Starting phenix.real_space_refine on Tue Aug 26 15:21:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u81_41996/08_2025/8u81_41996.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u81_41996/08_2025/8u81_41996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u81_41996/08_2025/8u81_41996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u81_41996/08_2025/8u81_41996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u81_41996/08_2025/8u81_41996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u81_41996/08_2025/8u81_41996.map" } resolution = 3.82 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= -0.007 sd= 1.074 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 275 5.16 5 C 23635 2.51 5 N 6635 2.21 5 O 7345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37890 Number of models: 1 Model: "" Number of chains: 20 Chain: "K1" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1559 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "K2" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1559 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "K3" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1559 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "K4" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1559 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "K5" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1559 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "C1" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2932 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 353} Chain: "C2" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2932 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 353} Chain: "C3" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2932 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 353} Chain: "C4" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2932 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 353} Chain: "C5" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2932 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 353} Chain: "B1" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "B2" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "B3" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "B4" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "B5" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G1" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "G2" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "G3" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "G4" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "G5" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Time building chain proxies: 8.13, per 1000 atoms: 0.21 Number of scatterers: 37890 At special positions: 0 Unit cell: (245.14, 246.17, 135.96, 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 275 16.00 O 7345 8.00 N 6635 7.00 C 23635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.96 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8970 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 45 sheets defined 48.4% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'K1' and resid 59 through 63 Processing helix chain 'K1' and resid 68 through 75 removed outlier: 3.688A pdb=" N ARGK1 72 " --> pdb=" O SERK1 68 " (cutoff:3.500A) Processing helix chain 'K1' and resid 95 through 109 removed outlier: 3.748A pdb=" N GLYK1 100 " --> pdb=" O PROK1 96 " (cutoff:3.500A) Proline residue: K1 101 - end of helix Processing helix chain 'K1' and resid 118 through 129 Processing helix chain 'K1' and resid 131 through 151 removed outlier: 4.230A pdb=" N GLNK1 151 " --> pdb=" O SERK1 147 " (cutoff:3.500A) Processing helix chain 'K1' and resid 164 through 174 removed outlier: 4.622A pdb=" N THRK1 169 " --> pdb=" O GLUK1 165 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLNK1 170 " --> pdb=" O GLUK1 166 " (cutoff:3.500A) Processing helix chain 'K1' and resid 221 through 233 Processing helix chain 'K2' and resid 59 through 63 Processing helix chain 'K2' and resid 70 through 75 removed outlier: 3.692A pdb=" N CYSK2 74 " --> pdb=" O LEUK2 70 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLNK2 75 " --> pdb=" O TYRK2 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'K2' and resid 70 through 75' Processing helix chain 'K2' and resid 95 through 109 Proline residue: K2 101 - end of helix Processing helix chain 'K2' and resid 118 through 129 Processing helix chain 'K2' and resid 131 through 151 Processing helix chain 'K2' and resid 152 through 154 No H-bonds generated for 'chain 'K2' and resid 152 through 154' Processing helix chain 'K2' and resid 164 through 174 removed outlier: 3.511A pdb=" N LEUK2 168 " --> pdb=" O GLNK2 164 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THRK2 169 " --> pdb=" O GLUK2 165 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLNK2 170 " --> pdb=" O GLUK2 166 " (cutoff:3.500A) Processing helix chain 'K2' and resid 221 through 233 removed outlier: 3.686A pdb=" N ARGK2 233 " --> pdb=" O GLUK2 229 " (cutoff:3.500A) Processing helix chain 'K3' and resid 59 through 63 Processing helix chain 'K3' and resid 68 through 75 removed outlier: 3.600A pdb=" N ARGK3 72 " --> pdb=" O SERK3 68 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLNK3 75 " --> pdb=" O TYRK3 71 " (cutoff:3.500A) Processing helix chain 'K3' and resid 98 through 109 removed outlier: 3.932A pdb=" N VALK3 102 " --> pdb=" O TYRK3 98 " (cutoff:3.500A) Processing helix chain 'K3' and resid 118 through 130 Processing helix chain 'K3' and resid 131 through 150 Processing helix chain 'K3' and resid 164 through 166 No H-bonds generated for 'chain 'K3' and resid 164 through 166' Processing helix chain 'K3' and resid 167 through 174 Processing helix chain 'K3' and resid 191 through 195 Processing helix chain 'K3' and resid 221 through 233 Processing helix chain 'K4' and resid 59 through 63 Processing helix chain 'K4' and resid 68 through 75 removed outlier: 3.637A pdb=" N ARGK4 72 " --> pdb=" O SERK4 68 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEUK4 73 " --> pdb=" O PHEK4 69 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLNK4 75 " --> pdb=" O TYRK4 71 " (cutoff:3.500A) Processing helix chain 'K4' and resid 98 through 109 removed outlier: 4.010A pdb=" N VALK4 102 " --> pdb=" O TYRK4 98 " (cutoff:3.500A) Processing helix chain 'K4' and resid 118 through 129 removed outlier: 3.564A pdb=" N VALK4 122 " --> pdb=" O ALAK4 118 " (cutoff:3.500A) Processing helix chain 'K4' and resid 131 through 150 Processing helix chain 'K4' and resid 164 through 174 removed outlier: 4.179A pdb=" N THRK4 169 " --> pdb=" O GLUK4 165 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLNK4 170 " --> pdb=" O GLUK4 166 " (cutoff:3.500A) Processing helix chain 'K4' and resid 222 through 233 removed outlier: 3.637A pdb=" N ARGK4 233 " --> pdb=" O GLUK4 229 " (cutoff:3.500A) Processing helix chain 'K5' and resid 59 through 63 Processing helix chain 'K5' and resid 68 through 75 removed outlier: 4.529A pdb=" N ARGK5 72 " --> pdb=" O SERK5 68 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEUK5 73 " --> pdb=" O PHEK5 69 " (cutoff:3.500A) Processing helix chain 'K5' and resid 95 through 109 Proline residue: K5 101 - end of helix Processing helix chain 'K5' and resid 118 through 130 Processing helix chain 'K5' and resid 131 through 149 Processing helix chain 'K5' and resid 164 through 174 removed outlier: 4.479A pdb=" N THRK5 169 " --> pdb=" O GLUK5 165 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLNK5 170 " --> pdb=" O GLUK5 166 " (cutoff:3.500A) Processing helix chain 'K5' and resid 210 through 215 removed outlier: 4.007A pdb=" N TYRK5 214 " --> pdb=" O HISK5 210 " (cutoff:3.500A) Processing helix chain 'K5' and resid 221 through 233 Processing helix chain 'C1' and resid 26 through 46 removed outlier: 3.807A pdb=" N SERC1 32 " --> pdb=" O LYSC1 28 " (cutoff:3.500A) Processing helix chain 'C1' and resid 53 through 67 removed outlier: 3.724A pdb=" N LEUC1 57 " --> pdb=" O SERC1 53 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HISC1 67 " --> pdb=" O THRC1 63 " (cutoff:3.500A) Processing helix chain 'C1' and resid 69 through 88 Processing helix chain 'C1' and resid 88 through 96 removed outlier: 3.531A pdb=" N ASPC1 92 " --> pdb=" O LYSC1 88 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SERC1 96 " --> pdb=" O ASPC1 92 " (cutoff:3.500A) Processing helix chain 'C1' and resid 100 through 123 Processing helix chain 'C1' and resid 124 through 135 removed outlier: 3.641A pdb=" N VALC1 129 " --> pdb=" O TYRC1 125 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VALC1 131 " --> pdb=" O ASPC1 127 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLNC1 132 " --> pdb=" O ARGC1 128 " (cutoff:3.500A) Processing helix chain 'C1' and resid 138 through 151 Processing helix chain 'C1' and resid 154 through 174 removed outlier: 3.776A pdb=" N HISC1 160 " --> pdb=" O CYSC1 156 " (cutoff:3.500A) Processing helix chain 'C1' and resid 179 through 195 removed outlier: 4.382A pdb=" N ILEC1 183 " --> pdb=" O ASPC1 179 " (cutoff:3.500A) Processing helix chain 'C1' and resid 198 through 205 Processing helix chain 'C1' and resid 205 through 228 Processing helix chain 'C1' and resid 229 through 250 Processing helix chain 'C1' and resid 256 through 268 Processing helix chain 'C1' and resid 273 through 278 removed outlier: 3.649A pdb=" N GLUC1 278 " --> pdb=" O THRC1 275 " (cutoff:3.500A) Processing helix chain 'C1' and resid 283 through 291 Processing helix chain 'C1' and resid 292 through 304 removed outlier: 3.511A pdb=" N LEUC1 296 " --> pdb=" O LYSC1 292 " (cutoff:3.500A) Processing helix chain 'C1' and resid 308 through 330 removed outlier: 3.912A pdb=" N THRC1 312 " --> pdb=" O ASNC1 308 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SERC1 330 " --> pdb=" O LYSC1 326 " (cutoff:3.500A) Processing helix chain 'C1' and resid 337 through 342 Processing helix chain 'C1' and resid 343 through 359 Processing helix chain 'C1' and resid 363 through 379 removed outlier: 3.964A pdb=" N ASNC1 379 " --> pdb=" O GLUC1 375 " (cutoff:3.500A) Processing helix chain 'C2' and resid 26 through 46 Processing helix chain 'C2' and resid 53 through 67 Processing helix chain 'C2' and resid 69 through 88 Processing helix chain 'C2' and resid 88 through 95 Processing helix chain 'C2' and resid 100 through 123 removed outlier: 4.100A pdb=" N THRC2 104 " --> pdb=" O ASNC2 100 " (cutoff:3.500A) Processing helix chain 'C2' and resid 124 through 129 Processing helix chain 'C2' and resid 129 through 135 Processing helix chain 'C2' and resid 138 through 151 Processing helix chain 'C2' and resid 154 through 174 Processing helix chain 'C2' and resid 179 through 194 removed outlier: 4.130A pdb=" N ILEC2 183 " --> pdb=" O ASPC2 179 " (cutoff:3.500A) Processing helix chain 'C2' and resid 198 through 205 Processing helix chain 'C2' and resid 205 through 228 Processing helix chain 'C2' and resid 229 through 251 Processing helix chain 'C2' and resid 256 through 268 removed outlier: 3.511A pdb=" N LYSC2 262 " --> pdb=" O GLUC2 258 " (cutoff:3.500A) Processing helix chain 'C2' and resid 284 through 291 removed outlier: 4.099A pdb=" N LEUC2 288 " --> pdb=" O LEUC2 284 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYSC2 289 " --> pdb=" O VALC2 285 " (cutoff:3.500A) Processing helix chain 'C2' and resid 293 through 304 Processing helix chain 'C2' and resid 308 through 330 Processing helix chain 'C2' and resid 343 through 359 removed outlier: 4.038A pdb=" N LYSC2 349 " --> pdb=" O LEUC2 345 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHEC2 355 " --> pdb=" O ARGC2 351 " (cutoff:3.500A) Processing helix chain 'C2' and resid 363 through 379 removed outlier: 3.837A pdb=" N LYSC2 367 " --> pdb=" O ASPC2 363 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASNC2 379 " --> pdb=" O GLUC2 375 " (cutoff:3.500A) Processing helix chain 'C3' and resid 26 through 46 removed outlier: 3.686A pdb=" N VALC3 30 " --> pdb=" O ASPC3 26 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SERC3 32 " --> pdb=" O LYSC3 28 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASPC3 35 " --> pdb=" O ASNC3 31 " (cutoff:3.500A) Processing helix chain 'C3' and resid 53 through 67 Processing helix chain 'C3' and resid 69 through 88 removed outlier: 3.669A pdb=" N LYSC3 88 " --> pdb=" O HISC3 84 " (cutoff:3.500A) Processing helix chain 'C3' and resid 88 through 95 Processing helix chain 'C3' and resid 100 through 123 removed outlier: 3.527A pdb=" N THRC3 104 " --> pdb=" O ASNC3 100 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N METC3 118 " --> pdb=" O THRC3 114 " (cutoff:3.500A) Processing helix chain 'C3' and resid 129 through 135 Processing helix chain 'C3' and resid 138 through 151 Processing helix chain 'C3' and resid 154 through 175 Processing helix chain 'C3' and resid 179 through 194 removed outlier: 3.832A pdb=" N ILEC3 183 " --> pdb=" O ASPC3 179 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLYC3 194 " --> pdb=" O LEUC3 190 " (cutoff:3.500A) Processing helix chain 'C3' and resid 198 through 205 removed outlier: 3.583A pdb=" N PHEC3 205 " --> pdb=" O TYRC3 201 " (cutoff:3.500A) Processing helix chain 'C3' and resid 205 through 226 removed outlier: 3.663A pdb=" N ALAC3 226 " --> pdb=" O GLNC3 222 " (cutoff:3.500A) Processing helix chain 'C3' and resid 229 through 251 Processing helix chain 'C3' and resid 253 through 255 No H-bonds generated for 'chain 'C3' and resid 253 through 255' Processing helix chain 'C3' and resid 256 through 269 removed outlier: 3.970A pdb=" N ILEC3 260 " --> pdb=" O THRC3 256 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VALC3 261 " --> pdb=" O GLUC3 257 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILEC3 269 " --> pdb=" O GLUC3 265 " (cutoff:3.500A) Processing helix chain 'C3' and resid 272 through 278 Processing helix chain 'C3' and resid 283 through 291 Processing helix chain 'C3' and resid 293 through 304 Processing helix chain 'C3' and resid 308 through 330 removed outlier: 4.091A pdb=" N THRC3 312 " --> pdb=" O ASNC3 308 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N METC3 313 " --> pdb=" O GLYC3 309 " (cutoff:3.500A) Processing helix chain 'C3' and resid 343 through 359 Processing helix chain 'C3' and resid 363 through 377 removed outlier: 3.634A pdb=" N LYSC3 367 " --> pdb=" O ASPC3 363 " (cutoff:3.500A) Processing helix chain 'C4' and resid 27 through 46 Processing helix chain 'C4' and resid 53 through 67 Processing helix chain 'C4' and resid 69 through 88 Processing helix chain 'C4' and resid 88 through 95 Processing helix chain 'C4' and resid 100 through 123 removed outlier: 3.697A pdb=" N METC4 118 " --> pdb=" O THRC4 114 " (cutoff:3.500A) Processing helix chain 'C4' and resid 123 through 129 Processing helix chain 'C4' and resid 129 through 135 Processing helix chain 'C4' and resid 138 through 151 Processing helix chain 'C4' and resid 154 through 175 Processing helix chain 'C4' and resid 179 through 193 Processing helix chain 'C4' and resid 198 through 205 Processing helix chain 'C4' and resid 205 through 228 Processing helix chain 'C4' and resid 229 through 251 Processing helix chain 'C4' and resid 253 through 255 No H-bonds generated for 'chain 'C4' and resid 253 through 255' Processing helix chain 'C4' and resid 256 through 269 removed outlier: 3.790A pdb=" N ILEC4 260 " --> pdb=" O THRC4 256 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYSC4 262 " --> pdb=" O GLUC4 258 " (cutoff:3.500A) Processing helix chain 'C4' and resid 272 through 278 Processing helix chain 'C4' and resid 283 through 