8497 (pm20) REVERT: B 201 PHE cc_start: 0.9310 (t80) cc_final: 0.8555 (t80) REVERT: B 234 PHE cc_start: 0.8821 (p90) cc_final: 0.8443 (p90) REVERT: B 242 GLU cc_start: 0.9526 (mp0) cc_final: 0.9130 (mp0) REVERT: B 243 ARG cc_start: 0.9611 (ttt-90) cc_final: 0.8940 (ttm170) REVERT: B 277 ILE cc_start: 0.9379 (mm) cc_final: 0.8896 (mm) REVERT: B 302 CYS cc_start: 0.5020 (t) cc_final: 0.4416 (t) REVERT: C 33 LEU cc_start: 0.9029 (mp) cc_final: 0.8182 (tp) REVERT: C 50 LYS cc_start: 0.9329 (tttt) cc_final: 0.8921 (mtmt) REVERT: C 88 MET cc_start: 0.9624 (mmm) cc_final: 0.8874 (tpp) REVERT: C 102 GLN cc_start: 0.8066 (tp-100) cc_final: 0.7847 (tp40) REVERT: C 103 MET cc_start: 0.3557 (tpp) cc_final: 0.3225 (tpp) REVERT: C 181 TYR cc_start: 0.8978 (t80) cc_final: 0.8763 (t80) REVERT: C 188 TYR cc_start: 0.9384 (t80) cc_final: 0.9100 (t80) REVERT: C 204 LEU cc_start: 0.8746 (tp) cc_final: 0.7561 (mp) REVERT: C 270 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8926 (mp0) REVERT: C 354 THR cc_start: 0.8669 (p) cc_final: 0.8395 (p) REVERT: D 33 LEU cc_start: 0.9616 (mp) cc_final: 0.9400 (tt) REVERT: D 52 LYS cc_start: 0.9800 (ttpt) cc_final: 0.9592 (mtmt) REVERT: D 117 ASP cc_start: 0.8895 (m-30) cc_final: 0.7989 (m-30) REVERT: D 152 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8733 (mm-30) REVERT: D 169 SER cc_start: 0.9360 (t) cc_final: 0.8994 (p) REVERT: D 175 ASP cc_start: 0.8999 (m-30) cc_final: 0.8523 (p0) REVERT: D 183 HIS cc_start: 0.9102 (t70) cc_final: 0.8840 (t70) REVERT: D 184 GLU cc_start: 0.8430 (pm20) cc_final: 0.8164 (pm20) REVERT: D 188 TYR cc_start: 0.9316 (t80) cc_final: 0.8662 (t80) REVERT: D 191 PRO cc_start: 0.9748 (Cg_exo) cc_final: 0.9533 (Cg_endo) REVERT: D 197 LYS cc_start: 0.9732 (mmmm) cc_final: 0.9529 (mmmm) REVERT: D 254 ASP cc_start: 0.9448 (m-30) cc_final: 0.8370 (p0) REVERT: D 255 VAL cc_start: 0.9710 (p) cc_final: 0.9249 (m) REVERT: D 277 ILE cc_start: 0.9379 (mm) cc_final: 0.8650 (mm) REVERT: P 10 ASP cc_start: 0.9233 (p0) cc_final: 0.8084 (p0) REVERT: P 16 MET cc_start: 0.4581 (mpp) cc_final: 0.3506 (tpp) REVERT: P 89 HIS cc_start: 0.9183 (m90) cc_final: 0.8774 (m90) REVERT: Q 82 PRO cc_start: 0.3954 (Cg_exo) cc_final: 0.3628 (Cg_endo) REVERT: R 16 MET cc_start: 0.8120 (mmm) cc_final: 0.7695 (mmm) REVERT: R 72 ASP cc_start: 0.7948 (t0) cc_final: 0.7604 (p0) REVERT: R 80 LYS cc_start: 0.7936 (mptt) cc_final: 0.7056 (mptt) REVERT: R 117 ASP cc_start: 0.8054 (p0) cc_final: 0.7354 (p0) REVERT: a 8 GLN cc_start: 0.8549 (tp40) cc_final: 0.8133 (pm20) REVERT: a 48 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7430 (tm-30) REVERT: a 71 LYS cc_start: 0.8710 (pttm) cc_final: 0.8094 (tttt) REVERT: a 126 HIS cc_start: 0.8211 (t-90) cc_final: 0.7686 (t-170) REVERT: a 302 ASN cc_start: 0.8418 (t0) cc_final: 0.7773 (p0) REVERT: a 316 PHE cc_start: 0.8151 (m-80) cc_final: 0.7856 (m-80) REVERT: b 8 GLN cc_start: 0.9191 (tp40) cc_final: 0.8803 (tt0) REVERT: b 45 ILE cc_start: 0.9847 (pt) cc_final: 0.9315 (mm) REVERT: b 53 PHE cc_start: 0.8650 (m-80) cc_final: 0.8121 (m-80) REVERT: b 65 MET cc_start: 0.9494 (ptm) cc_final: 0.9233 (ppp) REVERT: b 68 MET cc_start: 0.8753 (mmm) cc_final: 0.7988 (mmm) REVERT: b 102 GLN cc_start: 0.9664 (tt0) cc_final: 0.9405 (tp40) REVERT: b 139 ARG cc_start: 0.9683 (ttm-80) cc_final: 0.9239 (ttm110) REVERT: b 270 GLU cc_start: 0.9637 (tp30) cc_final: 0.8891 (tm-30) REVERT: b 294 THR cc_start: 0.9200 (p) cc_final: 0.8880 (t) REVERT: b 306 GLN cc_start: 0.9604 (pt0) cc_final: 0.9389 (pp30) REVERT: b 390 ARG cc_start: 0.9056 (tpt170) cc_final: 0.8668 (tpt170) REVERT: b 393 CYS cc_start: 0.8338 (t) cc_final: 0.7974 (t) REVERT: c 36 VAL cc_start: 0.9070 (t) cc_final: 0.8688 (t) REVERT: c 47 ILE cc_start: 0.9782 (pt) cc_final: 0.9561 (mm) REVERT: c 52 MET cc_start: 0.8463 (mmm) cc_final: 0.8248 (mmm) REVERT: c 139 ARG cc_start: 0.8717 (mtm110) cc_final: 0.8277 (mtm110) REVERT: c 300 ASP cc_start: 0.9636 (t0) cc_final: 0.9411 (t0) REVERT: c 306 GLN cc_start: 0.9017 (pm20) cc_final: 0.8744 (pm20) REVERT: c 316 PHE cc_start: 0.8802 (m-80) cc_final: 0.8519 (m-80) REVERT: c 327 TRP cc_start: 0.6633 (t-100) cc_final: 0.6169 (t-100) REVERT: c 339 GLU cc_start: 0.7547 (pm20) cc_final: 0.7158 (pm20) REVERT: c 386 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9353 (mm) REVERT: d 39 ASP cc_start: 0.8484 (p0) cc_final: 0.8146 (p0) REVERT: d 41 HIS cc_start: 0.8784 (m90) cc_final: 0.8446 (m90) REVERT: d 53 PHE cc_start: 0.9065 (m-80) cc_final: 0.8413 (m-80) REVERT: d 127 LYS cc_start: 0.9665 (tmtt) cc_final: 0.9465 (tptp) REVERT: d 151 ASN cc_start: 0.8462 (p0) cc_final: 0.7794 (p0) REVERT: d 200 LYS cc_start: 0.9686 (tptp) cc_final: 0.9356 (tppt) REVERT: d 274 GLU cc_start: 0.9701 (tp30) cc_final: 0.9435 (tm-30) REVERT: d 276 LYS cc_start: 0.9531 (mmpt) cc_final: 0.9146 (mtmm) REVERT: d 282 LEU cc_start: 0.9663 (mp) cc_final: 0.9451 (mp) REVERT: d 287 ASP cc_start: 0.9360 (p0) cc_final: 0.8624 (p0) REVERT: d 292 LEU cc_start: 0.9368 (tp) cc_final: 0.9028 (tp) REVERT: d 314 VAL cc_start: 0.9711 (m) cc_final: 0.9425 (p) REVERT: d 368 LEU cc_start: 0.9219 (mm) cc_final: 0.8956 (pp) REVERT: d 387 CYS cc_start: 0.8995 (m) cc_final: 0.8620 (p) REVERT: d 397 TYR cc_start: 0.8772 (m-80) cc_final: 0.8513 (m-80) outliers start: 8 outliers final: 4 residues processed: 734 average time/residue: 0.2171 time to fit residues: 251.9741 Evaluate side-chains 548 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 543 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 64 optimal weight: 20.0000 chunk 278 optimal weight: 6.9990 chunk 440 optimal weight: 8.9990 chunk 274 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 253 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 323 optimal weight: 7.9990 chunk 304 optimal weight: 30.0000 chunk 59 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 ASN C 332 HIS C 363 HIS ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 GLN ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 94 HIS a 162 HIS ** a 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 222 GLN ** a 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 5 HIS ** c 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 21 ASN ** d 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 285 HIS d 346 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.082706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.065526 restraints weight = 242442.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.067280 restraints weight = 164965.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.068599 restraints weight = 122108.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.069581 restraints weight = 95531.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.070371 restraints weight = 78193.254| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 36017 Z= 0.205 Angle : 0.789 12.134 49187 Z= 0.408 Chirality : 0.051 0.367 5519 Planarity : 0.006 0.102 6289 Dihedral : 10.049 103.688 5204 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.37 % Favored : 94.59 % Rotamer: Outliers : 0.16 % Allowed : 5.20 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.07 % 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: -1.33 (0.12), residues: 4473 helix: -0.29 (0.23), residues: 470 sheet: -0.72 (0.14), residues: 1336 loop : -1.05 (0.12), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG d 390 TYR 0.022 0.002 TYR 1 112 PHE 0.027 0.002 PHE A 421 TRP 0.025 0.002 TRP B 142 HIS 0.010 0.002 HIS A 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (35937) covalent geometry : angle 0.76945 / 0.40 (49011) SS BOND : bond 0.01120 / 0.71 ( 64) SS BOND : angle 1.70488 / 1.16 ( 128) hydrogen bonds : bond 0.04577 / 3.03 ( 1319) hydrogen bonds : angle 6.77098 / 4.67 ( 3423) link_BETA1-4 : bond 0.01156 / 0.55 ( 8) link_BETA1-4 : angle 3.94398 / 2.45 ( 24) link_NAG-ASN : bond 0.01222 / 0.63 ( 8) link_NAG-ASN : angle 5.97497 / 4.37 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 682 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 116 PHE cc_start: 0.8485 (m-80) cc_final: 0.7973 (m-80) REVERT: 1 192 TYR cc_start: 0.9555 (m-80) cc_final: 0.9274 (m-80) REVERT: 2 26 ASN cc_start: 0.9487 (t0) cc_final: 0.9187 (t0) REVERT: 2 57 ILE cc_start: 0.6818 (mp) cc_final: 0.6566 (mt) REVERT: 2 97 TYR cc_start: 0.9450 (m-10) cc_final: 0.9142 (m-80) REVERT: A 24 TYR cc_start: 0.9494 (m-80) cc_final: 0.8676 (m-80) REVERT: A 33 LEU cc_start: 0.9839 (mt) cc_final: 0.9557 (tp) REVERT: A 36 THR cc_start: 0.9757 (p) cc_final: 0.9479 (p) REVERT: A 45 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8995 (mm-30) REVERT: A 103 MET cc_start: 0.8900 (mtp) cc_final: 0.8615 (tpt) REVERT: A 128 THR cc_start: 0.9161 (t) cc_final: 0.8459 (t) REVERT: A 130 GLN cc_start: 0.9517 (pt0) cc_final: 0.9098 (mp10) REVERT: A 197 LYS cc_start: 0.9201 (tptt) cc_final: 0.8877 (mmtt) REVERT: A 285 ASP cc_start: 0.9870 (m-30) cc_final: 0.9664 (m-30) REVERT: A 343 ASN cc_start: 0.8728 (m-40) cc_final: 0.7992 (t0) REVERT: A 361 ASN cc_start: 0.9251 (t0) cc_final: 0.8979 (t0) REVERT: A 411 LEU cc_start: 0.9565 (mt) cc_final: 0.9255 (pp) REVERT: B 10 LYS cc_start: 0.9493 (mtmm) cc_final: 0.9235 (mmtm) REVERT: B 79 GLN cc_start: 0.8270 (tp-100) cc_final: 0.7738 (tm-30) REVERT: B 88 MET cc_start: 0.8273 (mpp) cc_final: 0.7965 (pmm) REVERT: B 201 PHE cc_start: 0.9403 (t80) cc_final: 0.9134 (t80) REVERT: B 242 GLU cc_start: 0.9674 (mp0) cc_final: 0.9329 (mp0) REVERT: B 341 LYS cc_start: 0.9509 (ptmt) cc_final: 0.9292 (pttp) REVERT: B 368 LEU cc_start: 0.9104 (tp) cc_final: 0.8902 (tp) REVERT: C 33 LEU cc_start: 0.9178 (mp) cc_final: 0.8285 (tp) REVERT: C 38 ILE cc_start: 0.9335 (mm) cc_final: 0.8127 (pt) REVERT: C 88 MET cc_start: 0.9659 (mmm) cc_final: 0.9086 (tpp) REVERT: C 102 GLN cc_start: 0.8449 (tp-100) cc_final: 0.8087 (tp40) REVERT: C 103 MET cc_start: 0.4936 (tpp) cc_final: 0.4224 (tpp) REVERT: C 181 TYR cc_start: 0.9043 (t80) cc_final: 0.8802 (t80) REVERT: C 