Starting phenix.real_space_refine on Tue Aug 26 15:23:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u84_42008/08_2025/8u84_42008.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u84_42008/08_2025/8u84_42008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u84_42008/08_2025/8u84_42008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u84_42008/08_2025/8u84_42008.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u84_42008/08_2025/8u84_42008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u84_42008/08_2025/8u84_42008.map" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 1.100 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 7340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.03s 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: 37885 Number of models: 1 Model: "" Number of chains: 20 Chain: "K1" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "K2" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "K3" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "K4" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "K5" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} 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: 7.65, per 1000 atoms: 0.20 Number of scatterers: 37885 At special positions: 0 Unit cell: (238.96, 250.29, 138.02, 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 7340 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: 2.79 Conformation dependent library (CDL) restraints added in 1.6 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: 159 helices and 47 sheets defined 48.3% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'K1' and resid 59 through 63 Processing helix chain 'K1' and resid 68 through 75 removed outlier: 3.683A pdb=" N GLNK1 75 " --> pdb=" O TYRK1 71 " (cutoff:3.500A) Processing helix chain 'K1' and resid 96 through 98 No H-bonds generated for 'chain 'K1' and resid 96 through 98' Processing helix chain 'K1' and resid 99 through 108 removed outlier: 3.537A pdb=" N LEUK1 106 " --> pdb=" O VALK1 102 " (cutoff:3.500A) Processing helix chain 'K1' and resid 118 through 129 Processing helix chain 'K1' and resid 131 through 150 Processing helix chain 'K1' and resid 164 through 174 removed outlier: 3.842A pdb=" N THRK1 169 " --> pdb=" O GLUK1 165 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLNK1 170 " --> pdb=" O GLUK1 166 " (cutoff:3.500A) Processing helix chain 'K1' and resid 221 through 233 removed outlier: 4.087A pdb=" N ARGK1 233 " --> pdb=" O GLUK1 229 " (cutoff:3.500A) Processing helix chain 'K2' and resid 59 through 63 Processing helix chain 'K2' and resid 69 through 75 Processing helix chain 'K2' and resid 95 through 109 Proline residue: K2 101 - end of helix removed outlier: 3.543A pdb=" N HISK2 108 " --> pdb=" O ASNK2 104 " (cutoff:3.500A) Processing helix chain 'K2' and resid 118 through 130 Processing helix chain 'K2' and resid 131 through 149 Processing helix chain 'K2' and resid 164 through 174 removed outlier: 4.390A pdb=" N THRK2 169 " --> pdb=" O GLUK2 165 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLNK2 170 " --> pdb=" O GLUK2 166 " (cutoff:3.500A) Processing helix chain 'K2' and resid 190 through 195 removed outlier: 4.209A pdb=" N TYRK2 193 " --> pdb=" O SERK2 190 " (cutoff:3.500A) Processing helix chain 'K2' and resid 221 through 233 Processing helix chain 'K3' and resid 59 through 63 Processing helix chain 'K3' and resid 70 through 76 removed outlier: 3.612A pdb=" N GLNK3 75 " --> pdb=" O TYRK3 71 " (cutoff:3.500A) Processing helix chain 'K3' and resid 98 through 109 removed outlier: 4.146A pdb=" N VALK3 102 " --> pdb=" O TYRK3 98 " (cutoff:3.500A) Processing helix chain 'K3' and resid 118 through 129 Processing helix chain 'K3' and resid 131 through 152 removed outlier: 4.563A pdb=" N VALK3 152 " --> pdb=" O LYSK3 148 " (cutoff:3.500A) Processing helix chain 'K3' and resid 167 through 174 removed outlier: 4.006A pdb=" N METK3 171 " --> pdb=" O GLUK3 167 " (cutoff:3.500A) Processing helix chain 'K3' and resid 191 through 195 removed outlier: 3.502A pdb=" N ASNK3 195 " --> pdb=" O ASNK3 192 " (cutoff:3.500A) 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: 3.524A pdb=" N ARGK4 72 " --> pdb=" O SERK4 68 " (cutoff:3.500A) Processing helix chain 'K4' and resid 98 through 109 Processing helix chain 'K4' and resid 118 through 130 removed outlier: 3.679A pdb=" N VALK4 122 " --> pdb=" O ALAK4 118 " (cutoff:3.500A) Processing helix chain 'K4' and resid 131 through 149 Processing helix chain 'K4' and resid 167 through 174 Processing helix chain 'K4' and resid 221 through 233 Processing helix chain 'K5' and resid 59 through 63 Processing helix chain 'K5' and resid 68 through 74 removed outlier: 3.606A pdb=" N ARGK5 72 " --> pdb=" O SERK5 68 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEUK5 73 " --> pdb=" O PHEK5 69 " (cutoff:3.500A) Processing helix chain 'K5' and resid 98 through 109 removed outlier: 3.760A pdb=" N VALK5 102 " --> pdb=" O TYRK5 98 " (cutoff:3.500A) Processing helix chain 'K5' and resid 118 through 129 removed outlier: 3.801A pdb=" N PHEK5 128 " --> pdb=" O GLUK5 