291 Processing helix chain 'C4' and resid 292 through 306 removed outlier: 3.719A pdb=" N ARGC4 305 " --> pdb=" O LYSC4 301 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VALC4 306 " --> pdb=" O LEUC4 302 " (cutoff:3.500A) Processing helix chain 'C4' and resid 308 through 330 Processing helix chain 'C4' and resid 342 through 359 removed outlier: 3.929A pdb=" N LEUC4 346 " --> pdb=" O ILEC4 342 " (cutoff:3.500A) Processing helix chain 'C4' and resid 363 through 379 Processing helix chain 'C5' and resid 26 through 46 removed outlier: 3.715A pdb=" N VALC5 30 " --> pdb=" O ASPC5 26 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SERC5 32 " --> pdb=" O LYSC5 28 " (cutoff:3.500A) Processing helix chain 'C5' and resid 53 through 67 Processing helix chain 'C5' and resid 69 through 88 removed outlier: 3.557A pdb=" N LYSC5 88 " --> pdb=" O HISC5 84 " (cutoff:3.500A) Processing helix chain 'C5' and resid 88 through 97 Processing helix chain 'C5' and resid 100 through 123 removed outlier: 3.691A pdb=" N THRC5 104 " --> pdb=" O ASNC5 100 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N METC5 118 " --> pdb=" O THRC5 114 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEUC5 123 " --> pdb=" O ILEC5 119 " (cutoff:3.500A) Processing helix chain 'C5' and resid 129 through 135 Processing helix chain 'C5' and resid 138 through 149 Processing helix chain 'C5' and resid 154 through 175 Processing helix chain 'C5' and resid 179 through 193 removed outlier: 3.826A pdb=" N ILEC5 183 " --> pdb=" O ASPC5 179 " (cutoff:3.500A) Processing helix chain 'C5' and resid 198 through 205 Processing helix chain 'C5' and resid 205 through 228 Processing helix chain 'C5' and resid 229 through 252 Processing helix chain 'C5' and resid 253 through 268 removed outlier: 3.530A pdb=" N GLUC5 257 " --> pdb=" O ASPC5 253 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLUC5 258 " --> pdb=" O LYSC5 254 " (cutoff:3.500A) Proline residue: C5 259 - end of helix removed outlier: 4.333A pdb=" N LYSC5 262 " --> pdb=" O GLUC5 258 " (cutoff:3.500A) Processing helix chain 'C5' and resid 272 through 279 removed outlier: 3.507A pdb=" N METC5 279 " --> pdb=" O THRC5 275 " (cutoff:3.500A) Processing helix chain 'C5' and resid 282 through 291 removed outlier: 4.240A pdb=" N HISC5 286 " --> pdb=" O SERC5 282 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYSC5 289 " --> pdb=" O VALC5 285 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLYC5 291 " --> pdb=" O METC5 287 " (cutoff:3.500A) Processing helix chain 'C5' and resid 292 through 304 removed outlier: 3.714A pdb=" N LEUC5 296 " --> pdb=" O LYSC5 292 " (cutoff:3.500A) Processing helix chain 'C5' and resid 308 through 330 removed outlier: 4.272A pdb=" N THRC5 312 " --> pdb=" O ASNC5 308 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N METC5 313 " --> pdb=" O GLYC5 309 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALAC5 327 " --> pdb=" O GLUC5 323 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SERC5 330 " --> pdb=" O LYSC5 326 " (cutoff:3.500A) Processing helix chain 'C5' and resid 337 through 342 Processing helix chain 'C5' and resid 343 through 359 Processing helix chain 'C5' and resid 363 through 378 Processing helix chain 'B1' and resid 3 through 25 Processing helix chain 'B1' and resid 29 through 34 removed outlier: 3.994A pdb=" N ILEB1 33 " --> pdb=" O THRB1 29 " (cutoff:3.500A) Processing helix chain 'B2' and resid 3 through 26 Processing helix chain 'B2' and resid 29 through 34 removed outlier: 3.645A pdb=" N ILEB2 33 " --> pdb=" O THRB2 29 " (cutoff:3.500A) Processing helix chain 'B3' and resid 3 through 26 removed outlier: 3.749A pdb=" N LEUB3 7 " --> pdb=" O GLUB3 3 " (cutoff:3.500A) Processing helix chain 'B3' and resid 29 through 34 removed outlier: 3.524A pdb=" N ILEB3 33 " --> pdb=" O THRB3 29 " (cutoff:3.500A) Processing helix chain 'B4' and resid 3 through 26 removed outlier: 3.520A pdb=" N LEUB4 7 " --> pdb=" O GLUB4 3 " (cutoff:3.500A) Processing helix chain 'B4' and resid 29 through 34 Processing helix chain 'B5' and resid 3 through 25 Processing helix chain 'B5' and resid 29 through 34 Processing helix chain 'G1' and resid 1 through 5 Processing helix chain 'G1' and resid 7 through 24 removed outlier: 3.639A pdb=" N GLNG1 11 " --> pdb=" O ALAG1 7 " (cutoff:3.500A) Processing helix chain 'G1' and resid 29 through 44 Processing helix chain 'G1' and resid 48 through 52 Processing helix chain 'G2' and resid 7 through 25 removed outlier: 3.985A pdb=" N GLNG2 11 " --> pdb=" O ALAG2 7 " (cutoff:3.500A) Processing helix chain 'G2' and resid 29 through 44 Processing helix chain 'G3' and resid 1 through 5 Processing helix chain 'G3' and resid 7 through 25 removed outlier: 3.700A pdb=" N GLNG3 11 " --> pdb=" O ALAG3 7 " (cutoff:3.500A) Processing helix chain 'G3' and resid 29 through 45 Processing helix chain 'G3' and resid 46 through 48 No H-bonds generated for 'chain 'G3' and resid 46 through 48' Processing helix chain 'G4' and resid 7 through 25 removed outlier: 4.223A pdb=" N GLNG4 11 " --> pdb=" O ALAG4 7 " (cutoff:3.500A) Processing helix chain 'G4' and resid 29 through 44 Processing helix chain 'G5' and resid 8 through 25 Processing helix chain 'G5' and resid 29 through 46 removed outlier: 4.246A pdb=" N LYSG5 46 " --> pdb=" O GLUG5 42 " (cutoff:3.500A) Processing helix chain 'G5' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'K1' and resid 53 through 58 removed outlier: 9.621A pdb=" N TYRK1 90 " --> pdb=" O TRPK1 45 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ARGK1 47 " --> pdb=" O TYRK1 90 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILEK1 92 " --> pdb=" O ARGK1 47 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASNK1 49 " --> pdb=" O ILEK1 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K1' and resid 157 through 163 removed outlier: 6.500A pdb=" N LEUK1 202 " --> pdb=" O LEUK1 184 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEUK1 184 " --> pdb=" O LEUK1 202 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VALK1 204 " --> pdb=" O GLUK1 182 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K2' and resid 53 through 58 removed outlier: 7.882A pdb=" N ILEK2 92 " --> pdb=" O ARGK2 47 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ASNK2 49 " --> pdb=" O ILEK2 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K2' and resid 156 through 163 removed outlier: 6.656A pdb=" N LEUK2 202 " --> pdb=" O LEUK2 184 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEUK2 184 " --> pdb=" O LEUK2 202 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VALK2 204 " --> pdb=" O GLUK2 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K3' and resid 53 through 58 Processing sheet with id=AA6, first strand: chain 'K3' and resid 156 through 163 removed outlier: 6.509A pdb=" N LEUK3 202 " --> pdb=" O LEUK3 184 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEUK3 184 " --> pdb=" O LEUK3 202 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VALK3 204 " --> pdb=" O GLUK3 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K4' and resid 53 through 58 removed outlier: 9.388A pdb=" N TYRK4 90 " --> pdb=" O TRPK4 45 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ARGK4 47 " --> pdb=" O TYRK4 90 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ILEK4 92 " --> pdb=" O ARGK4 47 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ASNK4 49 " --> pdb=" O ILEK4 92 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALAK4 89 " --> pdb=" O LYSK4 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K4' and resid 155 through 163 removed outlier: 3.625A pdb=" N LYSK4 155 " --> pdb=" O LEUK4 209 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N SERK4 206 " --> pdb=" O PHEK4 181 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N PHEK4 181 " --> pdb=" O SERK4 206 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLUK4 208 " --> pdb=" O TRPK4 179 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N TRPK4 179 " --> pdb=" O GLUK4 208 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K5' and resid 53 through 58 removed outlier: 10.035A pdb=" N TYRK5 90 " --> pdb=" O TRPK5 45 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ARGK5 47 " --> pdb=" O TYRK5 90 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILEK5 92 " --> pdb=" O ARGK5 47 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ASNK5 49 " --> pdb=" O ILEK5 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K5' and resid 157 through 163 removed outlier: 6.664A pdb=" N LEUK5 202 " --> pdb=" O LEUK5 184 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEUK5 184 " --> pdb=" O LEUK5 202 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VALK5 204 " --> pdb=" O GLUK5 182 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B1' and resid 47 through 52 removed outlier: 6.649A pdb=" N ILEB1 338 " --> pdb=" O ARGB1 48 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THRB1 50 " --> pdb=" O LEUB1 336 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEUB1 336 " --> pdb=" O THRB1 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B1' and resid 58 through 63 removed outlier: 3.804A pdb=" N ALAB1 60 " --> pdb=" O ALAB1 73 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYSB1 78 " --> pdb=" O SERB1 74 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEUB1 79 " --> pdb=" O ALAB1 92 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALAB1 92 " --> pdb=" O LEUB1 79 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILEB1 81 " --> pdb=" O VALB1 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B1' and resid 100 through 105 removed outlier: 6.001A pdb=" N CYSB1 121 " --> pdb=" O GLUB1 138 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLUB1 138 " --> pdb=" O CYSB1 121 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILEB1 123 " --> pdb=" O SERB1 136 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARGB1 134 " --> pdb=" O ASNB1 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B1' and resid 146 through 151 removed outlier: 3.599A pdb=" N CYSB1 148 " --> pdb=" O SERB1 160 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEUB1 168 " --> pdb=" O THRB1 177 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B1' and resid 191 through 192 removed outlier: 6.146A pdb=" N ASPB1 212 " --> pdb=" O CYSB1 218 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N CYSB1 218 " --> pdb=" O ASPB1 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B1' and resid 229 through 234 removed outlier: 3.537A pdb=" N ALAB1 231 " --> pdb=" O GLYB1 244 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYSB1 233 " --> pdb=" O ALAB1 242 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N CYSB1 250 " --> pdb=" O THRB1 263 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THRB1 263 " --> pdb=" O CYSB1 250 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEUB1 252 " --> pdb=" O LEUB1 261 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B1' and resid 273 through 278 removed outlier: 3.559A pdb=" N CYSB1 294 " --> pdb=" O LEUB1 308 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ASPB1 298 " --> pdb=" O ARGB1 304 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARGB1 304 " --> pdb=" O ASPB1 298 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B2' and resid 46 through 50 removed outlier: 6.612A pdb=" N ILEB2 338 " --> pdb=" O ARGB2 48 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THRB2 50 " --> pdb=" O LEUB2 336 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEUB2 336 " --> pdb=" O THRB2 50 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYSB2 337 " --> pdb=" O THRB2 329 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B2' and resid 58 through 63 removed outlier: 3.659A pdb=" N ALAB2 60 " --> pdb=" O ALAB2 73 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEUB2 70 " --> pdb=" O TRPB2 82 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYSB2 78 " --> pdb=" O SERB2 74 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B2' and resid 100 through 105 removed outlier: 5.664A pdb=" N ASNB2 125 " --> pdb=" O VALB2 135 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VALB2 135 " --> pdb=" O ASNB2 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B2' and resid 148 through 151 removed outlier: 6.235A pdb=" N LEUB2 168 " --> pdb=" O THRB2 177 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLNB2 175 " --> pdb=" O ASPB2 170 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B2' and resid 198 through 201 removed outlier: 5.788A pdb=" N ASPB2 212 " --> pdb=" O CYSB2 218 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYSB2 218 " --> pdb=" O ASPB2 212 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B2' and resid 229 through 234 removed outlier: 3.853A pdb=" N ALAB2 231 " --> pdb=" O GLYB2 244 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYSB2 233 " --> pdb=" O ALAB2 242 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N CYSB2 250 " --> pdb=" O THRB2 263 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THRB2 263 " --> pdb=" O CYSB2 250 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEUB2 252 " --> pdb=" O LEUB2 261 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B2' and resid 273 through 278 removed outlier: 5.753A pdb=" N ASPB2 298 " --> pdb=" O ARGB2 304 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARGB2 304 " --> pdb=" O ASPB2 298 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B3' and resid 46 through 50 removed outlier: 6.628A pdb=" N ILEB3 338 " --> pdb=" O ARGB3 48 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THRB3 50 " --> pdb=" O LEUB3 336 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEUB3 336 " --> pdb=" O THRB3 50 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYSB3 337 " --> pdb=" O THRB3 329 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B3' and resid 58 through 63 removed outlier: 3.526A pdb=" N ALAB3 60 " --> pdb=" O ALAB3 73 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYSB3 78 " --> pdb=" O SERB3 74 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEUB3 79 " --> pdb=" O ALAB3 92 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALAB3 92 " --> pdb=" O LEUB3 79 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILEB3 81 " --> pdb=" O VALB3 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B3' and resid 100 through 105 removed outlier: 4.850A pdb=" N GLYB3 116 " --> pdb=" O ILEB3 120 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILEB3 120 " --> pdb=" O GLYB3 116 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASNB3 125 " --> pdb=" O VALB3 135 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VALB3 135 " --> pdb=" O ASNB3 125 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B3' and resid 146 through 151 removed outlier: 7.115A pdb=" N SERB3 160 " --> pdb=" O SERB3 147 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N CYSB3 149 " --> pdb=" O VALB3 158 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VALB3 158 " --> pdb=" O CYSB3 149 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N PHEB3 151 " --> pdb=" O GLNB3 156 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLNB3 156 " --> pdb=" O PHEB3 151 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEUB3 168 " --> pdb=" O THRB3 177 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B3' and resid 191 through 192 removed outlier: 3.913A pdb=" N PHEB3 199 " --> pdb=" O TRPB3 211 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASPB3 212 " --> pdb=" O CYSB3 218 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N CYSB3 218 " --> pdb=" O ASPB3 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B3' and