188 TYR cc_start: 0.9415 (t80) cc_final: 0.9014 (t80) REVERT: C 191 PRO cc_start: 0.8924 (Cg_exo) cc_final: 0.8073 (Cg_endo) REVERT: C 242 GLU cc_start: 0.9516 (mm-30) cc_final: 0.8959 (tp30) REVERT: C 246 ARG cc_start: 0.9263 (mpt180) cc_final: 0.8558 (mmt180) REVERT: C 270 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8835 (mp0) REVERT: C 279 ILE cc_start: 0.9060 (pt) cc_final: 0.8469 (pt) REVERT: C 354 THR cc_start: 0.8681 (p) cc_final: 0.8407 (p) REVERT: D 33 LEU cc_start: 0.9646 (mp) cc_final: 0.9434 (tt) REVERT: D 103 MET cc_start: 0.8874 (tpt) cc_final: 0.8514 (tpp) REVERT: D 105 GLU cc_start: 0.8654 (tt0) cc_final: 0.8078 (pm20) REVERT: D 117 ASP cc_start: 0.9249 (m-30) cc_final: 0.8313 (m-30) REVERT: D 152 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8812 (mm-30) REVERT: D 169 SER cc_start: 0.9487 (t) cc_final: 0.9118 (p) REVERT: D 175 ASP cc_start: 0.9119 (m-30) cc_final: 0.8855 (p0) REVERT: D 176 ASN cc_start: 0.9762 (m-40) cc_final: 0.9161 (p0) REVERT: D 183 HIS cc_start: 0.9273 (t70) cc_final: 0.8992 (t70) REVERT: D 184 GLU cc_start: 0.8509 (pm20) cc_final: 0.8277 (pm20) REVERT: D 188 TYR cc_start: 0.9240 (t80) cc_final: 0.8473 (t80) REVERT: D 192 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8616 (mm-30) REVERT: D 197 LYS cc_start: 0.9770 (mmmm) cc_final: 0.9557 (mmmm) REVERT: D 254 ASP cc_start: 0.9511 (m-30) cc_final: 0.8474 (p0) REVERT: D 255 VAL cc_start: 0.9776 (p) cc_final: 0.9277 (m) REVERT: D 264 LEU cc_start: 0.9445 (mp) cc_final: 0.9167 (mt) REVERT: D 277 ILE cc_start: 0.9143 (mm) cc_final: 0.8359 (mm) REVERT: P 10 ASP cc_start: 0.9384 (p0) cc_final: 0.9087 (p0) REVERT: P 18 ASN cc_start: 0.8267 (p0) cc_final: 0.7885 (p0) REVERT: P 20 GLN cc_start: 0.9290 (mp10) cc_final: 0.9022 (pp30) REVERT: P 89 HIS cc_start: 0.9196 (m90) cc_final: 0.8687 (m90) REVERT: Q 16 MET cc_start: 0.7026 (mmp) cc_final: 0.5701 (tpp) REVERT: Q 31 ARG cc_start: 0.9288 (mmm160) cc_final: 0.8859 (tpp80) REVERT: Q 88 HIS cc_start: 0.6856 (t-170) cc_final: 0.6612 (t-170) REVERT: R 16 MET cc_start: 0.8064 (mmm) cc_final: 0.7675 (mmm) REVERT: R 33 PHE cc_start: 0.7106 (m-80) cc_final: 0.6896 (m-80) REVERT: R 72 ASP cc_start: 0.8328 (t0) cc_final: 0.7806 (p0) REVERT: R 80 LYS cc_start: 0.8163 (mptt) cc_final: 0.7741 (mptt) REVERT: R 117 ASP cc_start: 0.8444 (p0) cc_final: 0.7596 (p0) REVERT: S 33 PHE cc_start: 0.8644 (m-10) cc_final: 0.8332 (m-80) REVERT: a 8 GLN cc_start: 0.8658 (tp40) cc_final: 0.8106 (pt0) REVERT: a 48 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7966 (tm-30) REVERT: a 126 HIS cc_start: 0.8410 (t-90) cc_final: 0.7863 (t-170) REVERT: a 308 ILE cc_start: 0.8498 (mp) cc_final: 0.8018 (tp) REVERT: a 316 PHE cc_start: 0.8327 (m-80) cc_final: 0.7760 (m-80) REVERT: b 8 GLN cc_start: 0.9244 (tp40) cc_final: 0.8864 (tt0) REVERT: b 45 ILE cc_start: 0.9869 (pt) cc_final: 0.9369 (mm) REVERT: b 52 MET cc_start: 0.7786 (mmp) cc_final: 0.6914 (mmm) REVERT: b 53 PHE cc_start: 0.8988 (m-80) cc_final: 0.8431 (m-80) REVERT: b 65 MET cc_start: 0.9594 (ptm) cc_final: 0.9326 (ppp) REVERT: b 68 MET cc_start: 0.9066 (mmm) cc_final: 0.8361 (mmm) REVERT: b 97 TYR cc_start: 0.9561 (m-80) cc_final: 0.9241 (m-80) REVERT: b 102 GLN cc_start: 0.9698 (tt0) cc_final: 0.9476 (tp40) REVERT: b 127 LYS cc_start: 0.9447 (ttpp) cc_final: 0.9070 (ttpp) REVERT: b 129 GLU cc_start: 0.9014 (pt0) cc_final: 0.8733 (pt0) REVERT: b 139 ARG cc_start: 0.9653 (ttm-80) cc_final: 0.9420 (ttm110) REVERT: b 272 LEU cc_start: 0.9765 (tp) cc_final: 0.9562 (tp) REVERT: b 274 GLU cc_start: 0.9624 (tp30) cc_final: 0.9200 (tp30) REVERT: b 276 LYS cc_start: 0.9460 (mtmt) cc_final: 0.9064 (mttt) REVERT: b 287 ASP cc_start: 0.9494 (p0) cc_final: 0.9256 (p0) REVERT: b 300 ASP cc_start: 0.9493 (t0) cc_final: 0.9291 (t0) REVERT: b 306 GLN cc_start: 0.9609 (pt0) cc_final: 0.9206 (pm20) REVERT: b 358 ASN cc_start: 0.9640 (m-40) cc_final: 0.8642 (t0) REVERT: b 390 ARG cc_start: 0.9085 (tpt170) cc_final: 0.8696 (tpt-90) REVERT: c 52 MET cc_start: 0.8533 (mmm) cc_final: 0.8169 (mmm) REVERT: c 53 PHE cc_start: 0.9339 (m-80) cc_final: 0.8949 (m-80) REVERT: c 99 ILE cc_start: 0.9858 (pt) cc_final: 0.9590 (mm) REVERT: c 100 LEU cc_start: 0.9047 (tp) cc_final: 0.8837 (tp) REVERT: c 300 ASP cc_start: 0.9588 (t0) cc_final: 0.9325 (t0) REVERT: c 306 GLN cc_start: 0.9162 (pm20) cc_final: 0.8636 (pm20) REVERT: c 316 PHE cc_start: 0.8766 (m-80) cc_final: 0.8449 (m-80) REVERT: c 323 LEU cc_start: 0.9321 (tt) cc_final: 0.9117 (tt) REVERT: c 371 CYS cc_start: 0.9453 (m) cc_final: 0.9178 (p) REVERT: d 41 HIS cc_start: 0.8838 (m90) cc_final: 0.8543 (m90) REVERT: d 53 PHE cc_start: 0.8959 (m-80) cc_final: 0.8401 (m-10) REVERT: d 98 TYR cc_start: 0.9525 (m-10) cc_final: 0.9093 (m-10) REVERT: d 127 LYS cc_start: 0.9703 (tmtt) cc_final: 0.9483 (tptt) REVERT: d 151 ASN cc_start: 0.8716 (p0) cc_final: 0.7797 (p0) REVERT: d 200 LYS cc_start: 0.9760 (tptp) cc_final: 0.9508 (tppt) REVERT: d 274 GLU cc_start: 0.9752 (tp30) cc_final: 0.9277 (mp0) REVERT: d 282 LEU cc_start: 0.9751 (mp) cc_final: 0.9548 (mp) REVERT: d 287 ASP cc_start: 0.9350 (p0) cc_final: 0.8683 (p0) REVERT: d 292 LEU cc_start: 0.9442 (tp) cc_final: 0.9118 (tp) REVERT: d 314 VAL cc_start: 0.9702 (m) cc_final: 0.9262 (p) REVERT: d 316 PHE cc_start: 0.9301 (m-10) cc_final: 0.8789 (m-80) REVERT: d 368 LEU cc_start: 0.9253 (mm) cc_final: 0.8975 (pp) REVERT: d 385 LEU cc_start: 0.9345 (mm) cc_final: 0.9091 (pp) REVERT: d 397 TYR cc_start: 0.8833 (m-80) cc_final: 0.8616 (m-80) REVERT: d 399 LEU cc_start: 0.8570 (mt) cc_final: 0.7915 (mt) outliers start: 6 outliers final: 4 residues processed: 687 average time/residue: 0.2237 time to fit residues: 243.9531 Evaluate side-chains 524 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 520 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 149 optimal weight: 8.9990 chunk 5 optimal weight: 30.0000 chunk 198 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 313 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 325 optimal weight: 20.0000 chunk 238 optimal weight: 9.9990 chunk 423 optimal weight: 8.9990 chunk 27 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 196 GLN ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 131 ASN S 22 ASN ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 HIS a 120 HIS ** a 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 222 GLN ** b 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 402 ASN ** c 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 102 GLN c 160 GLN d 162 HIS d 277 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.076857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.060269 restraints weight = 235057.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.061789 restraints weight = 159527.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.062918 restraints weight = 118965.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.063762 restraints weight = 94653.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.064404 restraints weight = 78739.834| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 36017 Z= 0.241 Angle : 0.802 14.426 49187 Z= 0.414 Chirality : 0.050 0.327 5519 Planarity : 0.006 0.073 6289 Dihedral : 9.628 102.537 5204 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.99 % Favored : 93.99 % Rotamer: Outliers : 0.13 % Allowed : 4.86 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.12), residues: 4473 helix: 0.07 (0.23), residues: 464 sheet: -0.75 (0.14), residues: 1312 loop : -1.00 (0.12), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG R 135 TYR 0.030 0.002 TYR 1 104 PHE 0.033 0.002 PHE b 316 TRP 0.027 0.003 TRP A 244 HIS 0.013 0.002 HIS A 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.24 (35937) covalent geometry : angle 0.78498 / 0.41 (49011) SS BOND : bond 0.00712 / 0.47 ( 64) SS BOND : angle 1.59921 / 1.09 ( 128) hydrogen bonds : bond 0.04284 / 2.81 ( 1319) hydrogen bonds : angle 6.62049 / 4.56 ( 3423) link_BETA1-4 : bond 0.01477 / 0.73 ( 8) link_BETA1-4 : angle 3.90793 / 2.46 ( 24) link_NAG-ASN : bond 0.01648 / 0.79 ( 8) link_NAG-ASN : angle 5.62148 / 4.07 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 624 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 116 PHE cc_start: 0.8650 (m-80) cc_final: 0.7980 (m-80) REVERT: 2 16 GLN cc_start: 0.9762 (mm-40) cc_final: 0.9517 (mm110) REVERT: 2 19 ARG cc_start: 0.9677 (mpt180) cc_final: 0.9437 (mmt-90) REVERT: 2 26 ASN cc_start: 0.9575 (t0) cc_final: 0.9336 (t0) REVERT: 2 57 ILE cc_start: 0.7497 (mp) cc_final: 0.7282 (mp) REVERT: 2 97 TYR cc_start: 0.9417 (m-10) cc_final: 0.9209 (m-80) REVERT: A 2 GLU cc_start: 0.9482 (tm-30) cc_final: 0.9257 (tp30) REVERT: A 24 TYR cc_start: 0.9533 (m-80) cc_final: 0.9182 (m-80) REVERT: A 33 LEU cc_start: 0.9798 (mt) cc_final: 0.9589 (tp) REVERT: A 45 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9042 (mm-30) REVERT: A 103 MET cc_start: 0.9001 (mtp) cc_final: 0.8512 (tpp) REVERT: A 197 LYS cc_start: 0.9199 (tptt) cc_final: 0.8841 (mmtt) REVERT: A 343 ASN cc_start: 0.9052 (m-40) cc_final: 0.8493 (m-40) REVERT: A 361 ASN cc_start: 0.9492 (t0) cc_final: 0.9187 (t0) REVERT: A 411 LEU cc_start: 0.9471 (mt) cc_final: 0.9221 (pp) REVERT: B 50 LYS cc_start: 0.9527 (ttpt) cc_final: 0.8998 (ttpt) REVERT: B 79 GLN cc_start: 0.8343 (tp-100) cc_final: 0.7873 (tm-30) REVERT: B 88 MET cc_start: 0.8707 (mpp) cc_final: 0.8373 (pmm) REVERT: B 123 LYS cc_start: 0.9390 (mmpt) cc_final: 0.9178 (mmmt) REVERT: B 169 SER cc_start: 0.9151 (t) cc_final: 0.8917 (t) REVERT: B 184 GLU cc_start: 0.9047 (pm20) cc_final: 0.8659 (pm20) REVERT: B 242 GLU cc_start: 0.9495 (mp0) cc_final: 0.9250 (mp0) REVERT: B 243 ARG cc_start: 0.9521 (ttm170) cc_final: 0.9269 (ttm170) REVERT: B 246 ARG cc_start: 0.9426 (mmt180) cc_final: 0.8739 (mmt180) REVERT: C 88 MET cc_start: 0.9662 (mmm) cc_final: 0.9189 (tpp) REVERT: C 102 GLN cc_start: 0.8884 (tp-100) cc_final: 0.8624 (tp40) REVERT: C 103 MET cc_start: 0.6895 (tpp) cc_final: 