resid 229 through 234 removed outlier: 3.757A pdb=" N ALAB3 231 " --> pdb=" O GLYB3 244 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYSB3 233 " --> pdb=" O ALAB3 242 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASPB3 254 " --> pdb=" O GLUB3 260 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLUB3 260 " --> pdb=" O ASPB3 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B3' and resid 273 through 278 removed outlier: 6.211A pdb=" N GLYB3 288 " --> pdb=" O THRB3 274 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VALB3 276 " --> pdb=" O LEUB3 286 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEUB3 286 " --> pdb=" O VALB3 276 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHEB3 278 " --> pdb=" O LEUB3 284 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEUB3 284 " --> pdb=" O PHEB3 278 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASPB3 298 " --> pdb=" O ARGB3 304 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ARGB3 304 " --> pdb=" O ASPB3 298 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B4' and resid 46 through 50 removed outlier: 6.451A pdb=" N ILEB4 338 " --> pdb=" O ARGB4 48 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THRB4 50 " --> pdb=" O LEUB4 336 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEUB4 336 " --> pdb=" O THRB4 50 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYSB4 337 " --> pdb=" O THRB4 329 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B4' and resid 58 through 62 removed outlier: 3.761A pdb=" N ALAB4 60 " --> pdb=" O ALAB4 73 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYSB4 78 " --> pdb=" O SERB4 74 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEUB4 79 " --> pdb=" O ALAB4 92 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALAB4 92 " --> pdb=" O LEUB4 79 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILEB4 81 " --> pdb=" O VALB4 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B4' and resid 100 through 105 removed outlier: 6.082A pdb=" N CYSB4 121 " --> pdb=" O GLUB4 138 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLUB4 138 " --> pdb=" O CYSB4 121 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILEB4 123 " --> pdb=" O SERB4 136 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARGB4 134 " --> pdb=" O ASNB4 125 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B4' and resid 146 through 151 Processing sheet with id=AD9, first strand: chain 'B4' and resid 187 through 192 removed outlier: 5.685A pdb=" N ASPB4 212 " --> pdb=" O CYSB4 218 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N CYSB4 218 " --> pdb=" O ASPB4 212 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B4' and resid 229 through 234 removed outlier: 6.581A pdb=" N CYSB4 250 " --> pdb=" O THRB4 263 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THRB4 263 " --> pdb=" O CYSB4 250 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEUB4 252 " --> pdb=" O LEUB4 261 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B4' and resid 273 through 278 removed outlier: 5.423A pdb=" N ASPB4 298 " --> pdb=" O ARGB4 304 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARGB4 304 " --> pdb=" O ASPB4 298 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B5' and resid 46 through 51 removed outlier: 3.522A pdb=" N ARGB5 46 " --> pdb=" O ASNB5 340 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILEB5 338 " --> pdb=" O ARGB5 48 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N THRB5 50 " --> pdb=" O LEUB5 336 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEUB5 336 " --> pdb=" O THRB5 50 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYSB5 337 " --> pdb=" O THRB5 329 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B5' and resid 58 through 63 removed outlier: 3.677A pdb=" N ALAB5 60 " --> pdb=" O ALAB5 73 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SERB5 74 " --> pdb=" O LYSB5 78 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYSB5 78 " --> pdb=" O SERB5 74 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEUB5 79 " --> pdb=" O ALAB5 92 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALAB5 92 " --> pdb=" O LEUB5 79 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILEB5 81 " --> pdb=" O VALB5 90 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASNB5 88 " --> pdb=" O ASPB5 83 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B5' and resid 100 through 105 removed outlier: 5.892A pdb=" N CYSB5 121 " --> pdb=" O GLUB5 138 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLUB5 138 " --> pdb=" O CYSB5 121 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILEB5 123 " --> pdb=" O SERB5 136 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARGB5 134 " --> pdb=" O ASNB5 125 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B5' and resid 146 through 151 removed outlier: 6.617A pdb=" N LEUB5 168 " --> pdb=" O THRB5 177 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLNB5 175 " --> pdb=" O ASPB5 170 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B5' and resid 191 through 192 removed outlier: 5.954A pdb=" N ASPB5 212 " --> pdb=" O CYSB5 218 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N CYSB5 218 " --> pdb=" O ASPB5 212 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B5' and resid 229 through 231 removed outlier: 6.916A pdb=" N GLYB5 244 " --> pdb=" O ASNB5 230 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASPB5 254 " --> pdb=" O GLUB5 260 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLUB5 260 " --> pdb=" O ASPB5 254 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B5' and resid 273 through 278 removed outlier: 4.274A pdb=" N CYSB5 294 " --> pdb=" O LEUB5 308 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASPB5 298 " --> pdb=" O ARGB5 304 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ARGB5 304 " --> pdb=" O ASPB5 298 " (cutoff:3.500A) 1972 hydrogen bonds defined for protein. 5742 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.38 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12615 1.34 - 1.46: 7162 1.46 - 1.58: 18317 1.58 - 1.70: 1 1.70 - 1.82: 425 Bond restraints: 38520 Sorted by residual: bond pdb=" N VALK3 154 " pdb=" CA VALK3 154 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.80e+00 bond pdb=" N ILEK5 92 " pdb=" CA ILEK5 92 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.20e-02 6.94e+03 8.80e+00 bond pdb=" N ARGK5 94 " pdb=" CA ARGK5 94 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.39e+00 bond pdb=" N ILEB4 269 " pdb=" CA ILEB4 269 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.17e-02 7.31e+03 7.05e+00 bond pdb=" N GLYB3 202 " pdb=" CA GLYB3 202 " ideal model delta sigma weight residual 1.447 1.477 -0.030 1.17e-02 7.31e+03 6.70e+00 ... (remaining 38515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 51271 2.75 - 5.49: 606 5.49 - 8.24: 87 8.24 - 10.98: 28 10.98 - 13.73: 3 Bond angle restraints: 51995 Sorted by residual: angle pdb=" N LYSK2 44 " pdb=" CA LYSK2 44 " pdb=" C LYSK2 44 " ideal model delta sigma weight residual 114.75 103.04 11.71 1.26e+00 6.30e-01 8.64e+01 angle pdb=" C TYRK4 193 " pdb=" CA TYRK4 193 " pdb=" CB TYRK4 193 " ideal model delta sigma weight residual 116.54 109.72 6.82 1.15e+00 7.56e-01 3.52e+01 angle pdb=" C ASNK2 130 " pdb=" N ILEK2 131 " pdb=" CA ILEK2 131 " ideal model delta sigma weight residual 122.37 115.50 6.87 1.25e+00 6.40e-01 3.02e+01 angle pdb=" C LEUC1 195 " pdb=" CA LEUC1 195 " pdb=" CB LEUC1 195 " ideal model delta sigma weight residual 116.63 110.38 6.25 1.16e+00 7.43e-01 2.90e+01 angle pdb=" N ASPB3 118 " pdb=" CA ASPB3 118 " pdb=" C ASPB3 118 " ideal model delta sigma weight residual 114.56 108.28 6.28 1.27e+00 6.20e-01 2.44e+01 ... (remaining 51990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 20760 17.99 - 35.99: 1934 35.99 - 53.98: 376 53.98 - 71.98: 187 71.98 - 89.97: 128 Dihedral angle restraints: 23385 sinusoidal: 9500 harmonic: 13885 Sorted by residual: dihedral pdb=" CD ARGK5 94 " pdb=" NE ARGK5 94 " pdb=" CZ ARGK5 94 " pdb=" NH1 ARGK5 94 " ideal model delta sinusoidal sigma weight residual 0.00 -79.89 79.89 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CD ARGK4 72 " pdb=" NE ARGK4 72 " pdb=" CZ ARGK4 72 " pdb=" NH1 ARGK4 72 " ideal model delta sinusoidal sigma weight residual 0.00 -52.92 52.92 1 1.00e+01 1.00e-02 3.81e+01 dihedral pdb=" CG ARGK5 94 " pdb=" CD ARGK5 94 " pdb=" NE ARGK5 94 " pdb=" CZ ARGK5 94 " ideal model delta sinusoidal sigma weight residual -90.00 -19.02 -70.98 2 1.50e+01 4.44e-03 1.91e+01 ... (remaining 23382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4417 0.049 - 0.099: 1152 0.099 - 0.148: 189 0.148 - 0.197: 19 0.197 - 0.247: 3 Chirality restraints: 5780 Sorted by residual: chirality pdb=" CA ILEB4 270 " pdb=" N ILEB4 270 " pdb=" C ILEB4 270 " pdb=" CB ILEB4 270 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILEC1 33 " pdb=" CA ILEC1 33 " pdb=" CG1 ILEC1 33 " pdb=" CG2 ILEC1 33 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA METG3 21 " pdb=" N METG3 21 " pdb=" C METG3 21 " pdb=" CB METG3 21 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 5777 not shown) Planarity restraints: 6780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARGK5 94 " 1.079 9.50e-02 1.11e+02 4.83e-01 1.41e+02 pdb=" NE ARGK5 94 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARGK5 94 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARGK5 94 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARGK5 94 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGK4 72 " 0.867 9.50e-02 1.11e+02 3.89e-01 9.17e+01 pdb=" NE ARGK4 72 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARGK4 72 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARGK4 72 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARGK4 72 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRPC4 109 " 0.023 2.00e-02 2.50e+03 1.89e-02 8.93e+00 pdb=" CG TRPC4 109 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRPC4 109 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRPC4 109 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRPC4 109 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRPC4 109 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRPC4 109 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRPC4 109 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRPC4 109 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRPC4 109 " 0.001 2.00e-02 2.50e+03 ... (remaining 6777 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 664 2.66 - 3.22: 39180 3.22 - 3.78: 64235 3.78 - 4.34: 88904 4.34 - 4.90: 139762 Nonbonded interactions: 332745 Sorted by model distance: nonbonded pdb=" OG1 THRB2 321 " pdb=" OD1 ASPB2 323 " model vdw 2.097 3.040 nonbonded pdb=" O THRK5 58 " pdb=" OG1 THRK5 61 " model vdw 2.125 3.040 nonbonded pdb=" OG SERC5 53 " pdb=" OE1 GLUC5 55 " model vdw 2.144 3.040 nonbonded pdb=" OD2 ASPK1 95 " pdb=" OG1 THRK1 97 " model vdw 2.169 3.040 nonbonded pdb=" O CYSB3 148 " pdb=" OG SERB3 160 " model vdw 2.178 3.040 ... (remaining 332740 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'B1' selection = chain 'B2' selection = chain 'B3' selection = chain 'B4' selection = chain 'B5' } ncs_group { reference = chain 'C1' selection = chain 'C2' selection = chain 'C3' selection = chain 'C4' selection = chain 'C5' } ncs_group { reference = chain 'G1' selection = chain 'G2' selection = chain 'G3' selection = chain 'G4' selection = chain 'G5' } ncs_group { reference = chain 'K1' selection = chain 'K2' selection = chain 'K3' selection = chain 'K4' selection = chain 'K5' } 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 31.400 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 : 0.004 0.105 38520 Z= 0.200 Angle : 0.799 13.730 51995 Z= 0.455 Chirality : 0.044 0.247 5780 Planarity : 0.009 0.483 6780 Dihedral : 17.065 89.971 14415 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.97 % Favored : 94.90 % Rotamer: Outliers : 0.60 % Allowed : 16.57 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.12), residues: 4730 helix: 0.59 (0.11), residues: 2057 sheet: -1.54 (0.17), residues: 802 loop : -1.75 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGB2 46 TYR 0.037 0.002 TYRC5 376 PHE 0.033 0.002 PHEC3 54 TRP 0.051 0.002 TRPC4 109 HIS 0.011 0.002 HISC5 67 Details of bonding type rmsd covalent geometry : bond 0.00381 (38520) covalent geometry : angle 0.79895 (51995) hydrogen bonds : bond 0.14228 ( 1972) hydrogen bonds : angle 6.53609 ( 5742) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 253 time to evaluate : 1.173 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: K2 129 TYR cc_start: 0.8411 (m-80) cc_final: 0.7350 (m-80) REVERT: K2 171 MET cc_start: 0.9222 (ptp) cc_final: 0.9011 (ptp) REVERT: K2 198 GLN cc_start: 0.3998 (tp40) cc_final: 0.2981 (pp30) REVERT: K4 72 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7830 (mmm160) REVERT: C1 184 ARG cc_start: 0.9174 (mtm180) cc_final: 0.8602 (ptt-90) REVERT: C1 279 MET cc_start: 0.7670 (mtt) cc_final: 0.7184 (ptp) REVERT: C1 317 MET cc_start: 0.5619 (tpt) cc_final: 0.4705 (tmm) REVERT: C4 191 MET cc_start: 0.9508 (tpp) cc_final: 0.9216 (mmm) REVERT: C5 55 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8776 (mp0) REVERT: B2 61 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7451 (ptm) REVERT: B2 312 ASP cc_start: 0.9016 (p0) cc_final: 0.8719 (p0) REVERT: B4 45 MET cc_start: 0.8091 (mpp) cc_final: 0.7746 (mmt) REVERT: B4 188 MET cc_start: 0.8708 (ppp) cc_final: 0.8247 (ppp) outliers start: 25 outliers final: 12 residues processed: 275 average time/residue: 0.2005 time to fit residues: 91.9318 Evaluate side-chains 253 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 238 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K2 residue 44 LYS Chi-restraints excluded: chain K2 residue 77 ASP Chi-restraints excluded: chain K4 residue 72 ARG Chi-restraints excluded: chain K5 residue 93 ASP Chi-restraints excluded: chain K5 residue 94 ARG Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C2 residue 28 LYS Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C5 residue 55 GLU Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain B1 residue 276 VAL Chi-restraints excluded: chain B2 residue 61 MET Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B5 residue 82 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 50.0000 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 0.9980 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K2 60 GLN K2 108 HIS ** K2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 170 GLN ** K2 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K3 75 GLN ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K4 164 GLN ** K4 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 211 ASN C1 60 ASN ** C1 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 133 GLN ** C1 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 218 GLN ** C1 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 368 GLN C2 290 ASN C3 185 ASN ** C3 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 100 ASN C4 150 GLN C4 228 ASN C5 98 ASN ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 9 GLN ** B2 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3 142 HIS ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 220 GLN B3 237 ASN ** B3 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 125 ASN B5 32 GLN B5 36 ASN ** B5 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5 88 ASN ** G2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 24 ASN ** G2 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3 4 ASN ** G4 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.077518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.057996 restraints weight = 417603.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 83)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.052731 restraints weight = 267354.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.052730 restraints weight = 190348.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.052889 restraints weight = 157285.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.053011 restraints weight = 136690.996| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 38520 Z= 0.342 Angle : 0.828 10.670 51995 Z= 0.440 Chirality : 0.046 0.214 5780 Planarity : 0.006 0.090 6780 Dihedral : 6.453 64.244 5262 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.43 % Favored : 93.51 % Rotamer: Outliers : 3.43 % Allowed : 14.65 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.12), residues: 4730 helix: 0.41 (0.11), residues: 2056 sheet: -1.71 (0.17), residues: 759 loop : -1.90 (0.13), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGC5 120 TYR 0.033 0.003 TYRB4 105 PHE 0.032 0.003 PHEG5 61 TRP 0.026 0.003 TRPC4 34 HIS 0.011 0.002 HISC1 160 Details of bonding type rmsd covalent geometry : bond 0.00703 (38520) covalent geometry : angle 0.82774 (51995) hydrogen bonds : bond 0.04934 ( 1972) hydrogen bonds : angle 5.72889 ( 5742) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 249 time to evaluate : 1.274 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: K1 60 GLN cc_start: 0.9002 (mp10) cc_final: 0.8798 (mp10) REVERT: K1 155 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.9047 (mtmm) REVERT: K2 198 GLN cc_start: 0.4384 (tp40) cc_final: 0.2756 (pp30) REVERT: K3 129 TYR cc_start: 0.6646 (m-10) cc_final: 0.6237 (m-10) REVERT: K3 212 THR cc_start: 0.3876 (OUTLIER) cc_final: 0.3578 (p) REVERT: C1 184 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.9000 (mtm-85) REVERT: C1 212 MET cc_start: 0.3860 (ptm) cc_final: 0.3018 (ptt) REVERT: C1 317 MET cc_start: 0.5144 (tpt) cc_final: 0.4203 (tmm) REVERT: C2 116 MET cc_start: 0.2463 (ptm) cc_final: 0.2226 (ptm) REVERT: C2 212 MET cc_start: 0.8889 (ppp) cc_final: 0.8652 (ppp) REVERT: C3 29 TYR cc_start: -0.0054 (OUTLIER) cc_final: -0.1731 (p90) REVERT: C3 287 MET cc_start: -0.2590 (mtt) cc_final: -0.2878 (mtt) REVERT: C4 212 MET cc_start: 0.3338 (ppp) cc_final: 0.3044 (ppp) REVERT: C5 25 MET cc_start: 0.3189 (tpp) cc_final: 0.2933 (tpp) REVERT: C5 128 ARG cc_start: 0.9040 (tmt170) cc_final: 0.8591 (ttt-90) REVERT: C5 168 MET cc_start: 0.8735 (mmm) cc_final: 0.8469 (mmm) REVERT: B1 262 MET cc_start: 0.9024 (mmm) cc_final: 0.8799 (mmm) REVERT: B2 217 MET cc_start: 0.8294 (ppp) cc_final: 0.7990 (ppp) REVERT: B2 262 MET cc_start: 0.8509 (tpp) cc_final: 0.8190 (tpp) REVERT: B3 267 ASP cc_start: 0.8820 (p0) cc_final: 0.8592 (p0) REVERT: B4 45 MET cc_start: 0.8422 (mpp) cc_final: 0.7696 (mpp) REVERT: B4 188 MET cc_start: 0.8691 (ppp) cc_final: 0.8175 (ppp) REVERT: B4 273 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8443 (mt) REVERT: B5 325 MET cc_start: 0.9359 (tpp) cc_final: 0.9044 (tpp) REVERT: G4 9 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.7008 (pt) REVERT: G4 21 MET cc_start: 0.9376 (mpp) cc_final: 0.9168 (mpp) REVERT: G5 1 MET cc_start: 0.7821 (ppp) cc_final: 0.7354 (tmm) outliers start: 143 outliers final: 72 residues processed: 373 average time/residue: 0.1982 time to fit residues: 124.5001 Evaluate side-chains 298 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 220 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 97 THR Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 155 LYS Chi-restraints excluded: chain K1 residue 169 THR Chi-restraints excluded: chain K1 residue 187 ILE Chi-restraints excluded: chain K2 residue 62 LEU Chi-restraints excluded: chain K2 residue 77 ASP Chi-restraints excluded: chain K3 residue 70 LEU Chi-restraints excluded: chain K3 residue 97 THR Chi-restraints excluded: chain K3 residue 157 VAL Chi-restraints excluded: chain K3 residue 175 MET Chi-restraints excluded: chain K3 residue 206 SER Chi-restraints excluded: chain K3 residue 212 THR Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 111 LEU Chi-restraints excluded: chain K4 residue 169 THR Chi-restraints excluded: chain K4 residue 205 VAL Chi-restraints excluded: chain K5 residue 93 ASP Chi-restraints excluded: chain K5 residue 94 ARG Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 134 LEU Chi-restraints excluded: chain K5 residue 152 VAL Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 83 GLU Chi-restraints excluded: chain C1 residue 126 MET Chi-restraints excluded: chain C1 residue 144 LEU Chi-restraints excluded: chain C1 residue 169 ILE Chi-restraints excluded: chain C1 residue 172 GLU Chi-restraints excluded: chain C1 residue 184 ARG Chi-restraints excluded: chain C2 residue 278 GLU Chi-restraints excluded: chain C2 residue 293 THR Chi-restraints excluded: chain C2 residue 306 VAL Chi-restraints excluded: chain C3 residue 29 TYR Chi-restraints excluded: chain C3 residue 264 VAL Chi-restraints excluded: chain C3 residue 273 MET Chi-restraints excluded: chain C4 residue 39 ASN Chi-restraints excluded: chain C4 residue 206 GLU Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C5 residue 57 LEU Chi-restraints excluded: chain C5 residue 79 GLU Chi-restraints excluded: chain C5 residue 104 THR Chi-restraints excluded: chain C5 residue 132 GLN Chi-restraints excluded: chain C5 residue 293 THR Chi-restraints excluded: chain C5 residue 299 MET Chi-restraints excluded: chain C5 residue 354 ARG Chi-restraints excluded: chain B1 residue 40 VAL Chi-restraints excluded: chain B1 residue 187 VAL Chi-restraints excluded: chain B1 residue 307 VAL Chi-restraints excluded: chain B1 residue 325 MET Chi-restraints excluded: chain B2 residue 61 MET Chi-restraints excluded: chain B2 residue 112 VAL Chi-restraints excluded: chain B2 residue 152 LEU Chi-restraints excluded: chain B2 residue 187 VAL Chi-restraints excluded: chain B2 residue 286 LEU Chi-restraints excluded: chain B2 residue 318 LEU Chi-restraints excluded: chain B3 residue 3 GLU Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 169 TRP Chi-restraints excluded: chain B3 residue 187 VAL Chi-restraints excluded: chain B3 residue 336 LEU Chi-restraints excluded: chain B4 residue 20 ASP Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 136 SER Chi-restraints excluded: chain B4 residue 263 THR Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B4 residue 273 ILE Chi-restraints excluded: chain B4 residue 286 LEU Chi-restraints excluded: chain B5 residue 29 THR Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 273 ILE Chi-restraints excluded: chain B5 residue 338 ILE Chi-restraints excluded: chain G1 residue 3 SER Chi-restraints excluded: chain G2 residue 5 ASN Chi-restraints excluded: chain G2 residue 28 ILE Chi-restraints excluded: chain G4 residue 9 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 447 optimal weight: 3.9990 chunk 268 optimal weight: 40.0000 chunk 164 optimal weight: 50.0000 chunk 103 optimal weight: 6.9990 chunk 309 optimal weight: 0.9980 chunk 462 optimal weight: 10.0000 chunk 361 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 398 optimal weight: 10.0000 chunk 80 optimal weight: 40.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 192 ASN ** K2 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3 183 GLN K4 60 GLN ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K4 192 ASN ** K4 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K5 104 ASN ** K5 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 106 ASN C2 286 HIS ** C3 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 69 HIS C5 163 GLN B2 142 HIS ** B2 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 237 ASN ** B3 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 259 GLN ** G2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4 4 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 = 0.4280 r_free = 0.4280 target = 0.078417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.058999 restraints weight = 426148.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.059279 restraints weight = 254379.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.058540 restraints weight = 161789.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.058523 restraints weight = 133740.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.058574 restraints weight = 131027.374| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 38520 Z= 0.197 Angle : 0.665 12.067 51995 Z= 0.353 Chirality : 0.043 0.267 5780 Planarity : 0.004 0.055 6780 Dihedral : 5.890 56.142 5242 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 2.73 % Allowed : 16.57 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.12), residues: 4730 helix: 0.69 (0.11), residues: 2080 sheet: -1.78 (0.17), residues: 786 loop : -1.73 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGC5 120 TYR 0.041 0.002 TYRK5 54 PHE 0.024 0.002 PHEB4 199 TRP 0.018 0.002 TRPK4 45 HIS 0.007 0.002 HISB2 266 Details of bonding type rmsd covalent geometry : bond 0.00411 (38520) covalent geometry : angle 0.66498 (51995) hydrogen bonds : bond 0.04223 ( 1972) hydrogen bonds : angle 5.43093 ( 5742) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 234 time to evaluate : 1.433 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: K1 171 MET cc_start: 0.9022 (ppp) cc_final: 0.8737 (ppp) REVERT: K2 198 GLN cc_start: 0.3939 (tp40) cc_final: 0.2650 (pp30) REVERT: K3 129 TYR cc_start: 0.6641 (m-10) cc_final: 0.6353 (m-10) REVERT: K3 212 THR cc_start: 0.4150 (OUTLIER) cc_final: 0.3859 (p) REVERT: C1 212 MET cc_start: 0.4067 (ptm) cc_final: 0.3475 (ptt) REVERT: C1 317 MET cc_start: 0.5003 (tpt) cc_final: 0.4041 (tmm) REVERT: C3 126 MET cc_start: 0.5561 (ppp) cc_final: 0.5243 (ppp) REVERT: C3 287 MET cc_start: -0.2686 (mtt) cc_final: -0.2968 (mtt) REVERT: C4 64 MET cc_start: 0.5673 (mtp) cc_final: 0.5386 (ttp) REVERT: C4 73 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6645 (mt) REVERT: C5 128 ARG cc_start: 0.9031 (tmt170) cc_final: 0.8617 (ttt-90) REVERT: C5 144 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6600 (tt) REVERT: B2 262 MET cc_start: 0.8495 (tpp) cc_final: 0.8204 (tpp) REVERT: B3 260 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: B3 267 ASP cc_start: 0.8819 (p0) cc_final: 0.8610 (p0) REVERT: B4 45 MET cc_start: 0.8443 (mpp) cc_final: 0.7679 (mpp) REVERT: B4 61 MET cc_start: 0.8279 (tmm) cc_final: 0.8012 (tmm) REVERT: B4 188 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8280 (tmm) REVERT: B4 325 MET cc_start: 0.8085 (tpp) cc_final: 0.7738 (tpp) REVERT: B5 325 MET cc_start: 0.9104 (tpp) cc_final: 0.8844 (tpp) REVERT: G4 9 ILE cc_start: 0.7236 (OUTLIER) cc_final: 0.6969 (pt) REVERT: G4 21 MET cc_start: 0.9401 (mpp) cc_final: 0.9084 (mpp) REVERT: G5 1 MET cc_start: 0.7887 (ppp) cc_final: 0.7469 (tmm) outliers start: 114 outliers final: 68 residues processed: 334 average time/residue: 0.2004 time to fit residues: 112.9805 Evaluate side-chains 294 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 220 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 169 THR Chi-restraints excluded: chain K1 residue 187 ILE Chi-restraints excluded: chain K2 residue 62 LEU Chi-restraints excluded: chain K2 residue 70 LEU Chi-restraints excluded: chain K3 residue 90 TYR Chi-restraints excluded: chain K3 residue 97 THR Chi-restraints excluded: chain K3 residue 157 VAL Chi-restraints excluded: chain K3 residue 212 THR Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 111 LEU Chi-restraints excluded: chain K5 residue 50 VAL Chi-restraints excluded: chain K5 residue 93 ASP Chi-restraints excluded: chain K5 residue 94 ARG Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 111 LEU Chi-restraints excluded: chain K5 residue 134 LEU Chi-restraints excluded: chain K5 residue 152 VAL Chi-restraints excluded: chain K5 residue 161 LEU Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C1 residue 83 GLU Chi-restraints excluded: chain C1 residue 172 GLU Chi-restraints excluded: chain C1 residue 348 LEU Chi-restraints excluded: chain C2 residue 39 ASN Chi-restraints excluded: chain C2 residue 54 PHE Chi-restraints excluded: chain C2 residue 183 ILE Chi-restraints excluded: chain C2 residue 278 GLU Chi-restraints excluded: chain C2 residue 293 THR Chi-restraints excluded: chain C2 residue 306 VAL Chi-restraints excluded: chain C4 residue 73 LEU Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C4 residue 313 MET Chi-restraints excluded: chain C5 residue 57 LEU Chi-restraints excluded: chain C5 residue 79 GLU Chi-restraints excluded: chain C5 residue 104 THR Chi-restraints excluded: chain C5 residue 132 GLN Chi-restraints excluded: chain C5 residue 144 LEU Chi-restraints excluded: chain C5 residue 163 GLN Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 254 LYS Chi-restraints excluded: chain C5 residue 256 THR Chi-restraints excluded: chain C5 residue 299 MET Chi-restraints excluded: chain C5 residue 354 ARG Chi-restraints excluded: chain B1 residue 40 VAL Chi-restraints excluded: chain B1 residue 58 ILE Chi-restraints excluded: chain B1 residue 61 MET Chi-restraints excluded: chain B1 residue 187 VAL Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B1 residue 307 VAL Chi-restraints excluded: chain B1 residue 325 MET Chi-restraints excluded: chain B2 residue 136 SER Chi-restraints excluded: chain B2 residue 152 LEU Chi-restraints excluded: chain B2 residue 286 LEU Chi-restraints excluded: chain B2 residue 318 LEU Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 169 TRP Chi-restraints excluded: chain B3 residue 187 VAL Chi-restraints excluded: chain B3 residue 198 LEU Chi-restraints excluded: chain B3 residue 260 GLU Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 136 SER Chi-restraints excluded: chain B4 residue 146 LEU Chi-restraints excluded: chain B4 residue 188 MET Chi-restraints excluded: chain B4 residue 232 ILE Chi-restraints excluded: chain B4 residue 259 GLN Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B4 residue 286 LEU Chi-restraints excluded: chain B5 residue 29 THR Chi-restraints excluded: chain B5 residue 177 THR Chi-restraints excluded: chain B5 residue 213 VAL Chi-restraints excluded: chain B5 residue 284 LEU Chi-restraints excluded: chain G2 residue 5 ASN Chi-restraints excluded: chain G2 residue 28 ILE Chi-restraints excluded: chain G4 residue 9 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 381 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 413 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 180 optimal weight: 20.0000 chunk 420 optimal weight: 10.0000 chunk 464 optimal weight: 2.9990 chunk 262 optimal weight: 40.0000 chunk 439 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K5 75 GLN ** K5 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 106 ASN C1 250 HIS ** C3 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3 135 ASN C4 218 GLN C5 67 HIS B1 220 GLN ** B2 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 237 ASN ** B3 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 176 GLN B4 268 ASN B5 142 HIS ** G2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4 4 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 = 0.4277 r_free = 0.4277 target = 0.078315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.058614 restraints weight = 426960.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.054967 restraints weight = 249799.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.054943 restraints weight = 174783.