0.6339 (tpp) REVERT: C 105 GLU cc_start: 0.8587 (pt0) cc_final: 0.8385 (pp20) REVERT: C 113 GLU cc_start: 0.9422 (mp0) cc_final: 0.9035 (mp0) REVERT: C 181 TYR cc_start: 0.9240 (t80) cc_final: 0.8832 (t80) REVERT: C 188 TYR cc_start: 0.9276 (t80) cc_final: 0.8712 (t80) REVERT: C 191 PRO cc_start: 0.9212 (Cg_exo) cc_final: 0.8853 (Cg_endo) REVERT: C 220 LEU cc_start: 0.8871 (mt) cc_final: 0.8434 (mt) REVERT: C 221 LYS cc_start: 0.9464 (mmpt) cc_final: 0.9091 (mmtm) REVERT: C 242 GLU cc_start: 0.9528 (mm-30) cc_final: 0.8896 (tp30) REVERT: C 246 ARG cc_start: 0.9384 (mpt180) cc_final: 0.8380 (mmt180) REVERT: C 270 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8778 (mp0) REVERT: C 303 LYS cc_start: 0.9421 (mppt) cc_final: 0.9123 (mtmm) REVERT: C 395 HIS cc_start: 0.6955 (p-80) cc_final: 0.6524 (p-80) REVERT: D 2 GLU cc_start: 0.9621 (pm20) cc_final: 0.9162 (tp30) REVERT: D 33 LEU cc_start: 0.9647 (mp) cc_final: 0.9437 (tp) REVERT: D 103 MET cc_start: 0.8938 (tpt) cc_final: 0.8628 (tpp) REVERT: D 117 ASP cc_start: 0.9321 (m-30) cc_final: 0.8665 (m-30) REVERT: D 152 GLU cc_start: 0.9319 (mm-30) cc_final: 0.9073 (mp0) REVERT: D 175 ASP cc_start: 0.9151 (m-30) cc_final: 0.8654 (m-30) REVERT: D 176 ASN cc_start: 0.9808 (m-40) cc_final: 0.9384 (p0) REVERT: D 183 HIS cc_start: 0.9353 (t70) cc_final: 0.9117 (t70) REVERT: D 188 TYR cc_start: 0.9153 (t80) cc_final: 0.8328 (t80) REVERT: D 192 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8540 (mm-30) REVERT: D 243 ARG cc_start: 0.9624 (ttt90) cc_final: 0.9351 (ttm-80) REVERT: D 246 ARG cc_start: 0.9294 (mtm-85) cc_final: 0.8838 (ptt-90) REVERT: D 254 ASP cc_start: 0.9565 (m-30) cc_final: 0.8704 (p0) REVERT: D 277 ILE cc_start: 0.9332 (mm) cc_final: 0.8732 (mm) REVERT: P 74 LEU cc_start: 0.8733 (mt) cc_final: 0.8521 (mt) REVERT: Q 16 MET cc_start: 0.7582 (mmp) cc_final: 0.7373 (mmp) REVERT: Q 31 ARG cc_start: 0.9377 (mmm160) cc_final: 0.8902 (tpp80) REVERT: R 15 ILE cc_start: 0.9182 (tt) cc_final: 0.8867 (tt) REVERT: R 16 MET cc_start: 0.8139 (mmm) cc_final: 0.7921 (mmm) REVERT: R 72 ASP cc_start: 0.8951 (t0) cc_final: 0.8535 (p0) REVERT: R 80 LYS cc_start: 0.8325 (mptt) cc_final: 0.7370 (mptt) REVERT: S 33 PHE cc_start: 0.8714 (m-10) cc_final: 0.8280 (m-80) REVERT: a 41 HIS cc_start: 0.9488 (m90) cc_final: 0.9240 (m170) REVERT: a 126 HIS cc_start: 0.8609 (t-90) cc_final: 0.8036 (t-170) REVERT: a 260 LYS cc_start: 0.9579 (tppt) cc_final: 0.9341 (mmmt) REVERT: a 316 PHE cc_start: 0.8776 (m-80) cc_final: 0.8334 (m-80) REVERT: b 8 GLN cc_start: 0.9373 (tp40) cc_final: 0.8927 (tt0) REVERT: b 45 ILE cc_start: 0.9858 (pt) cc_final: 0.9434 (mm) REVERT: b 52 MET cc_start: 0.8634 (mmp) cc_final: 0.7842 (mmm) REVERT: b 53 PHE cc_start: 0.8993 (m-80) cc_final: 0.8378 (m-80) REVERT: b 65 MET cc_start: 0.9591 (ptm) cc_final: 0.9345 (ppp) REVERT: b 68 MET cc_start: 0.9160 (mmm) cc_final: 0.8946 (mmm) REVERT: b 100 LEU cc_start: 0.9831 (tp) cc_final: 0.9343 (mt) REVERT: b 274 GLU cc_start: 0.9679 (tp30) cc_final: 0.9438 (mp0) REVERT: b 287 ASP cc_start: 0.9455 (p0) cc_final: 0.9170 (p0) REVERT: b 302 ASN cc_start: 0.9622 (t0) cc_final: 0.9290 (t0) REVERT: b 306 GLN cc_start: 0.9632 (pt0) cc_final: 0.9263 (pm20) REVERT: b 390 ARG cc_start: 0.8992 (tpt170) cc_final: 0.8582 (tpt-90) REVERT: c 47 ILE cc_start: 0.9904 (pt) cc_final: 0.9697 (mp) REVERT: c 52 MET cc_start: 0.8679 (mmm) cc_final: 0.8449 (mmm) REVERT: c 53 PHE cc_start: 0.9274 (m-80) cc_final: 0.8765 (m-80) REVERT: c 99 ILE cc_start: 0.9927 (pt) cc_final: 0.9578 (mm) REVERT: c 287 ASP cc_start: 0.9494 (p0) cc_final: 0.9009 (p0) REVERT: c 300 ASP cc_start: 0.9468 (t0) cc_final: 0.9021 (t0) REVERT: c 302 ASN cc_start: 0.9271 (p0) cc_final: 0.9021 (p0) REVERT: c 306 GLN cc_start: 0.9163 (pm20) cc_final: 0.8772 (pm20) REVERT: c 371 CYS cc_start: 0.9633 (m) cc_final: 0.9411 (p) REVERT: c 397 TYR cc_start: 0.9103 (m-80) cc_final: 0.8630 (m-80) REVERT: c 414 CYS cc_start: 0.9427 (t) cc_final: 0.9041 (m) REVERT: d 41 HIS cc_start: 0.9219 (m90) cc_final: 0.8598 (m90) REVERT: d 53 PHE cc_start: 0.9054 (m-80) cc_final: 0.8461 (m-10) REVERT: d 151 ASN cc_start: 0.8965 (p0) cc_final: 0.8604 (p0) REVERT: d 274 GLU cc_start: 0.9739 (tp30) cc_final: 0.9442 (tm-30) REVERT: d 287 ASP cc_start: 0.9326 (p0) cc_final: 0.8841 (p0) REVERT: d 314 VAL cc_start: 0.9741 (m) cc_final: 0.9520 (p) REVERT: d 368 LEU cc_start: 0.9464 (mm) cc_final: 0.9208 (pp) REVERT: d 397 TYR cc_start: 0.8999 (m-80) cc_final: 0.8737 (m-80) REVERT: d 399 LEU cc_start: 0.8716 (mt) cc_final: 0.8025 (mt) outliers start: 5 outliers final: 0 residues processed: 629 average time/residue: 0.2348 time to fit residues: 234.6285 Evaluate side-chains 494 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 90 optimal weight: 6.9990 chunk 372 optimal weight: 4.9990 chunk 230 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 351 optimal weight: 0.0170 chunk 233 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 17 optimal weight: 50.0000 chunk 6 optimal weight: 0.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 HIS ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN C 30 GLN C 395 HIS ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN D 363 HIS Q 86 ASN Q 144 ASN R 89 HIS ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 162 HIS ** a 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 222 GLN ** a 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 277 HIS ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 236 ASN ** 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 = 0.3598 r_free = 0.3598 target = 0.081153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.063527 restraints weight = 203476.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.064868 restraints weight = 144854.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.065857 restraints weight = 113301.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.066539 restraints weight = 94484.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.067055 restraints weight = 82823.132| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.6546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36017 Z= 0.147 Angle : 0.720 12.633 49187 Z= 0.368 Chirality : 0.049 0.346 5519 Planarity : 0.006 0.080 6289 Dihedral : 9.223 103.689 5204 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.25 % Favored : 94.72 % Rotamer: Outliers : 0.03 % Allowed : 2.57 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: -1.21 (0.12), residues: 4473 helix: 0.13 (0.23), residues: 464 sheet: -0.69 (0.14), residues: 1340 loop : -1.01 (0.12), residues: 2669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG b 139 TYR 0.022 0.002 TYR b 360 PHE 0.034 0.002 PHE A 421 TRP 0.026 0.002 TRP C 89 HIS 0.011 0.001 HIS R 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (35937) covalent geometry : angle 0.70355 / 0.36 (49011) SS BOND : bond 0.00399 / 0.24 ( 64) SS BOND : angle 1.52689 / 1.03 ( 128) hydrogen bonds : bond 0.03823 / 2.50 ( 1319) hydrogen bonds : angle 6.32771 / 4.35 ( 3423) link_BETA1-4 : bond 0.00944 / 0.43 ( 8) link_BETA1-4 : angle 3.52539 / 2.22 ( 24) link_NAG-ASN : bond 0.00679 / 0.34 ( 8) link_NAG-ASN : angle 5.13325 / 3.66 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 618 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 116 PHE cc_start: 0.8680 (m-80) cc_final: 0.8007 (m-80) REVERT: 1 192 TYR cc_start: 0.9523 (m-80) cc_final: 0.9167 (m-80) REVERT: 2 19 ARG cc_start: 0.9627 (mpt180) cc_final: 0.9407 (mmt-90) REVERT: 2 25 ASN cc_start: 0.9267 (m-40) cc_final: 0.8570 (p0) REVERT: 2 26 ASN cc_start: 0.9547 (t0) cc_final: 0.9279 (t0) REVERT: A 2 GLU cc_start: 0.9474 (tm-30) cc_final: 0.9270 (tp30) REVERT: A 24 TYR cc_start: 0.9584 (m-80) cc_final: 0.9191 (m-80) REVERT: A 33 LEU cc_start: 0.9836 (mt) cc_final: 0.9545 (tp) REVERT: A 36 THR cc_start: 0.9772 (p) cc_final: 0.9529 (p) REVERT: A 45 GLU cc_start: 0.9349 (mm-30) cc_final: 0.9133 (mm-30) REVERT: A 103 MET cc_start: 0.9149 (mtp) cc_final: 0.8740 (tpt) REVERT: A 197 LYS cc_start: 0.9259 (tptt) cc_final: 0.8917 (mmtt) REVERT: A 285 ASP cc_start: 0.9871 (m-30) cc_final: 0.9538 (m-30) REVERT: A 361 ASN cc_start: 0.9491 (t0) cc_final: 0.9156 (t0) REVERT: A 411 LEU cc_start: 0.9573 (mt) cc_final: 0.9334 (pp) REVERT: B 50 LYS cc_start: 0.9485 (ttpt) cc_final: 0.8964 (ttpt) REVERT: B 79 GLN cc_start: 0.8400 (tp-100) cc_final: 0.7993 (tm-30) REVERT: B 88 MET cc_start: 0.8737 (mpp) cc_final: 0.8390 (pmm) REVERT: B 169 SER cc_start: 0.9152 (t) cc_final: 0.8875 (t) REVERT: B 183 HIS cc_start: 0.9304 (m-70) cc_final: 0.8939 (m-70) REVERT: B 246 ARG cc_start: 0.9453 (mmt180) cc_final: 0.8961 (mmt180) REVERT: C 2 GLU cc_start: 0.9534 (pm20) cc_final: 0.8980 (tp30) REVERT: C 102 GLN cc_start: 0.8846 (tp-100) cc_final: 0.8604 (tp40) REVERT: C 103 MET cc_start: 0.6806 (tpp) cc_final: 0.6403 (tpp) REVERT: C 176 ASN cc_start: 0.9623 (m-40) cc_final: 0.9322 (t0) REVERT: C 188 TYR cc_start: 0.9250 (t80) cc_final: 0.8601 (t80) REVERT: C 189 ASP cc_start: 0.9504 (t0) cc_final: 0.9273 (t0) REVERT: C 191 PRO cc_start: 0.9135 (Cg_exo) cc_final: 0.8450 (Cg_endo) REVERT: C 220 LEU cc_start: 0.8853 (mt) cc_final: 0.8354 (mt) REVERT: C 221 LYS cc_start: 0.9358 (mmpt) cc_final: 0.8959 (mmtm) REVERT: C 242 GLU cc_start: 0.9525 (mm-30) cc_final: 0.8916 (tp30) REVERT: C 246 ARG cc_start: 0.9364 (mpt180) cc_final: 0.8433 (mmt180) REVERT: C 270 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8823 (mp0) REVERT: C 283 ILE cc_start: 0.9048 (mm) cc_final: 0.8636 (mm) REVERT: C 303 LYS cc_start: 0.9387 (mppt) cc_final: 0.9029 (mtmm) REVERT: C 390 ASP cc_start: 0.9342 (p0) cc_final: 0.9038 (p0) REVERT: C 395 HIS cc_start: 0.6724 (p90) cc_final: 0.6509 (p90) REVERT: D 2 GLU cc_start: 0.9663 (pm20) cc_final: 0.9237 (tp30) REVERT: D 33 LEU cc_start: 0.9609 (mp) cc_final: 0.9340 (tt) REVERT: D 103 MET cc_start: 0.9000 (tpt) cc_final: 0.8677 (tpp) REVERT: D 117 ASP cc_start: 0.9337 (m-30) cc_final: 0.8675 (m-30) REVERT: D 152 GLU cc_start: 0.9378 (mm-30) cc_final: 0.9161 (mp0) REVERT: D 175 ASP cc_start: 0.9167 (m-30) cc_final: 0.8742 (m-30) REVERT: D 176 ASN cc_start: 0.9836 (m-40) cc_final: 0.9438 (p0) REVERT: D 183 HIS cc_start: 0.9380 (t70) cc_final: 0.9044 (t70) REVERT: D 184 GLU cc_start: 0.8692 (pm20) cc_final: 0.8298 (pm20) REVERT: D 188 TYR cc_start: 0.9102 (t80) cc_final: 0.8847 (t80) REVERT: D 197 LYS cc_start: 0.9759 (mmmm) cc_final: 0.9554 (mmmm) REVERT: D 243 ARG cc_start: 0.9620 (ttt90) cc_final: 0.9124 (tpt170) REVERT: D 254 ASP cc_start: 0.9540 (m-30) cc_final: 0.8873 (p0) REVERT: D 264 LEU cc_start: 0.9415 (mt) cc_final: 0.9161 (mt) REVERT: D 277 ILE cc_start: 0.9323 (mm) cc_final: 0.8725 (mm) REVERT: Q 16 MET cc_start: 0.7829 (mmp) cc_final: 0.7519 (mmp) REVERT: Q 31 ARG cc_start: 0.9390 (mmm160) cc_final: 0.8899 (tpp80) REVERT: Q 33 PHE cc_start: 0.6983 (m-80) cc_final: 0.6733 (m-80) REVERT: Q 144 ASN cc_start: 0.7251 (m110) cc_final: 0.7027 (m110) REVERT: R 26 CYS cc_start: 0.7740 (t) cc_final: 0.7113 (p) REVERT: R 72 ASP cc_start: 0.8940 (t0) cc_final: 0.8657 (p0) REVERT: S 33 PHE cc_start: 0.8661 (m-10) cc_final: 0.8348 (m-80) REVERT: a 8 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8727 (tm-30) REVERT: a 48 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7911 (tm-30) REVERT: a 126 HIS cc_start: 0.8831 (t-90) cc_final: 0.8135 (t-170) REVERT: a 128 VAL cc_start: 0.9165 (p) cc_final: 0.8927 (m) REVERT: a 260 LYS cc_start: 0.9560 (tppt) cc_final: 0.9206 (tppt) REVERT: a 278 ARG cc_start: 0.8438 (ttm110) cc_final: 0.7680 (mtp85) REVERT: a 302 ASN cc_start: 0.8925 (t0) cc_final: 0.8095 (p0) REVERT: a 316 PHE cc_start: 0.8635 (m-80) cc_final: 0.8210 (m-80) REVERT: b 8 GLN cc_start: 0.9299 (tp40) cc_final: 0.8880 (tt0) REVERT: b 41 HIS cc_start: 0.9522 (m170) cc_final: 0.9144 (m90) REVERT: b 45 ILE cc_start: 0.9848 (pt) cc_final: 0.9446 (mm) REVERT: b 52 MET cc_start: 0.8760 (mmp) cc_final: 0.7973 (mmm) REVERT: b 53 PHE cc_start: 0.9011 (m-80) cc_final: 0.8420 (m-80) REVERT: b 65 MET cc_start: 0.9579 (ptm) cc_final: 0.9355 (ppp) REVERT: b 68 MET cc_start: 0.9098 (mmm) cc_final: 0.8807 (mmm) REVERT: b 100 LEU cc_start: 0.9783 (tp) cc_final: 0.9281 (mt) REVERT: b 107 ASP cc_start: 0.9506 (p0) cc_final: 0.8873 (p0) REVERT: b 274 GLU cc_start: 0.9664 (tp30) cc_final: 0.9426 (mp0) REVERT: b 287 ASP cc_start: 0.9511 (p0) cc_final: 0.9243 (p0) REVERT: b 302 ASN cc_start: 0.9625 (t0) cc_final: 0.9307 (t0) REVERT: b 306 GLN cc_start: 0.9586 (pt0) cc_final: 0.9247 (pm20) REVERT: b 404 GLN cc_start: 0.4140 (tm-30) cc_final: 0.3931 (tm-30) REVERT: c 36 VAL cc_start: 0.9585 (t) cc_final: 0.9374 (t) REVERT: c 47 ILE cc_start: 0.9882 (pt) cc_final: 0.9676 (mp) REVERT: c 53 PHE cc_start: 0.9349 (m-80) cc_final: 0.8967 (m-80) REVERT: c 99 ILE cc_start: 0.9912 (pt) cc_final: 0.9576 (mm) REVERT: c 287 ASP cc_start: 0.9500 (p0) cc_final: 0.8963 (p0) REVERT: c 300 ASP cc_start: 0.9462 (t0) cc_final: 0.9018 (t0) REVERT: c 302 ASN cc_start: 0.9192 (p0) cc_final: 0.8961 (p0) REVERT: c 304 THR cc_start: 0.9489 (p) cc_final: 0.9230 (p) REVERT: c 306 GLN cc_start: 0.9069 (pm20) cc_final: 0.8561 (pm20) REVERT: c 371 CYS cc_start: 0.9691 (m) cc_final: 0.9473 (p) REVERT: d 41 HIS cc_start: 0.9184 (m90) cc_final: 0.8508 (m90) REVERT: d 53 PHE cc_start: 0.9054 (m-80) cc_final: 0.8486 (m-10) REVERT: d 151 ASN cc_start: 0.8836 (p0) cc_final: 0.8376 (p0) REVERT: d 252 LEU cc_start: 0.9629 (mp) cc_final: 0.9165 (tt) REVERT: d 274 GLU cc_start: 0.9751 (tp30) cc_final: 0.9412 (tm-30) REVERT: d 287 ASP cc_start: 0.9375 (p0) cc_final: 0.8991 (p0) REVERT: d 368 LEU cc_start: 0.9425 (mm) cc_final: 0.9169 (pp) outliers start: 1 outliers final: 1 residues processed: 619 average time/residue: 0.2239 time to fit residues: 221.8392 Evaluate side-chains 497 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 496 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 309 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 207 optimal weight: 30.0000 chunk 380 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 74 optimal weight: 30.0000 chunk 400 optimal weight: 6.9990 chunk 326 optimal weight: 9.9990 chunk 216 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 329 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 HIS ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 86 ASN ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 HIS R 86 ASN R 89 HIS S 22 ASN ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 222 GLN ** b 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 102 GLN b 277 HIS b 288 HIS ** c 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 82 HIS ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.067326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.051741 restraints weight = 251345.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.053093 restraints weight = 161301.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.054067 restraints weight = 115213.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.054832 restraints weight = 89903.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055377 restraints weight = 73441.629| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.8048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 36017 Z= 0.279 Angle : 0.851 13.339 49187 Z= 0.438 Chirality : 0.050 0.394 5519 Planarity : 0.007 0.069 6289 Dihedral : 9.376 102.015 5204 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 24.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.46 % Favored : 93.49 % Rotamer: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.12), residues: 4473 helix: -0.18 (0.23), residues: 470 sheet: -0.79 (0.14), residues: 1297 loop : -1.03 (0.12), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG c 388 TYR 0.032 0.003 TYR c 97 PHE 0.039 0.003 PHE A 421 TRP 0.026 0.002 TRP C 142 HIS 0.017 0.002 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.28 (35937) covalent geometry : angle 0.83484 / 0.43 (49011) SS BOND : bond 0.00767 / 0.46 ( 64) SS BOND : angle 1.90117 / 1.27 ( 128) hydrogen bonds : bond 0.04356 / 2.84 ( 1319) hydrogen bonds : angle 6.70558 / 4.64 ( 3423) link_BETA1-4 : bond 0.00936 / 0.45 ( 8) link_BETA1-4 : angle 3.56830 / 2.28 ( 24) link_NAG-ASN : bond 0.00758 / 0.37 ( 8) link_NAG-ASN : angle 5.47692 / 4.10 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 591 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 116 PHE cc_start: 0.8793 (m-80) cc_final: 0.7931 (m-80) REVERT: A 24 TYR cc_start: 0.9571 (m-80) cc_final: 0.9347 (m-10) REVERT: A 36 THR cc_start: 0.9793 (p) cc_final: 0.9585 (p) REVERT: A 45 GLU cc_start: 0.9377 (mm-30) cc_final: 0.9042 (tp30) REVERT: A 103 MET cc_start: 0.9130 (mtp) cc_final: 0.8766 (tpp) REVERT: A 178 VAL cc_start: 0.9628 (t) cc_final: 0.9358 (m) REVERT: A 197 LYS cc_start: 0.9411 (tptt) cc_final: 0.9099 (mmtm) REVERT: A 411 LEU cc_start: 0.9557 (mt) cc_final: 0.9316 (pp) REVERT: B 13 ILE cc_start: 0.9582 (pt) cc_final: 0.9041 (mt) REVERT: B 79 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8142 (tm-30) REVERT: B 175 ASP cc_start: 0.9140 (p0) cc_final: 0.8859 (p0) REVERT: B 197 LYS cc_start: 0.9534 (mmmt) cc_final: 0.9158 (mmtt) REVERT: B 242 GLU cc_start: 0.9573 (mp0) cc_final: 0.9307 (mp0) REVERT: B 243 ARG cc_start: 0.9481 (ttm170) cc_final: 0.9279 (ttm-80) REVERT: B 246 ARG cc_start: 0.9457 (mmt180) cc_final: 0.8892 (mmt180) REVERT: B 254 ASP cc_start: 0.9660 (m-30) cc_final: 0.9088 (p0) REVERT: C 2 GLU cc_start: 0.9503 (pm20) cc_final: 0.9005 (tp30) REVERT: C 88 MET cc_start: 0.9511 (mmm) cc_final: 0.9225 (tpp) REVERT: C 103 MET cc_start: 0.7924 (tpp) cc_final: 0.7633 (tpp) REVERT: C 188 TYR cc_start: 0.9178 (t80) cc_final: 0.8640 (t80) REVERT: C 189 ASP cc_start: 0.9594 (t0) cc_final: 0.9374 (t0) REVERT: C 197 LYS cc_start: 0.9886 (mppt) cc_final: 0.9663 (mmtm) REVERT: C 242 GLU cc_start: 0.9580 (mm-30) cc_final: 0.9038 (tp30) REVERT: C 254 ASP cc_start: 0.9169 (m-30) cc_final: 0.8958 (m-30) REVERT: C 270 GLU cc_start: 0.9280 (mt-10) cc_final: 0.8709 (mp0) REVERT: C 306 GLU cc_start: 0.9203 (tp30) cc_final: 0.8715 (tm-30) REVERT: C 439 HIS cc_start: 0.9213 (m90) cc_final: 0.8942 (m-70) REVERT: D 2 GLU cc_start: 0.9656 (pm20) cc_final: 0.9216 (tp30) REVERT: D 33 LEU cc_start: 0.9600 (mp) cc_final: 0.9255 (tp) REVERT: D 103 MET cc_start: 0.9011 (tpt) cc_final: 0.8666 (tpp) REVERT: D 117 ASP cc_start: 0.9394 (m-30) cc_final: 0.9121 (m-30) REVERT: D 175 ASP cc_start: 0.9075 (m-30) cc_final: 0.8643 (m-30) REVERT: D 176 ASN cc_start: 0.9798 (m-40) cc_final: 0.9387 (p0) REVERT: D 183 HIS cc_start: 0.9444 (t70) cc_final: 0.9171 (t70) REVERT: D 188 TYR cc_start: 0.9242 (t80) cc_final: 0.8953 (t80) REVERT: D 192 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8587 (mm-30) REVERT: D 243 ARG cc_start: 0.9617 (ttt90) cc_final: 0.8807 (ttm-80) REVERT: D 246 ARG cc_start: 0.9244 (mtm-85) cc_final: 0.8983 (mtm180) REVERT: D 264 LEU cc_start: 0.9488 (mt) cc_final: 0.9268 (mt) REVERT: D 395 HIS cc_start: 0.7665 (p90) cc_final: 0.7384 (p-80) REVERT: Q 16 MET cc_start: 0.8231 (mmp) cc_final: 0.7513 (mmp) REVERT: Q 31 ARG cc_start: 0.9402 (mmm160) cc_final: 0.9011 (tpp80) REVERT: Q 88 HIS cc_start: 0.7392 (t-170) cc_final: 0.7138 (t-170) REVERT: Q 89 HIS cc_start: 0.7552 (m90) cc_final: 0.7036 (m90) REVERT: Q 115 ILE cc_start: 0.9005 (mp) cc_final: 0.8533 (mp) REVERT: Q 144 ASN cc_start: 0.7328 (m110) cc_final: 0.7026 (m110) REVERT: R 15 ILE cc_start: 0.9084 (tt) cc_final: 0.8791 (tt) REVERT: R 26 CYS cc_start: 0.8378 (t) cc_final: 0.7411 (p) REVERT: R 53 LYS cc_start: 0.8947 (tppt) cc_final: 0.8661 (tppt) REVERT: R 80 LYS cc_start: 0.8311 (mptt) cc_final: 0.7014 (mptt) REVERT: R 85 TYR cc_start: 0.7556 (m-10) cc_final: 0.7317 (m-10) REVERT: R 87 TRP cc_start: 0.7221 (p90) cc_final: 0.6818 (p90) REVERT: R 121 ARG cc_start: 0.8655 (ttp-110) cc_final: 0.8391 (ttp-110) REVERT: S 33 PHE cc_start: 0.8628 (m-10) cc_final: 0.8423 (m-80) REVERT: S 85 TYR cc_start: 0.5226 (m-10) cc_final: 