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.055292 restraints weight = 144362.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.055318 restraints weight = 124653.816| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 38520 Z= 0.185 Angle : 0.646 14.065 51995 Z= 0.341 Chirality : 0.042 0.344 5780 Planarity : 0.004 0.051 6780 Dihedral : 5.632 58.972 5237 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.62 % Favored : 94.29 % Rotamer: Outliers : 3.07 % Allowed : 16.67 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.12), residues: 4730 helix: 0.85 (0.11), residues: 2082 sheet: -1.75 (0.17), residues: 780 loop : -1.66 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGC1 184 TYR 0.019 0.002 TYRK5 71 PHE 0.022 0.002 PHEB4 199 TRP 0.038 0.002 TRPC3 109 HIS 0.007 0.001 HISC1 112 Details of bonding type rmsd covalent geometry : bond 0.00387 (38520) covalent geometry : angle 0.64615 (51995) hydrogen bonds : bond 0.03961 ( 1972) hydrogen bonds : angle 5.26177 ( 5742) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 238 time to evaluate : 1.233 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: K2 198 GLN cc_start: 0.3579 (tp40) cc_final: 0.2326 (pp30) REVERT: K3 112 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8425 (p) REVERT: K3 124 GLU cc_start: 0.9402 (mt-10) cc_final: 0.9151 (tt0) REVERT: K3 129 TYR cc_start: 0.6456 (m-10) cc_final: 0.6073 (m-10) REVERT: K3 212 THR cc_start: 0.3834 (OUTLIER) cc_final: 0.3522 (p) REVERT: K5 93 ASP cc_start: 0.6384 (OUTLIER) cc_final: 0.5304 (t70) REVERT: C1 212 MET cc_start: 0.4188 (OUTLIER) cc_final: 0.3446 (ptt) REVERT: C1 317 MET cc_start: 0.4834 (tpt) cc_final: 0.3820 (tmm) REVERT: C3 124 MET cc_start: 0.7842 (mtt) cc_final: 0.7637 (mtt) REVERT: C3 126 MET cc_start: 0.5780 (ppp) cc_final: 0.5421 (ppp) REVERT: C3 287 MET cc_start: -0.2584 (mtt) cc_final: -0.2858 (mtt) REVERT: C4 28 LYS cc_start: 0.9428 (tptp) cc_final: 0.8892 (mmmt) REVERT: C4 64 MET cc_start: 0.5947 (OUTLIER) cc_final: 0.5681 (ttp) REVERT: C4 73 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6683 (mt) REVERT: C4 124 MET cc_start: 0.8014 (mmt) cc_final: 0.7685 (mmm) REVERT: C4 126 MET cc_start: 0.7954 (ppp) cc_final: 0.7694 (ppp) REVERT: C4 276 ILE cc_start: 0.3576 (OUTLIER) cc_final: 0.3135 (tp) REVERT: C4 302 LEU cc_start: -0.0115 (OUTLIER) cc_final: -0.0352 (tp) REVERT: C5 25 MET cc_start: 0.4038 (tpp) cc_final: 0.2843 (tmm) REVERT: C5 128 ARG cc_start: 0.8958 (tmt170) cc_final: 0.8528 (ttt-90) REVERT: C5 144 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6678 (tt) REVERT: B1 262 MET cc_start: 0.9172 (mmm) cc_final: 0.8839 (mmm) REVERT: B1 325 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8305 (ptm) REVERT: B2 262 MET cc_start: 0.8500 (tpp) cc_final: 0.8170 (tpp) REVERT: B3 188 MET cc_start: 0.8808 (ppp) cc_final: 0.8228 (ppp) REVERT: B3 260 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: B3 267 ASP cc_start: 0.8920 (p0) cc_final: 0.8714 (p0) REVERT: B4 61 MET cc_start: 0.8300 (tmm) cc_final: 0.8021 (tmm) REVERT: B4 188 MET cc_start: 0.8785 (ppp) cc_final: 0.8330 (tmm) REVERT: B4 273 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8192 (mt) REVERT: B5 325 MET cc_start: 0.9203 (tpp) cc_final: 0.8901 (tpp) REVERT: G4 9 ILE cc_start: 0.7049 (OUTLIER) cc_final: 0.6765 (pt) REVERT: G5 1 MET cc_start: 0.8106 (ppp) cc_final: 0.7682 (tmm) outliers start: 128 outliers final: 78 residues processed: 351 average time/residue: 0.1917 time to fit residues: 114.4050 Evaluate side-chains 314 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 223 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 58 THR Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 97 THR Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 169 THR Chi-restraints excluded: chain K1 residue 187 ILE Chi-restraints excluded: chain K2 residue 70 LEU Chi-restraints excluded: chain K2 residue 111 LEU Chi-restraints excluded: chain K3 residue 90 TYR Chi-restraints excluded: chain K3 residue 97 THR Chi-restraints excluded: chain K3 residue 112 VAL Chi-restraints excluded: chain K3 residue 157 VAL Chi-restraints excluded: chain K3 residue 161 LEU Chi-restraints excluded: chain K3 residue 175 MET Chi-restraints excluded: chain K3 residue 206 SER Chi-restraints excluded: chain K3 residue 212 THR Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 111 LEU Chi-restraints excluded: chain K4 residue 169 THR Chi-restraints excluded: chain K5 residue 93 ASP Chi-restraints excluded: chain K5 residue 94 ARG Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 152 VAL Chi-restraints excluded: chain K5 residue 154 VAL Chi-restraints excluded: chain K5 residue 161 LEU Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 83 GLU Chi-restraints excluded: chain C1 residue 144 LEU Chi-restraints excluded: chain C1 residue 172 GLU Chi-restraints excluded: chain C1 residue 212 MET Chi-restraints excluded: chain C1 residue 348 LEU Chi-restraints excluded: chain C2 residue 39 ASN Chi-restraints excluded: chain C2 residue 54 PHE Chi-restraints excluded: chain C2 residue 183 ILE Chi-restraints excluded: chain C2 residue 237 VAL Chi-restraints excluded: chain C2 residue 306 VAL Chi-restraints excluded: chain C2 residue 345 LEU Chi-restraints excluded: chain C4 residue 39 ASN Chi-restraints excluded: chain C4 residue 62 TYR Chi-restraints excluded: chain C4 residue 64 MET Chi-restraints excluded: chain C4 residue 73 LEU Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C4 residue 276 ILE Chi-restraints excluded: chain C4 residue 302 LEU Chi-restraints excluded: chain C4 residue 313 MET Chi-restraints excluded: chain C5 residue 57 LEU Chi-restraints excluded: chain C5 residue 79 GLU Chi-restraints excluded: chain C5 residue 104 THR Chi-restraints excluded: chain C5 residue 144 LEU Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 254 LYS Chi-restraints excluded: chain C5 residue 256 THR Chi-restraints excluded: chain C5 residue 299 MET Chi-restraints excluded: chain C5 residue 354 ARG Chi-restraints excluded: chain B1 residue 40 VAL Chi-restraints excluded: chain B1 residue 58 ILE Chi-restraints excluded: chain B1 residue 71 VAL Chi-restraints excluded: chain B1 residue 187 VAL Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B1 residue 307 VAL Chi-restraints excluded: chain B1 residue 325 MET Chi-restraints excluded: chain B2 residue 136 SER Chi-restraints excluded: chain B2 residue 152 LEU Chi-restraints excluded: chain B2 residue 187 VAL Chi-restraints excluded: chain B2 residue 213 VAL Chi-restraints excluded: chain B2 residue 286 LEU Chi-restraints excluded: chain B2 residue 318 LEU Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 169 TRP Chi-restraints excluded: chain B3 residue 187 VAL Chi-restraints excluded: chain B3 residue 198 LEU Chi-restraints excluded: chain B3 residue 260 GLU Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 136 SER Chi-restraints excluded: chain B4 residue 232 ILE Chi-restraints excluded: chain B4 residue 263 THR Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B4 residue 273 ILE Chi-restraints excluded: chain B4 residue 286 LEU Chi-restraints excluded: chain B5 residue 54 HIS Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 177 THR Chi-restraints excluded: chain B5 residue 213 VAL Chi-restraints excluded: chain B5 residue 284 LEU Chi-restraints excluded: chain B5 residue 286 LEU Chi-restraints excluded: chain G1 residue 3 SER Chi-restraints excluded: chain G2 residue 5 ASN Chi-restraints excluded: chain G2 residue 28 ILE Chi-restraints excluded: chain G4 residue 9 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 207 optimal weight: 8.9990 chunk 246 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 chunk 352 optimal weight: 9.9990 chunk 420 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 425 optimal weight: 0.8980 chunk 185 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 344 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3 195 ASN K4 49 ASN K4 130 ASN ** K4 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 195 ASN C1 60 ASN C1 250 HIS ** C2 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3 133 GLN C4 286 HIS B1 6 GLN ** B1 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 259 GLN ** G2 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.078302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.056035 restraints weight = 421118.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 84)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.055014 restraints weight = 254593.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.055149 restraints weight = 179291.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.055481 restraints weight = 152687.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 76)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.053412 restraints weight = 138285.431| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 38520 Z= 0.172 Angle : 0.640 14.480 51995 Z= 0.335 Chirality : 0.042 0.387 5780 Planarity : 0.004 0.048 6780 Dihedral : 5.509 59.945 5237 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.52 % Rotamer: Outliers : 3.26 % Allowed : 16.93 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.12), residues: 4730 helix: 0.97 (0.11), residues: 2082 sheet: -1.65 (0.17), residues: 750 loop : -1.61 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGC5 120 TYR 0.016 0.002 TYRC4 62 PHE 0.021 0.002 PHEB4 199 TRP 0.055 0.002 TRPC3 109 HIS 0.014 0.001 HISC5 67 Details of bonding type rmsd covalent geometry : bond 0.00360 (38520) covalent geometry : angle 0.64047 (51995) hydrogen bonds : bond 0.03813 ( 1972) hydrogen bonds : angle 5.18912 ( 5742) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 235 time to evaluate : 1.185 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: K2 171 MET cc_start: 0.9026 (ptp) cc_final: 0.8537 (ptp) REVERT: K2 198 GLN cc_start: 0.4023 (tp40) cc_final: 0.2580 (pp30) REVERT: K3 124 GLU cc_start: 0.9255 (mt-10) cc_final: 0.9035 (tt0) REVERT: K3 129 TYR cc_start: 0.6754 (m-10) cc_final: 0.6423 (m-10) REVERT: K3 212 THR cc_start: 0.4008 (OUTLIER) cc_final: 0.3728 (p) REVERT: C1 212 MET cc_start: 0.5428 (OUTLIER) cc_final: 0.4868 (ptt) REVERT: C1 317 MET cc_start: 0.4953 (tpt) cc_final: 0.4008 (tmm) REVERT: C3 116 MET cc_start: -0.1481 (tpp) cc_final: -0.1719 (tpp) REVERT: C3 126 MET cc_start: 0.5001 (ppp) cc_final: 0.4554 (ppp) REVERT: C4 28 LYS cc_start: 0.9403 (tptp) cc_final: 0.9031 (mmmt) REVERT: C4 73 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6740 (mt) REVERT: C4 124 MET cc_start: 0.7870 (mmt) cc_final: 0.7458 (mmm) REVERT: C4 273 MET cc_start: 0.6068 (pmm) cc_final: 0.5837 (mtm) REVERT: C4 276 ILE cc_start: 0.3367 (OUTLIER) cc_final: 0.2887 (tp) REVERT: C4 302 LEU cc_start: -0.0123 (OUTLIER) cc_final: -0.0678 (tp) REVERT: C5 59 ARG cc_start: 0.9400 (ttt180) cc_final: 0.9176 (mpt180) REVERT: C5 128 ARG cc_start: 0.8968 (tmt170) cc_final: 0.8546 (ttt180) REVERT: C5 144 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6718 (tt) REVERT: B1 325 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8356 (ptm) REVERT: B2 262 MET cc_start: 0.8510 (tpp) cc_final: 0.8153 (tpp) REVERT: B3 188 MET cc_start: 0.8826 (ppp) cc_final: 0.8201 (ppp) REVERT: B3 260 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: B3 267 ASP cc_start: 0.8945 (p0) cc_final: 0.8724 (p0) REVERT: B4 61 MET cc_start: 0.8440 (tmm) cc_final: 0.8090 (tmm) REVERT: B4 188 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8337 (tmm) REVERT: B4 273 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8141 (mt) REVERT: B4 325 MET cc_start: 0.8118 (tpp) cc_final: 0.7743 (tpp) REVERT: B5 102 THR cc_start: 0.7946 (OUTLIER) cc_final: 0.7739 (t) REVERT: B5 325 MET cc_start: 0.9221 (tpp) cc_final: 0.8924 (tpp) REVERT: G4 9 ILE cc_start: 0.6832 (OUTLIER) cc_final: 0.6584 (pt) REVERT: G5 1 MET cc_start: 0.8252 (ppp) cc_final: 0.7839 (tmm) outliers start: 136 outliers final: 89 residues processed: 353 average time/residue: 0.1988 time to fit residues: 119.4018 Evaluate side-chains 326 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 225 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 42 VAL Chi-restraints excluded: chain K1 residue 58 THR Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 97 THR Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 155 LYS Chi-restraints excluded: chain K1 residue 169 THR Chi-restraints excluded: chain K1 residue 185 VAL Chi-restraints excluded: chain K1 residue 187 ILE Chi-restraints excluded: chain K2 residue 70 LEU Chi-restraints excluded: chain K2 residue 111 LEU Chi-restraints excluded: chain K3 residue 90 TYR Chi-restraints excluded: chain K3 residue 97 THR Chi-restraints excluded: chain K3 residue 157 VAL Chi-restraints excluded: chain K3 residue 212 THR Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 111 LEU Chi-restraints excluded: chain K4 residue 169 THR Chi-restraints excluded: chain K4 residue 205 VAL Chi-restraints excluded: chain K5 residue 94 ARG Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 134 LEU Chi-restraints excluded: chain K5 residue 152 VAL Chi-restraints excluded: chain K5 residue 154 VAL Chi-restraints excluded: chain K5 residue 157 VAL Chi-restraints excluded: chain K5 residue 161 LEU Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 83 GLU Chi-restraints excluded: chain C1 residue 169 ILE Chi-restraints excluded: chain C1 residue 172 GLU Chi-restraints excluded: chain C1 residue 212 MET Chi-restraints excluded: chain C1 residue 348 LEU Chi-restraints excluded: chain C2 residue 39 ASN Chi-restraints excluded: chain C2 residue 54 PHE Chi-restraints excluded: chain C2 residue 183 ILE Chi-restraints excluded: chain C2 residue 184 ARG Chi-restraints excluded: chain C2 residue 237 VAL Chi-restraints excluded: chain C2 residue 306 VAL Chi-restraints excluded: chain C4 residue 39 ASN Chi-restraints excluded: chain C4 residue 73 LEU Chi-restraints excluded: chain C4 residue 153 ARG Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C4 residue 276 ILE Chi-restraints excluded: chain C4 residue 302 LEU Chi-restraints excluded: chain C4 residue 313 MET Chi-restraints excluded: chain C5 residue 57 LEU Chi-restraints excluded: chain C5 residue 79 GLU Chi-restraints excluded: chain C5 residue 91 GLU Chi-restraints excluded: chain C5 residue 104 THR Chi-restraints excluded: chain C5 residue 132 GLN Chi-restraints excluded: chain C5 residue 144 LEU Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 254 LYS Chi-restraints excluded: chain C5 residue 256 THR Chi-restraints excluded: chain C5 residue 354 ARG Chi-restraints excluded: chain B1 residue 40 VAL Chi-restraints excluded: chain B1 residue 58 ILE Chi-restraints excluded: chain B1 residue 71 VAL Chi-restraints excluded: chain B1 residue 187 VAL Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B1 residue 307 VAL Chi-restraints excluded: chain B1 residue 325 MET Chi-restraints excluded: chain B2 residue 61 MET Chi-restraints excluded: chain B2 residue 136 SER Chi-restraints excluded: chain B2 residue 152 LEU Chi-restraints excluded: chain B2 residue 181 THR Chi-restraints excluded: chain B2 residue 213 VAL Chi-restraints excluded: chain B2 residue 286 LEU Chi-restraints excluded: chain B2 residue 318 LEU Chi-restraints excluded: chain B3 residue 46 ARG Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 169 TRP Chi-restraints excluded: chain B3 residue 187 VAL Chi-restraints excluded: chain B3 residue 198 LEU Chi-restraints excluded: chain B3 residue 260 GLU Chi-restraints excluded: chain B3 residue 336 LEU Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 136 SER Chi-restraints excluded: chain B4 residue 188 MET Chi-restraints excluded: chain B4 residue 232 ILE Chi-restraints excluded: chain B4 residue 263 THR Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B4 residue 273 ILE Chi-restraints excluded: chain B4 residue 286 LEU Chi-restraints excluded: chain B5 residue 29 THR Chi-restraints excluded: chain B5 residue 54 HIS Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 177 THR Chi-restraints excluded: chain B5 residue 213 VAL Chi-restraints excluded: chain B5 residue 262 MET Chi-restraints excluded: chain B5 residue 268 ASN Chi-restraints excluded: chain B5 residue 273 ILE Chi-restraints excluded: chain B5 residue 284 LEU Chi-restraints excluded: chain B5 residue 286 LEU Chi-restraints excluded: chain G1 residue 3 SER Chi-restraints excluded: chain G1 residue 57 SER Chi-restraints excluded: chain G2 residue 5 ASN Chi-restraints excluded: chain G2 residue 28 ILE Chi-restraints excluded: chain G4 residue 9 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 399 optimal weight: 20.0000 chunk 176 optimal weight: 5.9990 chunk 4 optimal weight: 0.4980 chunk 104 optimal weight: 4.9990 chunk 276 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 318 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K3 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 222 GLN C1 250 HIS ** C2 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 11 GLN ** G2 59 ASN ** 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 = 0.4291 r_free = 0.4291 target = 0.078674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.060135 restraints weight = 420345.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.060435 restraints weight = 253591.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.059586 restraints weight = 156027.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.058188 restraints weight = 123532.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.058032 restraints weight = 115718.240| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 38520 Z= 0.142 Angle : 0.630 15.044 51995 Z= 0.326 Chirality : 0.042 0.370 5780 Planarity : 0.004 0.046 6780 Dihedral : 5.271 57.623 5235 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.84 % Favored : 95.07 % Rotamer: Outliers : 2.83 % Allowed : 17.58 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.12), residues: 4730 helix: 1.07 (0.11), residues: 2098 sheet: -1.56 (0.17), residues: 750 loop : -1.56 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGC5 120 TYR 0.029 0.001 TYRC4 62 PHE 0.027 0.002 PHEC2 147 TRP 0.068 0.002 TRPC3 109 HIS 0.008 0.001 HISC5 67 Details of bonding type rmsd covalent geometry : bond 0.00300 (38520) covalent geometry : angle 0.62952 (51995) hydrogen bonds : bond 0.03660 ( 1972) hydrogen bonds : angle 5.05748 ( 5742) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 236 time to evaluate : 1.019 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: K1 171 MET cc_start: 0.9259 (ptm) cc_final: 0.9026 (ptt) REVERT: K2 198 GLN cc_start: 0.4011 (tp40) cc_final: 0.2752 (pp30) REVERT: K3 112 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8137 (p) REVERT: K3 129 TYR cc_start: 0.6015 (m-10) cc_final: 0.5570 (m-10) REVERT: K5 93 ASP cc_start: 0.6666 (OUTLIER) cc_final: 0.5981 (t70) REVERT: C1 124 MET cc_start: 0.8637 (mmm) cc_final: 0.8433 (mmt) REVERT: C1 212 MET cc_start: 0.3930 (OUTLIER) cc_final: 0.3181 (ptt) REVERT: C1 317 MET cc_start: 0.5236 (tpt) cc_final: 0.4237 (tmm) REVERT: C3 126 MET cc_start: 0.6112 (ppp) cc_final: 0.5729 (ppp) REVERT: C3 287 MET cc_start: -0.2475 (mtt) cc_final: -0.2705 (mtt) REVERT: C4 28 LYS cc_start: 0.9372 (tptp) cc_final: 0.8836 (mmmt) REVERT: C4 124 MET cc_start: 0.7872 (mmt) cc_final: 0.7598 (mmt) REVERT: C5 124 MET cc_start: 0.8800 (mmm) cc_final: 0.8291 (mmt) REVERT: C5 128 ARG cc_start: 0.8837 (tmt170) cc_final: 0.8405 (ttt-90) REVERT: C5 144 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6659 (tt) REVERT: B1 61 MET cc_start: 0.7769 (tmm) cc_final: 0.7437 (tmm) REVERT: B1 262 MET cc_start: 0.9123 (mmm) cc_final: 0.8834 (mmm) REVERT: B1 325 MET cc_start: 0.8716 (ptm) cc_final: 0.8510 (ptm) REVERT: B2 188 MET cc_start: 0.9075 (ppp) cc_final: 0.8842 (ppp) REVERT: B2 262 MET cc_start: 0.8547 (tpp) cc_final: 0.8189 (tpp) REVERT: B3 188 MET cc_start: 0.8849 (ppp) cc_final: 0.8614 (tmm) REVERT: B3 260 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: B3 267 ASP cc_start: 0.8951 (p0) cc_final: 0.8726 (p0) REVERT: B4 45 MET cc_start: 0.8487 (mpp) cc_final: 0.7754 (mpp) REVERT: B4 61 MET cc_start: 0.8358 (tmm) cc_final: 0.7944 (tmm) REVERT: B4 188 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8205 (ppp) REVERT: B5 102 THR cc_start: 0.7934 (OUTLIER) cc_final: 0.7698 (t) REVERT: B5 325 MET cc_start: 0.9156 (tpp) cc_final: 0.8852 (tpp) REVERT: G2 28 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7458 (tp) REVERT: G4 9 ILE cc_start: 0.6986 (OUTLIER) cc_final: 0.6663 (pt) REVERT: G4 38 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7548 (tpp) REVERT: G5 1 MET cc_start: 0.8464 (ppp) cc_final: 0.8081 (tmm) outliers start: 118 outliers final: 74 residues processed: 339 average time/residue: 0.1856 time to fit residues: 106.3282 Evaluate side-chains 308 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 224 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 42 VAL Chi-restraints excluded: chain K1 residue 58 THR Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 164 GLN Chi-restraints excluded: chain K1 residue 169 THR Chi-restraints excluded: chain K1 residue 187 ILE Chi-restraints excluded: chain K2 residue 70 LEU Chi-restraints excluded: chain K2 residue 111 LEU Chi-restraints excluded: chain K3 residue 90 TYR Chi-restraints excluded: chain K3 residue 112 VAL Chi-restraints excluded: chain K3 residue 157 VAL Chi-restraints excluded: chain K3 residue 212 THR Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 111 LEU Chi-restraints excluded: chain K4 residue 169 THR Chi-restraints excluded: chain K5 residue 93 ASP Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 152 VAL Chi-restraints excluded: chain K5 residue 154 VAL Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C1 residue 36 LEU Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 144 LEU Chi-restraints excluded: chain C1 residue 169 ILE Chi-restraints excluded: chain C1 residue 172 GLU Chi-restraints excluded: chain C1 residue 212 MET Chi-restraints excluded: chain C1 residue 250 HIS Chi-restraints excluded: chain C1 residue 348 LEU Chi-restraints excluded: chain C2 residue 39 ASN Chi-restraints excluded: chain C2 residue 54 PHE Chi-restraints excluded: chain C2 residue 183 ILE Chi-restraints excluded: chain C2 residue 237 VAL Chi-restraints excluded: chain C2 residue 273 MET Chi-restraints excluded: chain C2 residue 306 VAL Chi-restraints excluded: chain C4 residue 39 ASN Chi-restraints excluded: chain C4 residue 153 ARG Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C4 residue 313 MET Chi-restraints excluded: chain C5 residue 57 LEU Chi-restraints excluded: chain C5 residue 79 GLU Chi-restraints excluded: chain C5 residue 91 GLU Chi-restraints excluded: chain C5 residue 144 LEU Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 254 LYS Chi-restraints excluded: chain C5 residue 354 ARG Chi-restraints excluded: chain B1 residue 40 VAL Chi-restraints excluded: chain B1 residue 71 VAL Chi-restraints excluded: chain B1 residue 114 CYS Chi-restraints excluded: chain B1 residue 187 VAL Chi-restraints excluded: chain B1 residue 307 VAL Chi-restraints excluded: chain B2 residue 61 MET Chi-restraints excluded: chain B2 residue 136 SER Chi-restraints excluded: chain B2 residue 152 LEU Chi-restraints excluded: chain B2 residue 181 THR Chi-restraints excluded: chain B2 residue 187 VAL Chi-restraints excluded: chain B2 residue 213 VAL Chi-restraints excluded: chain B2 residue 286 LEU Chi-restraints excluded: chain B2 residue 318 LEU Chi-restraints excluded: chain B3 residue 61 MET Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 169 TRP Chi-restraints excluded: chain B3 residue 187 VAL Chi-restraints excluded: chain B3 residue 198 LEU Chi-restraints excluded: chain B3 residue 260 GLU Chi-restraints excluded: chain B3 residue 336 LEU Chi-restraints excluded: chain B4 residue 136 SER Chi-restraints excluded: chain B4 residue 183 HIS Chi-restraints excluded: chain B4 residue 188 MET Chi-restraints excluded: chain B4 residue 232 ILE Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B4 residue 286 LEU Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 153 ASP Chi-restraints excluded: chain B5 residue 177 THR Chi-restraints excluded: chain B5 residue 213 VAL Chi-restraints excluded: chain B5 residue 262 MET Chi-restraints excluded: chain B5 residue 284 LEU Chi-restraints excluded: chain B5 residue 286 LEU Chi-restraints excluded: chain G1 residue 57 SER Chi-restraints excluded: chain G2 residue 11 GLN Chi-restraints excluded: chain G2 residue 28 ILE Chi-restraints excluded: chain G4 residue 9 ILE Chi-restraints excluded: chain G4 residue 38 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 219 optimal weight: 30.0000 chunk 441 optimal weight: 0.0370 chunk 199 optimal weight: 20.0000 chunk 144 optimal weight: 7.9990 chunk 209 optimal weight: 30.0000 chunk 357 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 206 optimal weight: 30.0000 chunk 374 optimal weight: 6.9990 chunk 379 optimal weight: 0.0370 chunk 97 optimal weight: 9.9990 overall best weight: 3.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K3 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 250 HIS ** C2 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 343 GLN ** C3 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3 4 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.078579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.058439 restraints weight = 422972.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.058082 restraints weight = 252042.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.058845 restraints weight = 203294.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.057869 restraints weight = 146422.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.058215 restraints weight = 132351.396| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 38520 Z= 0.153 Angle : 0.638 12.848 51995 Z= 0.331 Chirality : 0.042 0.336 5780 Planarity : 0.004 0.052 6780 Dihedral : 5.132 57.910 5231 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.90 % Favored : 95.01 % Rotamer: Outliers : 2.81 % Allowed : 18.15 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.12), residues: 4730 helix: 1.10 (0.11), residues: 2091 sheet: -1.61 (0.17), residues: 767 loop : -1.50 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGC4 171 TYR 0.021 0.001 TYRC5 233 PHE 0.024 0.002 PHEC2 147 TRP 0.047 0.002 TRPC3 109 HIS 0.017 0.001 HISC1 250 Details of bonding type rmsd covalent geometry : bond 0.00321 (38520) covalent geometry : angle 0.63811 (51995) hydrogen bonds : bond 0.03644 ( 1972) hydrogen bonds : angle 5.02911 ( 5742) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 230 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K2 198 GLN cc_start: 0.3797 (tp40) cc_final: 0.2592 (pp30) REVERT: K3 129 TYR cc_start: 0.6335 (m-10) cc_final: 0.6000 (m-10) REVERT: K5 93 ASP cc_start: 0.6218 (OUTLIER) cc_final: 0.5893 (t70) REVERT: C1 212 MET cc_start: 0.5014 (OUTLIER) cc_final: 0.4455 (ptt) REVERT: C3 126 MET cc_start: 0.5261 (ppp) cc_final: 0.4797 (ppp) REVERT: C4 28 LYS cc_start: 0.9457 (tptp) cc_final: 0.9174 (mmmt) REVERT: C4 273 MET cc_start: 0.6162 (pmm) cc_final: 0.5916 (mtm) REVERT: C5 25 MET cc_start: 0.4306 (tpp) cc_final: 0.3333 (tmm) REVERT: C5 128 ARG cc_start: 0.8910 (tmt170) cc_final: 0.8220 (ttp-170) REVERT: C5 144 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6814 (tt) REVERT: B1 61 MET cc_start: 0.7730 (tmm) cc_final: 0.7327 (tmm) REVERT: B1 262 MET cc_start: 0.9101 (mmm) cc_final: 0.8815 (mmm) REVERT: B1 325 MET cc_start: 0.8734 (ptm) cc_final: 0.8516 (ptm) REVERT: B2 262 MET cc_start: 0.8417 (tpp) cc_final: 0.8089 (tpp) REVERT: B3 188 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8599 (tmm) REVERT: B3 260 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: B3 267 ASP cc_start: 0.8921 (p0) cc_final: 0.8699 (p0) REVERT: B4 43 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6407 (tp) REVERT: B4 45 MET cc_start: 0.8472 (mpp) cc_final: 0.7464 (mpp) REVERT: B4 61 MET cc_start: 0.8363 (tmm) cc_final: 0.7885 (tmm) REVERT: B4 188 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8206 (ppp) REVERT: B4 273 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8059 (mt) REVERT: B4 325 MET cc_start: 0.8057 (tpp) cc_final: 0.7718 (tpp) REVERT: B5 102 THR cc_start: 0.7985 (OUTLIER) cc_final: 0.7705 (t) REVERT: B5 325 MET cc_start: 0.9105 (tpp) cc_final: 0.8824 (tpp) REVERT: G2 28 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7487 (tp) REVERT: G4 9 ILE cc_start: 0.6936 (OUTLIER) cc_final: 0.6660 (pt) REVERT: G4 38 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7524 (tpp) REVERT: G5 1 MET cc_start: 0.7842 (ppp) cc_final: 0.7467 (tmm) outliers start: 117 outliers final: 87 residues processed: 331 average time/residue: 0.1942 time to fit residues: 109.3816 Evaluate side-chains 323 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 224 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 42 VAL Chi-restraints excluded: chain K1 residue 58 THR Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 97 THR Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 155 LYS Chi-restraints excluded: chain K1 residue 164 GLN Chi-restraints excluded: chain K1 residue 169 THR Chi-restraints excluded: chain K1 residue 185 VAL Chi-restraints excluded: chain K1 residue 187 ILE Chi-restraints excluded: chain K2 residue 70 LEU Chi-restraints excluded: chain K2 residue 111 LEU Chi-restraints excluded: chain K3 residue 90 TYR Chi-restraints excluded: chain K3 residue 97 THR Chi-restraints excluded: chain K3 residue 157 VAL Chi-restraints excluded: chain K3 residue 161 LEU Chi-restraints excluded: chain K3 residue 206 SER Chi-restraints excluded: chain K3 residue 212 THR Chi-restraints excluded: chain K4 residue 111 LEU Chi-restraints excluded: chain K5 residue 93 ASP Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 152 VAL Chi-restraints excluded: chain K5 residue 154 VAL Chi-restraints excluded: chain K5 residue 157 VAL Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C1 residue 36 LEU Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 83 GLU Chi-restraints excluded: chain C1 residue 144 LEU Chi-restraints excluded: chain C1 residue 169 ILE Chi-restraints excluded: chain C1 residue 172 GLU Chi-restraints excluded: chain C1 residue 212 MET Chi-restraints excluded: chain C1 residue 348 LEU Chi-restraints excluded: chain C2 residue 25 MET Chi-restraints excluded: chain C2 residue 39 ASN Chi-restraints excluded: chain C2 residue 54 PHE Chi-restraints excluded: chain C2 residue 183 ILE Chi-restraints excluded: chain C2 residue 237 VAL Chi-restraints excluded: chain C2 residue 306 VAL Chi-restraints excluded: chain C4 residue 39 ASN Chi-restraints excluded: chain C4 residue 153 ARG Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C4 residue 313 MET Chi-restraints excluded: chain C5 residue 57 LEU Chi-restraints excluded: chain C5 residue 79 GLU Chi-restraints excluded: chain C5 residue 91 GLU Chi-restraints excluded: chain C5 residue 144 LEU Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 254 LYS