0.4949 (m-10) REVERT: a 8 GLN cc_start: 0.9234 (tm-30) cc_final: 0.8996 (tm-30) REVERT: a 165 GLU cc_start: 0.8082 (tt0) cc_final: 0.7661 (tp30) REVERT: a 166 MET cc_start: 0.3867 (pmm) cc_final: 0.2974 (pmm) REVERT: a 203 ASP cc_start: 0.9884 (m-30) cc_final: 0.9678 (t70) REVERT: a 260 LYS cc_start: 0.9592 (tppt) cc_final: 0.9297 (tppt) REVERT: a 384 TRP cc_start: 0.9440 (t-100) cc_final: 0.9192 (t60) REVERT: b 8 GLN cc_start: 0.9416 (tp40) cc_final: 0.8962 (tt0) REVERT: b 45 ILE cc_start: 0.9857 (pt) cc_final: 0.9566 (mm) REVERT: b 52 MET cc_start: 0.9094 (mmp) cc_final: 0.8604 (mmm) REVERT: b 53 PHE cc_start: 0.9143 (m-80) cc_final: 0.8597 (m-80) REVERT: b 68 MET cc_start: 0.9216 (mmm) cc_final: 0.8865 (mmm) REVERT: b 100 LEU cc_start: 0.9771 (tp) cc_final: 0.9277 (mt) REVERT: b 107 ASP cc_start: 0.9439 (p0) cc_final: 0.8970 (p0) REVERT: b 127 LYS cc_start: 0.9675 (tmtt) cc_final: 0.9470 (tptp) REVERT: b 274 GLU cc_start: 0.9733 (tp30) cc_final: 0.9431 (mp0) REVERT: b 287 ASP cc_start: 0.9319 (p0) cc_final: 0.9097 (p0) REVERT: b 302 ASN cc_start: 0.9645 (t0) cc_final: 0.9378 (t0) REVERT: b 306 GLN cc_start: 0.9637 (pt0) cc_final: 0.9211 (pm20) REVERT: b 391 ASN cc_start: 0.9633 (m110) cc_final: 0.9416 (m110) REVERT: c 53 PHE cc_start: 0.9340 (m-80) cc_final: 0.9008 (m-80) REVERT: c 80 ASN cc_start: 0.7998 (t0) cc_final: 0.7720 (t0) REVERT: c 97 TYR cc_start: 0.9015 (m-10) cc_final: 0.8607 (m-10) REVERT: c 99 ILE cc_start: 0.9944 (pt) cc_final: 0.9599 (mp) REVERT: c 139 ARG cc_start: 0.9102 (mtp-110) cc_final: 0.8658 (mtm110) REVERT: c 287 ASP cc_start: 0.9336 (p0) cc_final: 0.9021 (p0) REVERT: c 300 ASP cc_start: 0.9337 (t0) cc_final: 0.8869 (t0) REVERT: c 302 ASN cc_start: 0.9221 (p0) cc_final: 0.8925 (p0) REVERT: c 323 LEU cc_start: 0.9752 (mm) cc_final: 0.9447 (mp) REVERT: c 339 GLU cc_start: 0.8374 (pm20) cc_final: 0.7758 (tp30) REVERT: d 53 PHE cc_start: 0.9146 (m-80) cc_final: 0.8591 (m-10) REVERT: d 68 MET cc_start: 0.9568 (mmm) cc_final: 0.8809 (mmm) REVERT: d 274 GLU cc_start: 0.9771 (tp30) cc_final: 0.9448 (tm-30) REVERT: d 276 LYS cc_start: 0.9468 (mtmt) cc_final: 0.8985 (mtmt) REVERT: d 287 ASP cc_start: 0.9283 (p0) cc_final: 0.8931 (p0) REVERT: d 292 LEU cc_start: 0.9433 (tp) cc_final: 0.8841 (tp) REVERT: d 300 ASP cc_start: 0.9260 (t0) cc_final: 0.9046 (t0) REVERT: d 368 LEU cc_start: 0.9601 (mm) cc_final: 0.9366 (pp) REVERT: d 399 LEU cc_start: 0.8368 (mt) cc_final: 0.7741 (mt) outliers start: 1 outliers final: 0 residues processed: 592 average time/residue: 0.2253 time to fit residues: 213.1287 Evaluate side-chains 440 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 216 optimal weight: 10.0000 chunk 318 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 279 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 303 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 409 optimal weight: 0.5980 chunk 140 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS S 22 ASN ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 222 GLN ** b 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 94 HIS ** c 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 338 GLN ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.067556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.051551 restraints weight = 241165.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.052954 restraints weight = 153864.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.053960 restraints weight = 109317.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.054772 restraints weight = 84311.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.055457 restraints weight = 67527.935| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.8411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 36017 Z= 0.163 Angle : 0.725 12.732 49187 Z= 0.371 Chirality : 0.049 0.362 5519 Planarity : 0.006 0.071 6289 Dihedral : 9.071 101.284 5204 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.52 % Favored : 94.43 % Rotamer: Outliers : 0.03 % Allowed : 1.46 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: -1.26 (0.12), residues: 4473 helix: 0.02 (0.23), residues: 464 sheet: -0.79 (0.13), residues: 1383 loop : -0.98 (0.12), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 139 TYR 0.039 0.002 TYR R 76 PHE 0.037 0.002 PHE A 421 TRP 0.019 0.002 TRP 1 55 HIS 0.010 0.001 HIS a 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (35937) covalent geometry : angle 0.70602 / 0.37 (49011) SS BOND : bond 0.00564 / 0.37 ( 64) SS BOND : angle 1.54209 / 1.07 ( 128) hydrogen bonds : bond 0.03780 / 2.46 ( 1319) hydrogen bonds : angle 6.32623 / 4.36 ( 3423) link_BETA1-4 : bond 0.00937 / 0.44 ( 8) link_BETA1-4 : angle 3.45774 / 2.18 ( 24) link_NAG-ASN : bond 0.00983 / 0.48 ( 8) link_NAG-ASN : angle 5.88271 / 4.26 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 579 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 116 PHE cc_start: 0.8721 (m-80) cc_final: 0.7998 (m-80) REVERT: 2 25 ASN cc_start: 0.9455 (m-40) cc_final: 0.8946 (p0) REVERT: A 24 TYR cc_start: 0.9569 (m-80) cc_final: 0.9336 (m-10) REVERT: A 45 GLU cc_start: 0.9273 (mm-30) cc_final: 0.9000 (tp30) REVERT: A 197 LYS cc_start: 0.9448 (tptt) cc_final: 0.9217 (mmtt) REVERT: A 411 LEU cc_start: 0.9539 (mt) cc_final: 0.9293 (pp) REVERT: B 10 LYS cc_start: 0.9654 (mtmm) cc_final: 0.9446 (mmtt) REVERT: B 13 ILE cc_start: 0.9566 (pt) cc_final: 0.9064 (mt) REVERT: B 79 GLN cc_start: 0.8758 (tp-100) cc_final: 0.8182 (tm-30) REVERT: B 175 ASP cc_start: 0.9224 (p0) cc_final: 0.8883 (p0) REVERT: B 183 HIS cc_start: 0.9137 (m-70) cc_final: 0.8842 (m-70) REVERT: B 197 LYS cc_start: 0.9541 (mmmt) cc_final: 0.9151 (mmmm) REVERT: B 246 ARG cc_start: 0.9470 (mmt180) cc_final: 0.8901 (mmt180) REVERT: B 254 ASP cc_start: 0.9678 (m-30) cc_final: 0.9114 (p0) REVERT: B 279 ILE cc_start: 0.8926 (mp) cc_final: 0.8719 (mp) REVERT: C 2 GLU cc_start: 0.9543 (pm20) cc_final: 0.9076 (tp30) REVERT: C 88 MET cc_start: 0.9519 (mmm) cc_final: 0.9161 (tpp) REVERT: C 125 HIS cc_start: 0.9321 (t-90) cc_final: 0.9091 (t-90) REVERT: C 156 LYS cc_start: 0.9495 (mmpt) cc_final: 0.9114 (tmtt) REVERT: C 188 TYR cc_start: 0.9115 (t80) cc_final: 0.8579 (t80) REVERT: C 189 ASP cc_start: 0.9602 (t0) cc_final: 0.9397 (t0) REVERT: C 197 LYS cc_start: 0.9875 (mppt) cc_final: 0.9635 (mmtm) REVERT: C 220 LEU cc_start: 0.9180 (mt) cc_final: 0.8705 (mt) REVERT: C 242 GLU cc_start: 0.9551 (mm-30) cc_final: 0.9074 (tp30) REVERT: C 270 GLU cc_start: 0.9326 (mt-10) cc_final: 0.8765 (mp0) REVERT: C 306 GLU cc_start: 0.9170 (tp30) cc_final: 0.8602 (tm-30) REVERT: C 368 LEU cc_start: 0.9345 (tt) cc_final: 0.9029 (tt) REVERT: C 421 PHE cc_start: 0.9263 (m-80) cc_final: 0.8711 (m-80) REVERT: C 439 HIS cc_start: 0.9245 (m90) cc_final: 0.9025 (m90) REVERT: D 2 GLU cc_start: 0.9639 (pm20) cc_final: 0.9268 (tp30) REVERT: D 10 LYS cc_start: 0.9467 (mppt) cc_final: 0.9257 (mmtm) REVERT: D 33 LEU cc_start: 0.9655 (mp) cc_final: 0.9287 (tp) REVERT: D 103 MET cc_start: 0.9065 (tpt) cc_final: 0.8719 (tpp) REVERT: D 175 ASP cc_start: 0.9109 (m-30) cc_final: 0.8671 (m-30) REVERT: D 176 ASN cc_start: 0.9820 (m-40) cc_final: 0.9473 (p0) REVERT: D 183 HIS cc_start: 0.9300 (t70) cc_final: 0.9031 (t70) REVERT: D 188 TYR cc_start: 0.9172 (t80) cc_final: 0.8900 (t80) REVERT: D 192 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8691 (mm-30) REVERT: D 243 ARG cc_start: 0.9603 (ttt90) cc_final: 0.9026 (tpt90) REVERT: D 254 ASP cc_start: 0.9550 (m-30) cc_final: 0.8761 (p0) REVERT: P 20 GLN cc_start: 0.9621 (mp10) cc_final: 0.9332 (mp10) REVERT: Q 16 MET cc_start: 0.8197 (mmp) cc_final: 0.7932 (mmp) REVERT: Q 31 ARG cc_start: 0.9265 (mmm160) cc_final: 0.8802 (tpp80) REVERT: Q 115 ILE cc_start: 0.9002 (mp) cc_final: 0.8462 (mp) REVERT: R 10 ASP cc_start: 0.9331 (m-30) cc_final: 0.8978 (p0) REVERT: R 16 MET cc_start: 0.8696 (mmm) cc_final: 0.8228 (tpp) REVERT: R 26 CYS cc_start: 0.8540 (t) cc_final: 0.7620 (p) REVERT: R 54 LYS cc_start: 0.8948 (tttm) cc_final: 0.8658 (tptp) REVERT: R 72 ASP cc_start: 0.8997 (m-30) cc_final: 0.8740 (m-30) REVERT: R 80 LYS cc_start: 0.7902 (mptt) cc_final: 0.7243 (mptt) REVERT: R 87 TRP cc_start: 0.7268 (p90) cc_final: 0.6780 (p90) REVERT: S 33 PHE cc_start: 0.8681 (m-10) cc_final: 0.8274 (m-80) REVERT: a 8 GLN cc_start: 0.9347 (tm-30) cc_final: 0.8961 (pm20) REVERT: a 165 GLU cc_start: 0.8156 (tt0) cc_final: 0.7779 (tp30) REVERT: a 166 MET cc_start: 0.4332 (pmm) cc_final: 0.3405 (pmm) REVERT: a 203 ASP cc_start: 0.9854 (m-30) cc_final: 0.9583 (t70) REVERT: a 260 LYS cc_start: 0.9577 (tppt) cc_final: 0.9288 (tppt) REVERT: a 278 ARG cc_start: 0.8834 (ttm110) cc_final: 0.8005 (mtp85) REVERT: a 302 ASN cc_start: 0.9296 (t0) cc_final: 0.8508 (p0) REVERT: a 384 TRP cc_start: 0.9428 (t-100) cc_final: 0.9139 (t60) REVERT: b 8 GLN cc_start: 0.9388 (tp40) cc_final: 0.8893 (tt0) REVERT: b 41 HIS cc_start: 0.9618 (m170) cc_final: 0.9171 (m90) REVERT: b 45 ILE cc_start: 0.9839 (pt) cc_final: 0.9539 (mm) REVERT: b 52 MET cc_start: 0.9166 (mmp) cc_final: 0.8714 (mmm) REVERT: b 53 PHE cc_start: 0.9069 (m-80) cc_final: 0.8496 (m-80) REVERT: b 68 MET cc_start: 0.9034 (mmm) cc_final: 0.8692 (mmm) REVERT: b 100 LEU cc_start: 0.9743 (tp) cc_final: 0.9224 (mt) REVERT: b 107 ASP cc_start: 0.9429 (p0) cc_final: 0.8953 (p0) REVERT: b 166 MET cc_start: 0.8785 (ptm) cc_final: 0.8581 (ptt) REVERT: b 274 GLU cc_start: 0.9731 (tp30) cc_final: 0.9421 (mp0) REVERT: b 287 ASP cc_start: 0.9362 (p0) cc_final: 0.9142 (p0) REVERT: b 302 ASN cc_start: 0.9702 (t0) cc_final: 0.9329 (t0) REVERT: b 306 GLN cc_start: 0.9637 (pt0) cc_final: 0.9222 (pm20) REVERT: b 391 ASN cc_start: 0.9641 (m110) cc_final: 0.9432 (m110) REVERT: c 52 MET cc_start: 0.9568 (mmp) cc_final: 0.9007 (mmm) REVERT: c 53 PHE cc_start: 0.9465 (m-80) cc_final: 0.9047 (m-80) REVERT: c 80 ASN cc_start: 0.7865 (t0) cc_final: 0.7533 (t0) REVERT: c 97 TYR cc_start: 0.9282 (m-10) cc_final: 0.9037 (m-10) REVERT: c 99 ILE cc_start: 0.9937 (pt) cc_final: 0.9624 (mm) REVERT: c 139 ARG cc_start: 0.9016 (mtp-110) cc_final: 0.8796 (mtp85) REVERT: c 276 LYS cc_start: 0.9730 (mtmt) cc_final: 0.9422 (mppt) REVERT: c 287 ASP cc_start: 0.9329 (p0) cc_final: 0.9011 (p0) REVERT: c 300 ASP cc_start: 0.9400 (t0) cc_final: 0.8991 (t0) REVERT: c 302 ASN cc_start: 0.9200 (p0) cc_final: 0.8927 (p0) REVERT: c 304 THR cc_start: 0.9560 (p) cc_final: 0.9097 (p) REVERT: c 306 GLN cc_start: 0.8620 (pm20) cc_final: 0.8257 (pm20) REVERT: c 338 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7006 (mp10) REVERT: c 339 GLU cc_start: 0.8917 (pm20) cc_final: 0.8473 (pm20) REVERT: c 386 LEU cc_start: 0.9642 (mm) cc_final: 0.9408 (pp) REVERT: d 53 PHE cc_start: 0.9207 (m-80) cc_final: 0.8751 (m-10) REVERT: d 248 PHE cc_start: 0.8459 (m-10) cc_final: 0.8229 (m-10) REVERT: d 274 GLU cc_start: 0.9777 (tp30) cc_final: 0.9501 (tm-30) REVERT: d 276 LYS cc_start: 0.9518 (mtmt) cc_final: 0.9078 (mtmt) REVERT: d 287 ASP cc_start: 0.9363 (p0) cc_final: 0.9067 (p0) REVERT: d 292 LEU cc_start: 0.9495 (tp) cc_final: 0.8918 (tp) REVERT: d 300 ASP cc_start: 0.9281 (t0) cc_final: 0.9055 (t0) REVERT: d 368 LEU cc_start: 0.9586 (mm) cc_final: 0.9338 (pp) REVERT: d 387 CYS cc_start: 0.9367 (m) cc_final: 0.9167 (m) REVERT: d 399 LEU cc_start: 0.8602 (mt) cc_final: 0.7815 (mt) outliers start: 1 outliers final: 0 residues processed: 580 average time/residue: 0.2349 time to fit residues: 217.9338 Evaluate side-chains 458 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 457 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 278 optimal weight: 20.0000 chunk 424 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 chunk 265 optimal weight: 4.9990 chunk 410 optimal weight: 6.9990 chunk 197 optimal weight: 30.0000 chunk 418 optimal weight: 30.0000 chunk 177 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 334 optimal weight: 30.0000 chunk 282 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 196 GLN ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN R 89 HIS S 22 ASN ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 222 GLN ** b 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.065657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.050061 restraints weight = 247596.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.051398 restraints weight = 156398.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.052438 restraints weight = 110247.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.053197 restraints weight = 84861.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.053794 restraints weight = 69320.170| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.8942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 36017 Z= 0.178 Angle : 0.724 11.291 49187 Z= 0.371 Chirality : 0.048 0.328 5519 Planarity : 0.006 0.068 6289 Dihedral : 8.849 95.851 5204 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.33 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.12), residues: 4473 helix: 0.08 (0.23), residues: 471 sheet: -0.89 (0.13), residues: 1373 loop : -0.96 (0.12), residues: 2629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 440 TYR 0.027 0.002 TYR R 76 PHE 0.034 0.002 PHE A 421 TRP 0.022 0.002 TRP C 142 HIS 0.010 0.001 HIS a 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 (35937) covalent geometry : angle 0.70466 / 0.37 (49011) SS BOND : bond 0.00501 / 0.30 ( 64) SS BOND : angle 1.59957 / 1.08 ( 128) hydrogen bonds : bond 0.03842 / 2.49 ( 1319) hydrogen bonds : angle 6.32312 / 4.36 ( 3423) link_BETA1-4 : bond 0.01068 / 0.51 ( 8) link_BETA1-4 : angle 3.53012 / 2.20 ( 24) link_NAG-ASN : bond 0.00890 / 0.45 ( 8) link_NAG-ASN : angle 5.79203 / 4.06 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 567 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 60 PHE cc_start: 0.9357 (m-10) cc_final: 0.9033 (m-80) REVERT: 1 116 PHE cc_start: 0.8829 (m-80) cc_final: 0.8146 (m-80) REVERT: 2 25 ASN cc_start: 0.9435 (m-40) cc_final: 0.8914 (p0) REVERT: A 24 TYR cc_start: 0.9567 (m-80) cc_final: 0.9342 (m-10) REVERT: A 45 GLU cc_start: 0.9279 (mm-30) cc_final: 0.9021 (tp30) REVERT: A 197 LYS cc_start: 0.9489 (tptt) cc_final: 0.9265 (mmtt) REVERT: A 246 ARG cc_start: 0.9683 (tpp80) cc_final: 0.9345 (ttm-80) REVERT: A 411 LEU cc_start: 0.9553 (mt) cc_final: 0.9313 (pp) REVERT: B 13 ILE cc_start: 0.9596 (pt) cc_final: 0.9082 (mt) REVERT: B 79 GLN cc_start: 0.8771 (tp-100) cc_final: 0.8224 (tm-30) REVERT: B 183 HIS cc_start: 0.9040 (m-70) cc_final: 0.8752 (m-70) REVERT: B 197 LYS cc_start: 0.9633 (mmmt) cc_final: 0.9279 (mmmm) REVERT: B 254 ASP cc_start: 0.9659 (m-30) cc_final: 0.9121 (p0) REVERT: B 279 ILE cc_start: 0.9072 (mp) cc_final: 0.8821 (mp) REVERT: C 2 GLU cc_start: 0.9546 (pm20) cc_final: 0.9151 (tp30) REVERT: C 88 MET cc_start: 0.9528 (mmm) cc_final: 0.9274 (tpp) REVERT: C 125 HIS cc_start: 0.9301 (t-90) cc_final: 0.9037 (t-90) REVERT: C 188 TYR cc_start: 0.9076 (t80) cc_final: 0.8587 (t80) REVERT: C 197 LYS cc_start: 0.9862 (mppt) cc_final: 0.9618 (mmtm) REVERT: C 220 LEU cc_start: 0.9295 (mt) cc_final: 0.8789 (mt) REVERT: C 242 GLU cc_start: 0.9613 (mm-30) cc_final: 0.9213 (tp30) REVERT: C 270 GLU cc_start: 0.9382 (mt-10) cc_final: 0.8767 (mp0) REVERT: C 368 LEU cc_start: 0.9468 (tt) cc_final: 0.9144 (tt) REVERT: C 421 PHE cc_start: 0.9315 (m-80) cc_final: 0.8811 (m-80) REVERT: D 2 GLU cc_start: 0.9679 (pm20) cc_final: 0.9395 (tp30) REVERT: D 33 LEU cc_start: 0.9692 (mp) cc_final: 0.9348 (tp) REVERT: D 103 MET cc_start: 0.9117 (tpt) cc_final: 0.8729 (tpp) REVERT: D 175 ASP cc_start: 0.9128 (m-30) cc_final: 0.8717 (m-30) REVERT: D 176 ASN cc_start: 0.9820 (m-40) cc_final: 0.9458 (p0) REVERT: D 183 HIS cc_start: 0.9353 (t70) cc_final: 0.9006 (t70) REVERT: D 188 TYR cc_start: 0.9190 (t80) cc_final: 0.8918 (t80) REVERT: D 192 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8689 (mm-30) REVERT: D 243 ARG cc_start: 0.9600 (ttt90) cc_final: 0.8955 (tpt-90) REVERT: D 246 ARG cc_start: 0.9233 (mtm-85) cc_final: 0.8409 (ptp-170) REVERT: D 254 ASP cc_start: 0.9560 (m-30) cc_final: 0.9070 (p0) REVERT: P 18 ASN cc_start: 0.9242 (p0) cc_final: 0.9039 (p0) REVERT: P 20 GLN cc_start: 0.9638 (mp10) cc_final: 0.9327 (mp10) REVERT: P 74 LEU cc_start: 0.8808 (mt) cc_final: 0.8553 (mt) REVERT: Q 16 MET cc_start: 0.8505 (mmp) cc_final: 0.7796 (mmp) REVERT: Q 31 ARG cc_start: 0.9181 (mmm160) cc_final: 0.8676 (tpp80) REVERT: Q 88 HIS cc_start: 0.7849 (t-170) cc_final: 0.7591 (t-170) REVERT: Q 89 HIS cc_start: 0.8414 (m90) cc_final: 0.7899 (m90) REVERT: Q 115 ILE cc_start: 0.8990 (mp) cc_final: 0.8570 (mp) REVERT: R 10 ASP cc_start: 0.9298 (m-30) cc_final: 0.8988 (p0) REVERT: R 16 MET cc_start: 0.8854 (mmm) cc_final: 0.8478 (tpp) REVERT: R 26 CYS cc_start: 0.8561 (t) cc_final: 0.7889 (p) REVERT: R 72 ASP cc_start: 0.9084 (m-30) cc_final: 0.8791 (m-30) REVERT: R 87 TRP cc_start: 0.7524 (p90) cc_final: 0.7112 (p90) REVERT: R 96 ASN cc_start: 0.8739 (m-40) cc_final: 0.8398 (p0) REVERT: R 143 TRP cc_start: 0.8225 (m-10) cc_final: 0.7920 (m-10) REVERT: S 33 PHE cc_start: 0.8698 (m-10) cc_final: 0.8333 (m-80) REVERT: S 85 TYR cc_start: 0.5943 (m-10) cc_final: 0.5579 (m-10) REVERT: a 8 GLN cc_start: 0.9363 (tm-30) cc_final: 0.8899 (pm20) REVERT: a 165 GLU cc_start: 0.8073 (tt0) cc_final: 0.7699 (tp30) REVERT: a 166 MET cc_start: 0.4869 (pmm) cc_final: 0.4130 (pmm) REVERT: a 203 ASP cc_start: 0.9844 (m-30) cc_final: 0.9608 (t70) REVERT: a 278 ARG cc_start: 0.8935 (ttm110) cc_final: 0.8034 (mtp85) REVERT: a 384 TRP cc_start: 0.9456 (t-100) cc_final: 0.9182 (t60) REVERT: b 8 GLN cc_start: 0.9392 (tp40) cc_final: 0.8936 (tt0) REVERT: b 41 HIS cc_start: 0.9594 (m170) cc_final: 0.9179 (m90) REVERT: b 52 MET cc_start: 0.9180 (mmp) cc_final: 0.8788 (mmm) REVERT: b 53 PHE cc_start: 0.9123 (m-80) cc_final: 0.8570 (m-80) REVERT: b 68 MET cc_start: 0.9005 (mmm) cc_final: 0.8765 (mmm) REVERT: b 100 LEU cc_start: 0.9727 (tp) cc_final: 0.9217 (mt) REVERT: b 107 ASP cc_start: 0.9438 (p0) cc_final: 0.8916 (p0) REVERT: b 274 GLU cc_start: 0.9747 (tp30) cc_final: 0.9433 (mp0) REVERT: b 287 ASP cc_start: 0.9387 (p0) cc_final: 0.9155 (p0) REVERT: b 302 ASN cc_start: 0.9727 (t0) cc_final: 0.9357 (t0) REVERT: b 306 GLN cc_start: 0.9647 (pt0) cc_final: 0.9255 (pm20) REVERT: c 52 MET cc_start: 0.9532 (mmp) cc_final: 0.9100 (mmt) REVERT: c 53 PHE cc_start: 0.9493 (m-80) cc_final: 0.9084 (m-80) REVERT: c 80 ASN cc_start: 0.7803 (t0) cc_final: 0.7546 (t0) REVERT: c 99 ILE cc_start: 0.9909 (pt) cc_final: 0.9634 (mm) REVERT: c 276 LYS cc_start: 0.9752 (mtmt) cc_final: 0.9430 (mppt) REVERT: c 287 ASP cc_start: 0.9340 (p0) cc_final: 0.9036 (p0) REVERT: c 300 ASP cc_start: 0.9378 (t0) cc_final: 0.8960 (t0) REVERT: c 302 ASN cc_start: 0.9219 (p0) cc_final: 0.8918 (p0) REVERT: c 304 THR cc_start: 0.9517 (p) cc_final: 0.8971 (p) REVERT: c 306 GLN cc_start: 0.8581 (pm20) cc_final: 0.8226 (pm20) REVERT: d 53 PHE cc_start: 0.9196 (m-80) cc_final: 0.8958 (m-10) REVERT: d 68 MET cc_start: 0.9574 (mmm) cc_final: 0.8900 (mmm) REVERT: d 248 PHE cc_start: 0.8419 (m-10) cc_final: 0.8179 (m-10) REVERT: d 252 LEU cc_start: 0.9615 (mp) cc_final: 0.9183 (tp) REVERT: d 274 GLU cc_start: 0.9772 (tp30) cc_final: 0.9513 (tm-30) REVERT: d 276 LYS cc_start: 0.9577 (mtmt) cc_final: 0.9124 (mtpt) REVERT: d 287 ASP cc_start: 0.9348 (p0) cc_final: 0.9020 (p0) REVERT: d 292 LEU cc_start: 0.9475 (tp) cc_final: 0.8946 (tp) REVERT: d 300 ASP cc_start: 0.9271 (t0) cc_final: 0.9036 (t0) REVERT: d 321 GLU cc_start: 0.8903 (pm20) cc_final: 0.8601 (pm20) REVERT: d 368 LEU cc_start: 0.9636 (mm) cc_final: 0.9391 (pp) REVERT: d 399 LEU cc_start: 0.8361 (mt) cc_final: 0.8103 (mt) outliers start: 0 outliers final: 0 residues processed: 567 average time/residue: 0.2357 time to fit residues: 214.1781 Evaluate side-chains 458 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 19 optimal weight: 20.0000 chunk 327 optimal weight: 0.6980 chunk 399 optimal weight: 7.9990 chunk 263 optimal weight: 8.9990 chunk 202 optimal weight: 0.5980 chunk 349 optimal weight: 1.9990 chunk 116 optimal weight: 30.0000 chunk 226 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 287 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 ASN ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 222 GLN ** b 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 118 ASN ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.070764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.054620 restraints weight = 211186.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.055831 restraints weight = 143957.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.056700 restraints weight = 110005.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.057329 restraints weight = 90615.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.057726 restraints weight = 78597.503| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.9283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36017 Z= 0.147 Angle : 0.708 10.375 49187 Z= 0.363 Chirality : 0.048 0.310 5519 Planarity : 0.005 0.066 6289 Dihedral : 8.629 92.793 5204 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.75 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.12), residues: 4473 helix: 0.18 (0.24), residues: 465 sheet: -0.81 (0.14), residues: 1370 loop : -0.97 (0.12), residues: 2638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 440 TYR 0.026 0.002 TYR R 76 PHE 0.038 0.002 PHE A 421 TRP 0.068 0.002 TRP R 87 HIS 0.011 0.001 HIS a 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (35937) covalent geometry : angle 0.69235 / 0.36 (49011) SS BOND : bond 0.00480 / 0.28 ( 64) SS BOND : angle 1.45219 / 0.98 ( 128) hydrogen bonds : bond 0.03737 / 2.46 ( 1319) hydrogen bonds : angle 6.20813 / 4.26 ( 3423) link_BETA1-4 : bond 0.00985 / 0.47 ( 8) link_BETA1-4 : angle 3.43525 / 2.16 ( 24) link_NAG-ASN : bond 0.00709 / 0.37 ( 8) link_NAG-ASN : angle 5.17769 / 3.63 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 116 PHE cc_start: 0.8933 (m-80) cc_final: 0.8267 (m-80) REVERT: 2 25 ASN cc_start: 0.9464 (m-40) cc_final: 0.8958 (p0) REVERT: 2 72 LEU cc_start: 0.9674 (tp) cc_final: 0.9473 (tp) REVERT: A 24 TYR cc_start: 0.9602 (m-80) cc_final: 0.9330 (m-80) REVERT: A 267 LEU cc_start: 0.9656 (tt) cc_final: 0.9312 (mt) REVERT: A 411 LEU cc_start: 0.9551 (mt) cc_final: 0.9302 (pp) REVERT: B 13 ILE cc_start: 0.9600 (pt) cc_final: 0.9114 (mt) REVERT: B 79 GLN cc_start: 0.8633 (tp-100) cc_final: 0.8229 (tm-30) REVERT: B 103 MET cc_start: 0.8998 (tpt) cc_final: 0.8721 (tpp) REVERT: B 197 LYS cc_start: 0.9652 (mmmt) cc_final: 0.9305 (mmmm) REVERT: B 242 GLU cc_start: 0.9631 (pm20) cc_final: 0.9418 (pm20) REVERT: B 246 ARG cc_start: 0.9524 (mmt180) cc_final: 0.8896 (mmt180) REVERT: B 254 ASP cc_start: 0.9702 (m-30) cc_final: 0.9125 (p0) REVERT: B 279 ILE cc_start: 0.9164 (mp) cc_final: 0.8916 (mp) REVERT: C 2 GLU cc_start: 0.9487 (pm20) cc_final: 0.9123 (tp30) REVERT: C 88 MET cc_start: 0.9588 (mmm) cc_final: 0.9266 (tpp) REVERT: C 102 GLN cc_start: 0.9218 (tp40) cc_final: 0.8970 (tp40) REVERT: C 103 MET cc_start: 0.8180 (tpt) cc_final: 0.7807 (tpt) REVERT: C 125 HIS cc_start: 0.9309 (t-90) cc_final: 0.9041 (t-90) REVERT: C 156 LYS cc_start: 0.9496 (mmpt) cc_final: 0.9214 (tmtt) REVERT: C 162 LEU cc_start: 0.9408 (mm) cc_final: 0.9050 (mm) REVERT: C 164 ILE cc_start: 0.9695 (mm) cc_final: 0.9341 (pt) REVERT: C 188 TYR cc_start: 0.8886 (t80) cc_final: 0.8405 (t80) REVERT: C 197 LYS cc_start: 0.9832 (mppt) cc_final: 0.9588 (mmtm) REVERT: C 220 LEU cc_start: 0.9235 (mt) cc_final: 0.8979 (mt) REVERT: C 242 GLU cc_start: 0.9618 (mm-30) cc_final: 0.9219 (tp30) REVERT: C 270 GLU cc_start: 0.9390 (mt-10) cc_final: 0.8839 (mp0) REVERT: C 306 GLU cc_start: 0.9217 (tp30) cc_final: 0.8844 (mp0) REVERT: C 368 LEU cc_start: 0.9504 (tt) cc_final: 0.9191 (tt) REVERT: D 2 GLU cc_start: 0.9701 (pm20) cc_final: 0.9433 (tp30) REVERT: D 10 LYS cc_start: 0.9441 (mppt) cc_final: 0.9223 (mmtm) REVERT: D 103 MET cc_start: 0.9228 (tpt) cc_final: 0.8754 (tpp) REVERT: D 125 HIS cc_start: 0.8903 (t-90) cc_final: 0.8292 (t-90) REVERT: D 175 ASP cc_start: 0.9193 (m-30) cc_final: 0.8789 (m-30) REVERT: D 176 ASN cc_start: 0.9855 (m-40) cc_final: 0.9513 (p0) REVERT: D 183 HIS cc_start: 0.9331 (t70) cc_final: 0.9026 (t70) REVERT: D 188 TYR cc_start: 0.9020 (t80) cc_final: 0.8763 (t80) REVERT: D 192 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8668 (mm-30) REVERT: D 243 ARG cc_start: 0.9597 (ttt90) cc_final: 0.9116 (tpt-90) REVERT: D 254 ASP cc_start: 0.9537 (m-30) cc_final: 0.8778 (p0) REVERT: P 18 ASN cc_start: 0.9224 (p0) cc_final: 0.8952 (p0) REVERT: P 20 GLN cc_start: 0.9657 (mp10) cc_final: 0.9274 (mp10) REVERT: Q 16 MET cc_start: 0.8589 (mmp) cc_final: 0.8192 (mmp) REVERT: Q 28 VAL cc_start: 0.9685 (t) cc_final: 0.9392 (m) REVERT: Q 31 ARG cc_start: 0.9266 (mmm160) cc_final: 0.8633 (tpp80) REVERT: Q 115 ILE cc_start: 0.8759 (mp) cc_final: 0.8224 (mp) REVERT: R 26 CYS cc_start: 0.8537 (t) cc_final: 0.7844 (p) REVERT: R 72 ASP cc_start: 0.9097 (m-30) cc_final: 0.8886 (m-30) REVERT: R 85 TYR cc_start: 0.7166 (m-10) cc_final: 0.6789 (m-10) REVERT: S 33 PHE cc_start: 0.8696 (m-10) cc_final: 0.8437 (m-80) REVERT: S 61 GLU cc_start: 0.9195 (pp20) cc_final: 0.8709 (tm-30) REVERT: S 85 TYR cc_start: 0.6273 (m-10) cc_final: 0.5841 (m-10) REVERT: S 119 LYS cc_start: 0.9575 (mmpt) cc_final: 0.9346 (mmtm) REVERT: a 78 ILE cc_start: 0.8618 (mp) cc_final: 0.8246 (mp) REVERT: a 165 GLU cc_start: 0.8213 (tt0) cc_final: 0.7793 (tp30) REVERT: a 166 MET cc_start: 0.4863 (pmm) cc_final: 0.3869 (pmm) REVERT: a 278 ARG cc_start: 0.8859 (ttm110) cc_final: 0.7951 (mtp85) REVERT: a 310 ARG cc_start: 0.8954 (tmm-80) cc_final: 0.8681 (tmm-80) REVERT: a 384 TRP cc_start: 0.9349 (t-100) cc_final: 0.9028 (t60) REVERT: b 8 GLN cc_start: 0.9391 (tp40) cc_final: 0.8972 (tt0) REVERT: b 41 HIS cc_start: 0.9620 (m170) cc_final: 0.9201 (m90) REVERT: b 52 MET cc_start: 0.9157 (mmp) cc_final: 0.8798 (mmm) REVERT: b 53 PHE cc_start: 0.9123 (m-80) cc_final: 0.8566 (m-80) REVERT: b 68 MET cc_start: 0.8938 (mmm) cc_final: 0.8667 (mmm) REVERT: b 100 LEU cc_start: 0.9705 (tp) cc_final: 0.9175 (mt) REVERT: b 107 ASP cc_start: 0.9457 (p0) cc_final: 0.8884 (p0) REVERT: b 274 GLU cc_start: 0.9735 (tp30) cc_final: 0.9428 (mp0) REVERT: b 287 ASP cc_start: 0.9376 (p0) cc_final: 0.9143 (p0) REVERT: b 302 ASN cc_start: 0.9751 (t0) cc_final: 0.9390 (t0) REVERT: b 306 GLN cc_start: 0.9650 (pt0) cc_final: 0.9270 (pm20) REVERT: b 391 ASN cc_start: 0.9639 (m110) cc_final: 0.9425 (m110) REVERT: c 52 MET cc_start: 0.9385 (mmp) cc_final: 0.8914 (mmm) REVERT: c 53 PHE cc_start: 0.9440 (m-80) cc_final: 0.8994 (m-80) REVERT: c 80 ASN cc_start: 0.7740 (t0) cc_final: 0.7365 (t0) REVERT: c 99 ILE cc_start: 0.9888 (pt) cc_final: 0.9656 (mm) REVERT: c 100 LEU cc_start: 0.9856 (tp) cc_final: 0.9411 (mt) REVERT: c 139 ARG cc_start: 0.9038 (mtp-110) cc_final: 0.8559 (mtm110) REVERT: c 276 LYS cc_start: 0.9742 (mtmt) cc_final: 0.9414 (mppt) REVERT: c 287 ASP cc_start: 0.9361 (p0) cc_final: 0.9072 (p0) REVERT: c 300 ASP cc_start: 0.9286 (t0) cc_final: 0.8883 (t0) REVERT: c 302 ASN cc_start: 0.9239 (p0) cc_final: 0.9001 (p0) REVERT: c 304 THR cc_start: 0.9514 (p) cc_final: 0.9047 (p) REVERT: c 306 GLN cc_start: 0.8468 (pm20) cc_final: 0.8150 (pm20) REVERT: c 309 GLU cc_start: 0.9594 (pm20) cc_final: 0.9339 (mp0) REVERT: c 316 PHE cc_start: 0.9151 (m-80) cc_final: 0.8951 (m-80) REVERT: c 368 LEU cc_start: 0.9638 (mm) cc_final: 0.9401 (pp) REVERT: d 21 ASN cc_start: 0.9444 (t0) cc_final: 0.9021 (t0) REVERT: d 53 PHE cc_start: 0.9416 (m-80) cc_final: 0.8939 (m-80) REVERT: d 68 MET cc_start: 0.9527 (mmm) cc_final: 0.8785 (mmm) REVERT: d 98 TYR cc_start: 0.9618 (m-10) cc_final: 0.9409 (m-10) REVERT: d 248 PHE cc_start: 0.8613 (m-10) cc_final: 0.8405 (m-10) REVERT: d 252 LEU cc_start: 0.9662 (mp) cc_final: 0.9257 (tp) REVERT: d 274 GLU cc_start: 0.9791 (tp30) cc_final: 0.9506 (tm-30) REVERT: d 276 LYS cc_start: 0.9601 (mtmt) cc_final: 0.9176 (mtmt) REVERT: d 287 ASP cc_start: 0.9418 (p0) cc_final: 0.9140 (p0) REVERT: d 292 LEU cc_start: 0.9479 (tp) cc_final: 0.8938 (tp) REVERT: d 300 ASP cc_start: 0.9257 (t0) cc_final: 0.9014 (t0) REVERT: d 321 GLU cc_start: 0.8953 (pm20) cc_final: 0.8502 (pm20) REVERT: d 368 LEU cc_start: 0.9636 (mm) cc_final: 0.9422 (pp) REVERT: d 387 CYS cc_start: 0.9356 (m) cc_final: 0.9101 (m) REVERT: d 399 LEU cc_start: 0.8560 (mt) cc_final: 0.7945 (mt) outliers start: 0 outliers final: 0 residues processed: 580 average time/residue: 0.2393 time to fit residues: 222.0937 Evaluate side-chains 460 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 460 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 75 optimal weight: 8.9990 chunk 294 optimal weight: 4.9990 chunk 379 optimal weight: 0.6980 chunk 380 optimal weight: 2.9990 chunk 386 optimal weight: 3.9990 chunk 322 optimal weight: 7.9990 chunk 370 optimal weight: 7.9990 chunk 311 optimal weight: 9.9990 chunk 43 optimal weight: 40.0000 chunk 250 optimal weight: 2.9990 chunk 336 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 GLN ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 ASN ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 222 GLN ** b 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.066420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.051459 restraints weight = 250764.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.052928 restraints weight = 155073.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.053987 restraints weight = 109296.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.054791 restraints weight = 83631.