Chi-restraints excluded: chain C5 residue 299 MET Chi-restraints excluded: chain C5 residue 354 ARG Chi-restraints excluded: chain B1 residue 40 VAL Chi-restraints excluded: chain B1 residue 71 VAL Chi-restraints excluded: chain B1 residue 114 CYS Chi-restraints excluded: chain B1 residue 187 VAL Chi-restraints excluded: chain B1 residue 307 VAL Chi-restraints excluded: chain B2 residue 61 MET Chi-restraints excluded: chain B2 residue 136 SER Chi-restraints excluded: chain B2 residue 152 LEU Chi-restraints excluded: chain B2 residue 181 THR Chi-restraints excluded: chain B2 residue 187 VAL Chi-restraints excluded: chain B2 residue 213 VAL Chi-restraints excluded: chain B2 residue 286 LEU Chi-restraints excluded: chain B2 residue 318 LEU Chi-restraints excluded: chain B3 residue 61 MET Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 169 TRP Chi-restraints excluded: chain B3 residue 187 VAL Chi-restraints excluded: chain B3 residue 188 MET Chi-restraints excluded: chain B3 residue 198 LEU Chi-restraints excluded: chain B3 residue 260 GLU Chi-restraints excluded: chain B3 residue 336 LEU Chi-restraints excluded: chain B4 residue 43 ILE Chi-restraints excluded: chain B4 residue 93 ILE Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 136 SER Chi-restraints excluded: chain B4 residue 183 HIS Chi-restraints excluded: chain B4 residue 188 MET Chi-restraints excluded: chain B4 residue 232 ILE Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B4 residue 273 ILE Chi-restraints excluded: chain B4 residue 286 LEU Chi-restraints excluded: chain B5 residue 29 THR Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 153 ASP Chi-restraints excluded: chain B5 residue 177 THR Chi-restraints excluded: chain B5 residue 213 VAL Chi-restraints excluded: chain B5 residue 262 MET Chi-restraints excluded: chain B5 residue 268 ASN Chi-restraints excluded: chain B5 residue 273 ILE Chi-restraints excluded: chain B5 residue 284 LEU Chi-restraints excluded: chain B5 residue 286 LEU Chi-restraints excluded: chain B5 residue 331 SER Chi-restraints excluded: chain G1 residue 3 SER Chi-restraints excluded: chain G1 residue 57 SER Chi-restraints excluded: chain G2 residue 28 ILE Chi-restraints excluded: chain G4 residue 9 ILE Chi-restraints excluded: chain G4 residue 38 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 385 optimal weight: 10.0000 chunk 431 optimal weight: 20.0000 chunk 395 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 461 optimal weight: 9.9990 chunk 254 optimal weight: 20.0000 chunk 208 optimal weight: 10.0000 chunk 216 optimal weight: 8.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 150 GLN ** C1 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 48 ASN ** C2 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3 160 HIS ** C3 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C5 84 HIS ** B1 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 340 ASN B2 16 ASN ** B2 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3 142 HIS ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 259 GLN ** B5 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.075476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.056458 restraints weight = 426759.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.057161 restraints weight = 268255.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.056041 restraints weight = 177319.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.055971 restraints weight = 139995.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.055957 restraints weight = 132943.208| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 38520 Z= 0.304 Angle : 0.793 14.261 51995 Z= 0.413 Chirality : 0.044 0.228 5780 Planarity : 0.005 0.049 6780 Dihedral : 5.669 53.060 5231 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 25.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.08 % Favored : 92.83 % Rotamer: Outliers : 3.07 % Allowed : 18.51 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.12), residues: 4730 helix: 0.59 (0.11), residues: 2102 sheet: -1.82 (0.18), residues: 717 loop : -1.72 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGC5 120 TYR 0.023 0.002 TYRK1 71 PHE 0.026 0.003 PHEG1 61 TRP 0.082 0.003 TRPC3 109 HIS 0.011 0.002 HISC1 69 Details of bonding type rmsd covalent geometry : bond 0.00631 (38520) covalent geometry : angle 0.79273 (51995) hydrogen bonds : bond 0.04398 ( 1972) hydrogen bonds : angle 5.53321 ( 5742) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 232 time to evaluate : 1.096 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: K2 171 MET cc_start: 0.8989 (ptp) cc_final: 0.8763 (ptp) REVERT: K2 198 GLN cc_start: 0.4206 (tp40) cc_final: 0.2514 (pp30) REVERT: K3 124 GLU cc_start: 0.9406 (mt-10) cc_final: 0.9178 (tt0) REVERT: K3 129 TYR cc_start: 0.6604 (m-10) cc_final: 0.6170 (m-10) REVERT: K5 93 ASP cc_start: 0.6250 (OUTLIER) cc_final: 0.5708 (t70) REVERT: C1 212 MET cc_start: 0.4610 (OUTLIER) cc_final: 0.3831 (ptt) REVERT: C3 29 TYR cc_start: 0.1055 (OUTLIER) cc_final: -0.0733 (p90) REVERT: C3 126 MET cc_start: 0.5966 (ppp) cc_final: 0.5766 (ppp) REVERT: C4 28 LYS cc_start: 0.9597 (tptp) cc_final: 0.9283 (mmmt) REVERT: C4 276 ILE cc_start: 0.2984 (OUTLIER) cc_final: 0.2636 (tp) REVERT: C5 25 MET cc_start: 0.4374 (tpp) cc_final: 0.3379 (tmm) REVERT: C5 128 ARG cc_start: 0.9121 (tmt170) cc_final: 0.8530 (ttp-170) REVERT: B1 61 MET cc_start: 0.7537 (tmm) cc_final: 0.7207 (tmm) REVERT: B1 172 GLU cc_start: 0.8787 (tp30) cc_final: 0.8547 (tp30) REVERT: B1 262 MET cc_start: 0.9312 (mmm) cc_final: 0.9012 (mmm) REVERT: B1 325 MET cc_start: 0.8946 (ptm) cc_final: 0.8489 (ptm) REVERT: B2 262 MET cc_start: 0.8814 (tpp) cc_final: 0.8502 (tpp) REVERT: B3 188 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8521 (tmm) REVERT: B3 267 ASP cc_start: 0.8932 (p0) cc_final: 0.8675 (p0) REVERT: B4 45 MET cc_start: 0.8452 (mpp) cc_final: 0.8018 (mmp) REVERT: B4 61 MET cc_start: 0.8287 (tmm) cc_final: 0.7902 (tmm) REVERT: B4 188 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8277 (tmm) REVERT: B4 273 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8359 (mt) REVERT: B5 325 MET cc_start: 0.9297 (tpp) cc_final: 0.8908 (tpp) REVERT: G3 38 MET cc_start: 0.7404 (mtm) cc_final: 0.7025 (mtm) REVERT: G4 9 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6873 (pt) REVERT: G5 1 MET cc_start: 0.8144 (ppp) cc_final: 0.7716 (tmm) outliers start: 128 outliers final: 98 residues processed: 343 average time/residue: 0.1855 time to fit residues: 107.6723 Evaluate side-chains 327 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 221 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 42 VAL Chi-restraints excluded: chain K1 residue 58 THR Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 97 THR Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 155 LYS Chi-restraints excluded: chain K1 residue 169 THR Chi-restraints excluded: chain K1 residue 185 VAL Chi-restraints excluded: chain K1 residue 187 ILE Chi-restraints excluded: chain K2 residue 70 LEU Chi-restraints excluded: chain K2 residue 111 LEU Chi-restraints excluded: chain K3 residue 90 TYR Chi-restraints excluded: chain K3 residue 97 THR Chi-restraints excluded: chain K3 residue 157 VAL Chi-restraints excluded: chain K3 residue 206 SER Chi-restraints excluded: chain K3 residue 212 THR Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 111 LEU Chi-restraints excluded: chain K4 residue 169 THR Chi-restraints excluded: chain K4 residue 205 VAL Chi-restraints excluded: chain K5 residue 93 ASP Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 134 LEU Chi-restraints excluded: chain K5 residue 152 VAL Chi-restraints excluded: chain K5 residue 154 VAL Chi-restraints excluded: chain K5 residue 157 VAL Chi-restraints excluded: chain K5 residue 161 LEU Chi-restraints excluded: chain K5 residue 169 THR Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C1 residue 36 LEU Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 83 GLU Chi-restraints excluded: chain C1 residue 126 MET Chi-restraints excluded: chain C1 residue 169 ILE Chi-restraints excluded: chain C1 residue 172 GLU Chi-restraints excluded: chain C1 residue 212 MET Chi-restraints excluded: chain C1 residue 348 LEU Chi-restraints excluded: chain C2 residue 25 MET Chi-restraints excluded: chain C2 residue 39 ASN Chi-restraints excluded: chain C2 residue 54 PHE Chi-restraints excluded: chain C2 residue 183 ILE Chi-restraints excluded: chain C2 residue 184 ARG Chi-restraints excluded: chain C2 residue 191 MET Chi-restraints excluded: chain C2 residue 306 VAL Chi-restraints excluded: chain C3 residue 29 TYR Chi-restraints excluded: chain C3 residue 130 TYR Chi-restraints excluded: chain C3 residue 273 MET Chi-restraints excluded: chain C4 residue 39 ASN Chi-restraints excluded: chain C4 residue 153 ARG Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C4 residue 276 ILE Chi-restraints excluded: chain C4 residue 313 MET Chi-restraints excluded: chain C5 residue 57 LEU Chi-restraints excluded: chain C5 residue 79 GLU Chi-restraints excluded: chain C5 residue 91 GLU Chi-restraints excluded: chain C5 residue 104 THR Chi-restraints excluded: chain C5 residue 132 GLN Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 254 LYS Chi-restraints excluded: chain C5 residue 256 THR Chi-restraints excluded: chain C5 residue 299 MET Chi-restraints excluded: chain C5 residue 354 ARG Chi-restraints excluded: chain B1 residue 40 VAL Chi-restraints excluded: chain B1 residue 71 VAL Chi-restraints excluded: chain B1 residue 114 CYS Chi-restraints excluded: chain B1 residue 187 VAL Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B1 residue 307 VAL Chi-restraints excluded: chain B2 residue 136 SER Chi-restraints excluded: chain B2 residue 152 LEU Chi-restraints excluded: chain B2 residue 181 THR Chi-restraints excluded: chain B2 residue 187 VAL Chi-restraints excluded: chain B2 residue 213 VAL Chi-restraints excluded: chain B2 residue 286 LEU Chi-restraints excluded: chain B2 residue 318 LEU Chi-restraints excluded: chain B3 residue 46 ARG Chi-restraints excluded: chain B3 residue 61 MET Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 187 VAL Chi-restraints excluded: chain B3 residue 188 MET Chi-restraints excluded: chain B3 residue 198 LEU Chi-restraints excluded: chain B3 residue 336 LEU Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 136 SER Chi-restraints excluded: chain B4 residue 146 LEU Chi-restraints excluded: chain B4 residue 188 MET Chi-restraints excluded: chain B4 residue 213 VAL Chi-restraints excluded: chain B4 residue 263 THR Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B4 residue 273 ILE Chi-restraints excluded: chain B4 residue 286 LEU Chi-restraints excluded: chain B5 residue 29 THR Chi-restraints excluded: chain B5 residue 54 HIS Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 153 ASP Chi-restraints excluded: chain B5 residue 177 THR Chi-restraints excluded: chain B5 residue 268 ASN Chi-restraints excluded: chain B5 residue 273 ILE Chi-restraints excluded: chain B5 residue 284 LEU Chi-restraints excluded: chain B5 residue 286 LEU Chi-restraints excluded: chain B5 residue 331 SER Chi-restraints excluded: chain G1 residue 57 SER Chi-restraints excluded: chain G2 residue 28 ILE Chi-restraints excluded: chain G4 residue 9 ILE Chi-restraints excluded: chain G4 residue 38 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 154 optimal weight: 40.0000 chunk 329 optimal weight: 3.9990 chunk 129 optimal weight: 30.0000 chunk 65 optimal weight: 20.0000 chunk 163 optimal weight: 7.9990 chunk 375 optimal weight: 0.8980 chunk 273 optimal weight: 20.0000 chunk 363 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 80 optimal weight: 50.0000 chunk 84 optimal weight: 5.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K1 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 150 GLN ** C1 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 250 HIS C2 110 ASN ** C2 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3 160 HIS ** C4 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C5 160 HIS ** B1 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 259 GLN ** B5 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.077290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.058417 restraints weight = 425345.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 82)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.057781 restraints weight = 261922.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.057950 restraints weight = 173958.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.057509 restraints weight = 124558.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.057303 restraints weight = 139452.882| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 38520 Z= 0.200 Angle : 0.706 12.805 51995 Z= 0.367 Chirality : 0.043 0.239 5780 Planarity : 0.004 0.042 6780 Dihedral : 5.484 53.644 5231 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.73 % Favored : 94.19 % Rotamer: Outliers : 2.61 % Allowed : 19.42 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.12), residues: 4730 helix: 0.71 (0.11), residues: 2105 sheet: -1.76 (0.18), residues: 707 loop : -1.59 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGG3 27 TYR 0.019 0.002 TYRK5 71 PHE 0.025 0.002 PHEB3 292 TRP 0.085 0.002 TRPC3 109 HIS 0.016 0.002 HISC1 69 Details of bonding type rmsd covalent geometry : bond 0.00420 (38520) covalent geometry : angle 0.70586 (51995) hydrogen bonds : bond 0.03991 ( 1972) hydrogen bonds : angle 5.34253 ( 5742) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 230 time to evaluate : 1.457 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: K1 162 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7405 (tm-30) REVERT: K2 198 GLN cc_start: 0.3784 (tp40) cc_final: 0.2241 (pp30) REVERT: K3 124 GLU cc_start: 0.9338 (mt-10) cc_final: 0.9067 (tt0) REVERT: K3 129 TYR cc_start: 0.6462 (m-10) cc_final: 0.6026 (m-10) REVERT: C1 124 MET cc_start: 0.8291 (mmm) cc_final: 0.8084 (mmm) REVERT: C1 212 MET cc_start: 0.4046 (OUTLIER) cc_final: 0.3288 (ptt) REVERT: C3 34 TRP cc_start: 0.8397 (m100) cc_final: 0.8066 (m100) REVERT: C3 189 MET cc_start: 0.8065 (mtt) cc_final: 0.7510 (mtt) REVERT: C4 28 LYS cc_start: 0.9601 (tptp) cc_final: 0.9195 (mmmt) REVERT: C5 128 ARG cc_start: 0.9082 (tmt170) cc_final: 0.8565 (ttt180) REVERT: B1 61 MET cc_start: 0.7714 (tmm) cc_final: 0.7376 (tmm) REVERT: B1 123 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8475 (tp) REVERT: B1 262 MET cc_start: 0.9236 (mmm) cc_final: 0.8979 (mmm) REVERT: B1 325 MET cc_start: 0.8888 (ptm) cc_final: 0.8680 (ptm) REVERT: B2 262 MET cc_start: 0.8712 (tpp) cc_final: 0.8373 (tpp) REVERT: B3 188 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8635 (tmm) REVERT: B3 267 ASP cc_start: 0.8967 (p0) cc_final: 0.8712 (p0) REVERT: B4 45 MET cc_start: 0.8481 (mpp) cc_final: 0.8241 (mmp) REVERT: B4 61 MET cc_start: 0.8314 (tmm) cc_final: 0.7934 (tmm) REVERT: B4 188 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8260 (tmm) REVERT: B4 273 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8190 (mt) REVERT: B4 325 MET cc_start: 0.8173 (tpp) cc_final: 0.7885 (tpp) REVERT: B5 325 MET cc_start: 0.9238 (tpp) cc_final: 0.8887 (tpp) REVERT: G3 38 MET cc_start: 0.7295 (mtm) cc_final: 0.6896 (mtm) REVERT: G4 9 ILE cc_start: 0.7216 (OUTLIER) cc_final: 0.6912 (pt) REVERT: G5 1 MET cc_start: 0.7710 (ppp) cc_final: 0.7359 (tmm) outliers start: 109 outliers final: 87 residues processed: 324 average time/residue: 0.2107 time to fit residues: 116.0698 Evaluate side-chains 318 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 224 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 42 VAL Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 97 THR Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 155 LYS Chi-restraints excluded: chain K1 residue 162 GLN Chi-restraints excluded: chain K1 residue 169 THR Chi-restraints excluded: chain K1 residue 185 VAL Chi-restraints excluded: chain K1 residue 187 ILE Chi-restraints excluded: chain K2 residue 70 LEU Chi-restraints excluded: chain K2 residue 111 LEU Chi-restraints excluded: chain K3 residue 90 TYR Chi-restraints excluded: chain K3 residue 97 THR Chi-restraints excluded: chain K3 residue 157 VAL Chi-restraints excluded: chain K3 residue 161 LEU Chi-restraints excluded: chain K3 residue 206 SER Chi-restraints excluded: chain K3 residue 212 THR Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 111 LEU Chi-restraints excluded: chain K4 residue 169 THR Chi-restraints excluded: chain K4 residue 205 VAL Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 152 VAL Chi-restraints excluded: chain K5 residue 154 VAL Chi-restraints excluded: chain K5 residue 157 VAL Chi-restraints excluded: chain K5 residue 161 LEU Chi-restraints excluded: chain K5 residue 169 THR Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C1 residue 36 LEU Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 144 LEU Chi-restraints excluded: chain C1 residue 169 ILE Chi-restraints excluded: chain C1 residue 172 GLU Chi-restraints excluded: chain C1 residue 212 MET Chi-restraints excluded: chain C1 residue 250 HIS Chi-restraints excluded: chain C1 residue 348 LEU Chi-restraints excluded: chain C2 residue 39 ASN Chi-restraints excluded: chain C2 residue 54 PHE Chi-restraints excluded: chain C2 residue 183 ILE Chi-restraints excluded: chain C2 residue 306 VAL Chi-restraints excluded: chain C3 residue 273 MET Chi-restraints excluded: chain C4 residue 39 ASN Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C4 residue 313 MET Chi-restraints excluded: chain C5 residue 57 LEU Chi-restraints excluded: chain C5 residue 79 GLU Chi-restraints excluded: chain C5 residue 91 GLU Chi-restraints excluded: chain C5 residue 104 THR Chi-restraints excluded: chain C5 residue 132 GLN Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 254 LYS Chi-restraints excluded: chain C5 residue 256 THR Chi-restraints excluded: chain C5 residue 273 MET Chi-restraints excluded: chain C5 residue 299 MET Chi-restraints excluded: chain C5 residue 354 ARG Chi-restraints excluded: chain B1 residue 40 VAL Chi-restraints excluded: chain B1 residue 71 VAL Chi-restraints excluded: chain B1 residue 114 CYS Chi-restraints excluded: chain B1 residue 123 ILE Chi-restraints excluded: chain B1 residue 187 VAL Chi-restraints excluded: chain B1 residue 307 VAL Chi-restraints excluded: chain B2 residue 136 SER Chi-restraints excluded: chain B2 residue 152 LEU Chi-restraints excluded: chain B2 residue 187 VAL Chi-restraints excluded: chain B2 residue 213 VAL Chi-restraints excluded: chain B2 residue 286 LEU Chi-restraints excluded: chain B2 residue 318 LEU Chi-restraints excluded: chain B3 residue 61 MET Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 187 VAL Chi-restraints excluded: chain B3 residue 188 MET Chi-restraints excluded: chain B3 residue 198 LEU Chi-restraints excluded: chain B3 residue 336 LEU Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 136 SER Chi-restraints excluded: chain B4 residue 146 LEU Chi-restraints excluded: chain B4 residue 188 MET Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B4 residue 273 ILE Chi-restraints excluded: chain B4 residue 286 LEU Chi-restraints excluded: chain B5 residue 29 THR Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 153 ASP Chi-restraints excluded: chain B5 residue 177 THR Chi-restraints excluded: chain B5 residue 213 VAL Chi-restraints excluded: chain B5 residue 268 ASN Chi-restraints excluded: chain B5 residue 273 ILE Chi-restraints excluded: chain B5 residue 284 LEU Chi-restraints excluded: chain B5 residue 286 LEU Chi-restraints excluded: chain B5 residue 331 SER Chi-restraints excluded: chain G1 residue 57 SER Chi-restraints excluded: chain G2 residue 28 ILE Chi-restraints excluded: chain G4 residue 9 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 380 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 170 optimal weight: 30.0000 chunk 177 optimal weight: 30.0000 chunk 164 optimal weight: 7.9990 chunk 310 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 299 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K1 162 GLN ** K3 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 150 GLN ** C1 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 250 HIS ** C2 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3 160 HIS ** C3 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 242 ASN ** C4 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 220 GLN ** B2 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3 142 HIS ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.076790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.058241 restraints weight = 428876.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.058964 restraints weight = 267131.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.058890 restraints weight = 186558.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.058341 restraints weight = 130788.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.058291 restraints weight = 100856.472| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 38520 Z= 0.239 Angle : 0.748 12.716 51995 Z= 0.388 Chirality : 0.043 0.210 5780 Planarity : 0.004 0.042 6780 Dihedral : 5.567 51.772 5231 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 22.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.77 % Favored : 93.15 % Rotamer: Outliers : 2.76 % Allowed : 19.40 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.12), residues: 4730 helix: 0.61 (0.11), residues: 2100 sheet: -1.83 (0.18), residues: 707 loop : -1.64 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGC2 184 TYR 0.022 0.002 TYRK5 71 PHE 0.037 0.003 PHEC3 224 TRP 0.025 0.002 TRPC3 34 HIS 0.028 0.002 HISC1 250 Details of bonding type rmsd covalent geometry : bond 0.00499 (38520) covalent geometry : angle 0.74779 (51995) hydrogen bonds : bond 0.04104 ( 1972) hydrogen bonds : angle 5.45424 ( 5742) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9460 Ramachandran restraints generated. 4730 Oldfield, 0 Emsley, 4730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 230 time to evaluate : 1.648 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: K2 198 GLN cc_start: 0.3465 (tp40) cc_final: 0.1869 (pp30) REVERT: K3 129 TYR cc_start: 0.6456 (m-10) cc_final: 0.6008 (m-10) REVERT: C1 212 MET cc_start: 0.4656 (OUTLIER) cc_final: 0.3883 (ptt) REVERT: C3 29 TYR cc_start: 0.0316 (OUTLIER) cc_final: -0.1389 (p90) REVERT: C3 34 TRP cc_start: 0.8621 (m100) cc_final: 0.8295 (m100) REVERT: C3 126 MET cc_start: 0.5981 (ppp) cc_final: 0.5735 (ppp) REVERT: C3 189 MET cc_start: 0.7776 (mtt) cc_final: 0.6922 (mtt) REVERT: C4 28 LYS cc_start: 0.9628 (tptp) cc_final: 0.9286 (mmmt) REVERT: C4 273 MET cc_start: 0.6523 (pmm) cc_final: 0.6215 (mtm) REVERT: C5 55 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8584 (mp0) REVERT: C5 128 ARG cc_start: 0.9107 (tmt170) cc_final: 0.8563 (ttt180) REVERT: B1 61 MET cc_start: 0.7719 (tmm) cc_final: 0.7343 (tmm) REVERT: B1 123 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8552 (tp) REVERT: B1 262 MET cc_start: 0.9288 (mmm) cc_final: 0.9023 (mmm) REVERT: B1 325 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8480 (ptm) REVERT: B2 262 MET cc_start: 0.8731 (tpp) cc_final: 0.8398 (tpp) REVERT: B3 188 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8591 (tmm) REVERT: B3 267 ASP cc_start: 0.8875 (p0) cc_final: 0.8623 (p0) REVERT: B4 45 MET cc_start: 0.8471 (mpp) cc_final: 0.8059 (mmp) REVERT: B4 61 MET cc_start: 0.8317 (tmm) cc_final: 0.7934 (tmm) REVERT: B4 188 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8260 (tmm) REVERT: B4 273 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8250 (mp) REVERT: B4 325 MET cc_start: 0.8164 (tpp) cc_final: 0.7870 (tpp) REVERT: B5 325 MET cc_start: 0.9241 (tpp) cc_final: 0.8884 (tpp) REVERT: G3 38 MET cc_start: 0.7348 (mtm) cc_final: 0.6918 (mtm) REVERT: G4 9 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6933 (pt) REVERT: G5 1 MET cc_start: 0.7947 (ppp) cc_final: 0.7574 (tmm) outliers start: 115 outliers final: 93 residues processed: 330 average time/residue: 0.1875 time to fit residues: 105.2002 Evaluate side-chains 326 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 224 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 42 VAL Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 97 THR Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 155 LYS Chi-restraints excluded: chain K1 residue 169 THR Chi-restraints excluded: chain K1 residue 185 VAL Chi-restraints excluded: chain K1 residue 187 ILE Chi-restraints excluded: chain K2 residue 42 VAL Chi-restraints excluded: chain K2 residue 70 LEU Chi-restraints excluded: chain K3 residue 90 TYR Chi-restraints excluded: chain K3 residue 97 THR Chi-restraints excluded: chain K3 residue 157 VAL Chi-restraints excluded: chain K3 residue 161 LEU Chi-restraints excluded: chain K3 residue 206 SER Chi-restraints excluded: chain K3 residue 212 THR Chi-restraints excluded: chain K4 residue 58 THR Chi-restraints excluded: chain K4 residue 111 LEU Chi-restraints excluded: chain K4 residue 169 THR Chi-restraints excluded: chain K4 residue 205 VAL Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 152 VAL Chi-restraints excluded: chain K5 residue 154 VAL Chi-restraints excluded: chain K5 residue 157 VAL Chi-restraints excluded: chain K5 residue 161 LEU Chi-restraints excluded: chain K5 residue 169 THR Chi-restraints excluded: chain K5 residue 212 THR Chi-restraints excluded: chain C1 residue 36 LEU Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 144 LEU Chi-restraints excluded: chain C1 residue 169 ILE Chi-restraints excluded: chain C1 residue 172 GLU Chi-restraints excluded: chain C1 residue 212 MET Chi-restraints excluded: chain C1 residue 348 LEU Chi-restraints excluded: chain C2 residue 39 ASN Chi-restraints excluded: chain C2 residue 54 PHE Chi-restraints excluded: chain C2 residue 183 ILE Chi-restraints excluded: chain C2 residue 306 VAL Chi-restraints excluded: chain C3 residue 29 TYR Chi-restraints excluded: chain C3 residue 273 MET Chi-restraints excluded: chain C4 residue 39 ASN Chi-restraints excluded: chain C4 residue 153 ARG Chi-restraints excluded: chain C4 residue 242 ASN Chi-restraints excluded: chain C4 residue 313 MET Chi-restraints excluded: chain C5 residue 55 GLU Chi-restraints excluded: chain C5 residue 57 LEU Chi-restraints excluded: chain C5 residue 79 GLU Chi-restraints excluded: chain C5 residue 91 GLU Chi-restraints excluded: chain C5 residue 104 THR Chi-restraints excluded: chain C5 residue 132 GLN Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 254 LYS Chi-restraints excluded: chain C5 residue 256 THR Chi-restraints excluded: chain C5 residue 273 MET Chi-restraints excluded: chain C5 residue 299 MET Chi-restraints excluded: chain C5 residue 354 ARG Chi-restraints excluded: chain B1 residue 40 VAL Chi-restraints excluded: chain B1 residue 71 VAL Chi-restraints excluded: chain B1 residue 114 CYS Chi-restraints excluded: chain B1 residue 123 ILE Chi-restraints excluded: chain B1 residue 187 VAL Chi-restraints excluded: chain B1 residue 215 GLU Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B1 residue 307 VAL Chi-restraints excluded: chain B1 residue 325 MET Chi-restraints excluded: chain B2 residue 136 SER Chi-restraints excluded: chain B2 residue 152 LEU Chi-restraints excluded: chain B2 residue 187 VAL Chi-restraints excluded: chain B2 residue 213 VAL Chi-restraints excluded: chain B2 residue 273 ILE Chi-restraints excluded: chain B2 residue 286 LEU Chi-restraints excluded: chain B2 residue 318 LEU Chi-restraints excluded: chain B3 residue 61 MET Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 142 HIS Chi-restraints excluded: chain B3 residue 187 VAL Chi-restraints excluded: chain B3 residue 188 MET Chi-restraints excluded: chain B3 residue 198 LEU Chi-restraints excluded: chain B3 residue 336 LEU Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 136 SER Chi-restraints excluded: chain B4 residue 146 LEU Chi-restraints excluded: chain B4 residue 188 MET Chi-restraints excluded: chain B4 residue 263 THR Chi-restraints excluded: chain B4 residue 270 ILE Chi-restraints excluded: chain B4 residue 273 ILE Chi-restraints excluded: chain B4 residue 286 LEU Chi-restraints excluded: chain B5 residue 29 THR Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 153 ASP Chi-restraints excluded: chain B5 residue 177 THR Chi-restraints excluded: chain B5 residue 213 VAL Chi-restraints excluded: chain B5 residue 268 ASN Chi-restraints excluded: chain B5 residue 273 ILE Chi-restraints excluded: chain B5 residue 284 LEU Chi-restraints excluded: chain B5 residue 286 LEU Chi-restraints excluded: chain B5 residue 331 SER Chi-restraints excluded: chain G1 residue 3 SER Chi-restraints excluded: chain G1 residue 57 SER Chi-restraints excluded: chain G2 residue 28 ILE Chi-restraints excluded: chain G4 residue 9 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 65 optimal weight: 20.0000 chunk 380 optimal weight: 4.9990 chunk 255 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 61 optimal weight: 40.0000 chunk 232 optimal weight: 6.9990 chunk 452 optimal weight: 0.0670 chunk 63 optimal weight: 20.0000 chunk 174 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K2 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3 192 ASN ** K4 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 250 HIS C2 218 GLN ** C2 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 272 HIS ** C3 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3 160 HIS ** C3 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.077232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.059030 restraints weight = 424440.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 82)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.051757 restraints weight = 251101.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.051530 restraints weight = 195649.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.051824 restraints weight = 154215.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.051949 restraints weight = 139590.850| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 38520 Z= 0.195 Angle : 0.716 12.610 51995 Z= 0.371 Chirality : 0.043 0.204 5780 Planarity : 0.004 0.044 6780 Dihedral : 5.463 51.803 5231 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.79 % Favored : 94.12 % Rotamer: Outliers : 2.52 % Allowed : 19.64 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.12), residues: 4730 helix: 0.69 (0.11), residues: 2104 sheet: -1.84 (0.18), residues: 717 loop : -1.55 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARGC2 184 TYR 0.019 0.002 TYRK5 71 PHE 0.039 0.002 PHEC3 224 TRP 0.042 0.002 TRPC3 109 HIS 0.021 0.002 HISC5 67 Details of bonding type rmsd covalent geometry : bond 0.00410 (38520) covalent geometry : angle 0.71570 (51995) hydrogen bonds : bond 0.03940 ( 1972) hydrogen bonds : angle 5.36236 ( 5742) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14147.51 seconds wall clock time: 241 minutes 58.82 seconds (14518.82 seconds total)