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.055395 restraints weight = 67696.499| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.9501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36017 Z= 0.137 Angle : 0.720 12.166 49187 Z= 0.367 Chirality : 0.049 0.304 5519 Planarity : 0.006 0.067 6289 Dihedral : 8.438 87.662 5204 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.84 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.12), residues: 4473 helix: 0.13 (0.24), residues: 465 sheet: -0.78 (0.14), residues: 1374 loop : -0.95 (0.12), residues: 2634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG d 390 TYR 0.031 0.002 TYR P 94 PHE 0.039 0.002 PHE A 421 TRP 0.045 0.002 TRP R 87 HIS 0.010 0.001 HIS S 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (35937) covalent geometry : angle 0.70524 / 0.36 (49011) SS BOND : bond 0.00354 / 0.21 ( 64) SS BOND : angle 1.45068 / 0.97 ( 128) hydrogen bonds : bond 0.03664 / 2.42 ( 1319) hydrogen bonds : angle 6.13176 / 4.20 ( 3423) link_BETA1-4 : bond 0.00963 / 0.46 ( 8) link_BETA1-4 : angle 3.44035 / 2.17 ( 24) link_NAG-ASN : bond 0.00604 / 0.31 ( 8) link_NAG-ASN : angle 4.74552 / 3.33 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8946 Ramachandran restraints generated. 4473 Oldfield, 0 Emsley, 4473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 573 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 116 PHE cc_start: 0.8926 (m-80) cc_final: 0.8279 (m-80) REVERT: 2 25 ASN cc_start: 0.9441 (m-40) cc_final: 0.8921 (p0) REVERT: 2 72 LEU cc_start: 0.9662 (tp) cc_final: 0.9456 (tp) REVERT: A 24 TYR cc_start: 0.9553 (m-80) cc_final: 0.9287 (m-80) REVERT: A 267 LEU cc_start: 0.9680 (tt) cc_final: 0.9368 (mt) REVERT: A 411 LEU cc_start: 0.9666 (mt) cc_final: 0.9425 (pp) REVERT: B 13 ILE cc_start: 0.9592 (pt) cc_final: 0.9110 (mt) REVERT: B 79 GLN cc_start: 0.8816 (tp-100) cc_final: 0.8373 (tm-30) REVERT: B 197 LYS cc_start: 0.9680 (mmmt) cc_final: 0.9307 (mmmm) REVERT: B 254 ASP cc_start: 0.9674 (m-30) cc_final: 0.9129 (p0) REVERT: B 279 ILE cc_start: 0.9174 (mp) cc_final: 0.8887 (mp) REVERT: C 2 GLU cc_start: 0.9508 (pm20) cc_final: 0.9144 (tp30) REVERT: C 88 MET cc_start: 0.9558 (mmm) cc_final: 0.9318 (tpp) REVERT: C 102 GLN cc_start: 0.9270 (tp40) cc_final: 0.8999 (tp40) REVERT: C 103 MET cc_start: 0.8242 (tpt) cc_final: 0.7790 (tpt) REVERT: C 123 LYS cc_start: 0.9659 (tptp) cc_final: 0.9452 (tppt) REVERT: C 125 HIS cc_start: 0.9233 (t-90) cc_final: 0.8992 (t-90) REVERT: C 156 LYS cc_start: 0.9489 (mmpt) cc_final: 0.9197 (tptt) REVERT: C 162 LEU cc_start: 0.9450 (mm) cc_final: 0.9050 (mm) REVERT: C 164 ILE cc_start: 0.9761 (mm) cc_final: 0.9434 (pt) REVERT: C 188 TYR cc_start: 0.8944 (t80) cc_final: 0.8447 (t80) REVERT: C 197 LYS cc_start: 0.9826 (mppt) cc_final: 0.9561 (mmtm) REVERT: C 220 LEU cc_start: 0.9204 (mt) cc_final: 0.8933 (mt) REVERT: C 242 GLU cc_start: 0.9577 (mm-30) cc_final: 0.9207 (tp30) REVERT: C 270 GLU cc_start: 0.9396 (mt-10) cc_final: 0.8802 (mp0) REVERT: C 306 GLU cc_start: 0.9164 (tp30) cc_final: 0.8822 (mp0) REVERT: C 333 SER cc_start: 0.8983 (p) cc_final: 0.8631 (p) REVERT: C 368 LEU cc_start: 0.9538 (tt) cc_final: 0.9263 (tt) REVERT: D 2 GLU cc_start: 0.9684 (pm20) cc_final: 0.9419 (tp30) REVERT: D 10 LYS cc_start: 0.9415 (mppt) cc_final: 0.9192 (mmtm) REVERT: D 103 MET cc_start: 0.9217 (tpt) cc_final: 0.8774 (tpp) REVERT: D 125 HIS cc_start: 0.8780 (t-90) cc_final: 0.8144 (t-90) REVERT: D 175 ASP cc_start: 0.9141 (m-30) cc_final: 0.8749 (m-30) REVERT: D 176 ASN cc_start: 0.9829 (m-40) cc_final: 0.9475 (p0) REVERT: D 183 HIS cc_start: 0.9360 (t70) cc_final: 0.9022 (t70) REVERT: D 188 TYR cc_start: 0.9065 (t80) cc_final: 0.8804 (t80) REVERT: D 219 ASN cc_start: 0.9085 (t0) cc_final: 0.8841 (t0) REVERT: D 243 ARG cc_start: 0.9588 (ttt90) cc_final: 0.9133 (tpt-90) REVERT: D 254 ASP cc_start: 0.9534 (m-30) cc_final: 0.8782 (p0) REVERT: P 20 GLN cc_start: 0.9660 (mp10) cc_final: 0.9315 (mp10) REVERT: Q 16 MET cc_start: 0.8538 (mmp) cc_final: 0.7647 (mmp) REVERT: Q 28 VAL cc_start: 0.9708 (t) cc_final: 0.9395 (m) REVERT: Q 31 ARG cc_start: 0.9215 (mmm160) cc_final: 0.8661 (tpp80) REVERT: Q 33 PHE cc_start: 0.7406 (m-80) cc_final: 0.7165 (m-80) REVERT: Q 115 ILE cc_start: 0.8862 (mp) cc_final: 0.8296 (mp) REVERT: Q 152 ASP cc_start: 0.6089 (t0) cc_final: 0.5597 (t0) REVERT: R 15 ILE cc_start: 0.9282 (tt) cc_final: 0.9021 (tt) REVERT: R 16 MET cc_start: 0.9103 (mmp) cc_final: 0.8582 (tpp) REVERT: R 26 CYS cc_start: 0.8539 (t) cc_final: 0.7887 (p) REVERT: R 72 ASP cc_start: 0.9170 (m-30) cc_final: 0.8965 (m-30) REVERT: R 96 ASN cc_start: 0.8949 (m-40) cc_final: 0.8655 (p0) REVERT: S 85 TYR cc_start: 0.6336 (m-10) cc_final: 0.5990 (m-10) REVERT: S 119 LYS cc_start: 0.9605 (mmpt) cc_final: 0.9376 (mmtm) REVERT: a 165 GLU cc_start: 0.8137 (tt0) cc_final: 0.7775 (tp30) REVERT: a 166 MET cc_start: 0.4955 (pmm) cc_final: 0.3744 (pmm) REVERT: a 278 ARG cc_start: 0.8924 (ttm110) cc_final: 0.7981 (mtp85) REVERT: a 310 ARG cc_start: 0.8962 (tmm-80) cc_final: 0.8658 (tmm-80) REVERT: a 384 TRP cc_start: 0.9426 (t-100) cc_final: 0.9085 (t60) REVERT: b 8 GLN cc_start: 0.9391 (tp40) cc_final: 0.8997 (tt0) REVERT: b 41 HIS cc_start: 0.9606 (m170) cc_final: 0.9177 (m90) REVERT: b 52 MET cc_start: 0.9192 (mmp) cc_final: 0.8791 (mmm) REVERT: b 53 PHE cc_start: 0.9119 (m-80) cc_final: 0.8544 (m-80) REVERT: b 68 MET cc_start: 0.8920 (mmm) cc_final: 0.8667 (mmm) REVERT: b 100 LEU cc_start: 0.9690 (tp) cc_final: 0.9109 (mt) REVERT: b 107 ASP cc_start: 0.9383 (p0) cc_final: 0.8737 (p0) REVERT: b 274 GLU cc_start: 0.9692 (tp30) cc_final: 0.9407 (mp0) REVERT: b 287 ASP cc_start: 0.9389 (p0) cc_final: 0.9154 (p0) REVERT: b 302 ASN cc_start: 0.9764 (t0) cc_final: 0.9418 (t0) REVERT: b 306 GLN cc_start: 0.9641 (pt0) cc_final: 0.9268 (pm20) REVERT: b 391 ASN cc_start: 0.9687 (m110) cc_final: 0.9473 (m110) REVERT: c 52 MET cc_start: 0.9413 (mmp) cc_final: 0.8909 (mmp) REVERT: c 53 PHE cc_start: 0.9459 (m-80) cc_final: 0.8975 (m-80) REVERT: c 80 ASN cc_start: 0.7647 (t0) cc_final: 0.7250 (t0) REVERT: c 97 TYR cc_start: 0.9092 (m-10) cc_final: 0.8527 (m-80) REVERT: c 100 LEU cc_start: 0.9859 (tp) cc_final: 0.9440 (mt) REVERT: c 139 ARG cc_start: 0.9058 (mtp-110) cc_final: 0.8622 (mtm110) REVERT: c 287 ASP cc_start: 0.9346 (p0) cc_final: 0.9035 (p0) REVERT: c 304 THR cc_start: 0.9517 (p) cc_final: 0.9028 (p) REVERT: c 306 GLN cc_start: 0.8422 (pm20) cc_final: 0.8119 (pm20) REVERT: c 309 GLU cc_start: 0.9529 (pm20) cc_final: 0.9319 (mp0) REVERT: c 316 PHE cc_start: 0.9155 (m-80) cc_final: 0.8953 (m-80) REVERT: c 358 ASN cc_start: 0.9522 (m110) cc_final: 0.9322 (m110) REVERT: c 368 LEU cc_start: 0.9636 (mm) cc_final: 0.9424 (pp) REVERT: c 376 MET cc_start: 0.9122 (tpt) cc_final: 0.8868 (tpt) REVERT: d 21 ASN cc_start: 0.9421 (t0) cc_final: 0.8962 (t0) REVERT: d 53 PHE cc_start: 0.9378 (m-80) cc_final: 0.8908 (m-80) REVERT: d 68 MET cc_start: 0.9546 (mmm) cc_final: 0.8834 (mmm) REVERT: d 98 TYR cc_start: 0.9616 (m-10) cc_final: 0.9414 (m-10) REVERT: d 127 LYS cc_start: 0.9744 (tmtt) cc_final: 0.9525 (tptp) REVERT: d 248 PHE cc_start: 0.8580 (m-10) cc_final: 0.8346 (m-10) REVERT: d 252 LEU cc_start: 0.9608 (mp) cc_final: 0.9119 (tp) REVERT: d 274 GLU cc_start: 0.9750 (tp30) cc_final: 0.9482 (tm-30) REVERT: d 276 LYS cc_start: 0.9578 (mtmt) cc_final: 0.9058 (mtpt) REVERT: d 287 ASP cc_start: 0.9389 (p0) cc_final: 0.9060 (p0) REVERT: d 292 LEU cc_start: 0.9474 (tp) cc_final: 0.8952 (tp) REVERT: d 300 ASP cc_start: 0.9293 (t0) cc_final: 0.9052 (t0) REVERT: d 321 GLU cc_start: 0.9016 (pm20) cc_final: 0.8619 (pm20) REVERT: d 368 LEU cc_start: 0.9641 (mm) cc_final: 0.9416 (pp) REVERT: d 399 LEU cc_start: 0.8473 (mt) cc_final: 0.8055 (mt) outliers start: 0 outliers final: 0 residues processed: 573 average time/residue: 0.2359 time to fit residues: 217.6083 Evaluate side-chains 465 residues out of total 3845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 465 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 283 optimal weight: 30.0000 chunk 245 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 94 optimal weight: 30.0000 chunk 96 optimal weight: 0.5980 chunk 167 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 373 optimal weight: 5.9990 chunk 339 optimal weight: 0.0980 chunk 57 optimal weight: 9.9990 chunk 429 optimal weight: 9.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 HIS a 222 GLN ** b 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 160 GLN ** c 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.066620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.051777 restraints weight = 244996.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.053198 restraints weight = 153053.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.054242 restraints weight = 108891.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.055008 restraints weight = 83856.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.055576 restraints weight = 68447.106| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.9723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 36017 Z= 0.138 Angle : 0.713 11.345 49187 Z= 0.364 Chirality : 0.048 0.314 5519 Planarity : 0.006 0.066 6289 Dihedral : 8.220 83.713 5204 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.50 % Favored : 94.48 % Rotamer: Outliers : 0.03 % Allowed : 0.34 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.12), residues: 4473 helix: 0.08 (0.24), residues: 473 sheet: -0.81 (0.14), residues: 1373 loop : -0.93 (0.12), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 246 TYR 0.026 0.001 TYR R 76 PHE 0.036 0.002 PHE a 316 TRP 0.043 0.002 TRP R 87 HIS 0.014 0.001 HIS c 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (35937) covalent geometry : angle 0.69958 / 0.36 (49011) SS BOND : bond 0.00334 / 0.19 ( 64) SS BOND : angle 1.41015 / 0.95 ( 128) hydrogen bonds : bond 0.03668 / 2.42 ( 1319) hydrogen bonds : angle 6.04291 / 4.15 ( 3423) link_BETA1-4 : bond 0.00996 / 0.47 ( 8) link_BETA1-4 : angle 3.45135 / 2.17 ( 24) link_NAG-ASN : bond 0.00627 / 0.32 ( 8) link_NAG-ASN : angle 4.56451 / 3.19 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6993.98 seconds wall clock time: 122 minutes 23.27 seconds (7343.27 seconds total)