124 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYRK5 129 " --> pdb=" O GLUK5 125 " (cutoff:3.500A) Processing helix chain 'K5' and resid 131 through 150 Processing helix chain 'K5' and resid 164 through 174 removed outlier: 4.717A pdb=" N THRK5 169 " --> pdb=" O GLUK5 165 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLNK5 170 " --> pdb=" O GLUK5 166 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N METK5 171 " --> pdb=" O GLUK5 167 " (cutoff:3.500A) Processing helix chain 'K5' and resid 197 through 199 No H-bonds generated for 'chain 'K5' and resid 197 through 199' Processing helix chain 'K5' and resid 221 through 233 removed outlier: 3.612A pdb=" N LYSK5 225 " --> pdb=" O SERK5 221 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARGK5 233 " --> pdb=" O GLUK5 229 " (cutoff:3.500A) Processing helix chain 'C1' and resid 27 through 46 Processing helix chain 'C1' and resid 53 through 67 removed outlier: 3.595A pdb=" N LEUC1 57 " --> pdb=" O SERC1 53 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VALC1 65 " --> pdb=" O ALAC1 61 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEUC1 66 " --> pdb=" O TYRC1 62 " (cutoff:3.500A) removed outlier: 3.984A 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 95 Processing helix chain 'C1' and resid 100 through 123 Processing helix chain 'C1' and resid 123 through 134 removed outlier: 3.603A pdb=" N ASPC1 127 " --> pdb=" O LEUC1 123 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VALC1 131 " --> pdb=" O ASPC1 127 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLNC1 132 " --> pdb=" O ARGC1 128 " (cutoff:3.500A) Processing helix chain 'C1' and resid 138 through 152 removed outlier: 3.864A pdb=" N PHEC1 147 " --> pdb=" O GLYC1 143 " (cutoff:3.500A) Processing helix chain 'C1' and resid 154 through 175 Processing helix chain 'C1' and resid 179 through 194 Processing helix chain 'C1' and resid 198 through 205 removed outlier: 3.539A pdb=" N PHEC1 205 " --> pdb=" O TYRC1 201 " (cutoff:3.500A) Processing helix chain 'C1' and resid 205 through 228 Processing helix chain 'C1' and resid 229 through 252 Processing helix chain 'C1' and resid 253 through 255 No H-bonds generated for 'chain 'C1' and resid 253 through 255' Processing helix chain 'C1' and resid 256 through 269 removed outlier: 3.901A pdb=" N ILEC1 260 " --> pdb=" O THRC1 256 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILEC1 269 " --> pdb=" O GLUC1 265 " (cutoff:3.500A) Processing helix chain 'C1' and resid 272 through 277 removed outlier: 3.710A pdb=" N ILEC1 276 " --> pdb=" O HISC1 272 " (cutoff:3.500A) Processing helix chain 'C1' and resid 284 through 289 Processing helix chain 'C1' and resid 292 through 304 removed outlier: 3.986A pdb=" N LEUC1 296 " --> pdb=" O LYSC1 292 " (cutoff:3.500A) Processing helix chain 'C1' and resid 308 through 330 Processing helix chain 'C1' and resid 337 through 342 removed outlier: 3.545A pdb=" N ILEC1 342 " --> pdb=" O PROC1 338 " (cutoff:3.500A) Processing helix chain 'C1' and resid 343 through 359 Processing helix chain 'C1' and resid 363 through 379 removed outlier: 3.567A pdb=" N ASNC1 379 " --> pdb=" O GLUC1 375 " (cutoff:3.500A) Processing helix chain 'C2' and resid 26 through 46 removed outlier: 4.215A pdb=" N SERC2 32 " --> pdb=" O LYSC2 28 " (cutoff:3.500A) Processing helix chain 'C2' and resid 53 through 66 removed outlier: 3.805A pdb=" N LEUC2 66 " --> pdb=" O TYRC2 62 " (cutoff:3.500A) Processing helix chain 'C2' and resid 69 through 88 Processing helix chain 'C2' and resid 88 through 96 removed outlier: 3.781A pdb=" N SERC2 96 " --> pdb=" O ASPC2 92 " (cutoff:3.500A) Processing helix chain 'C2' and resid 100 through 123 removed outlier: 4.155A pdb=" N METC2 118 " --> pdb=" O THRC2 114 " (cutoff:3.500A) Processing helix chain 'C2' and resid 129 through 134 Processing helix chain 'C2' and resid 138 through 151 removed outlier: 4.007A pdb=" N PHEC2 147 " --> pdb=" O GLYC2 143 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VALC2 151 " --> pdb=" O PHEC2 147 " (cutoff:3.500A) Processing helix chain 'C2' and resid 154 through 174 removed outlier: 4.113A pdb=" N HISC2 160 " --> pdb=" O CYSC2 156 " (cutoff:3.500A) Processing helix chain 'C2' and resid 179 through 194 removed outlier: 4.191A 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 252 Processing helix chain 'C2' and resid 253 through 255 No H-bonds generated for 'chain 'C2' and resid 253 through 255' Processing helix chain 'C2' and resid 256 through 268 removed outlier: 3.701A pdb=" N ILEC2 260 " --> pdb=" O THRC2 256 " (cutoff:3.500A) Processing helix chain 'C2' and resid 284 through 291 removed outlier: 3.704A pdb=" N LEUC2 288 " --> pdb=" O LEUC2 284 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYSC2 289 " --> pdb=" O VALC2 285 " (cutoff:3.500A) Processing helix chain 'C2' and resid 292 through 304 removed outlier: 3.783A pdb=" N LEUC2 296 " --> pdb=" O LYSC2 292 " (cutoff:3.500A) Processing helix chain 'C2' and resid 310 through 330 Processing helix chain 'C2' and resid 343 through 359 Processing helix chain 'C2' and resid 363 through 380 Processing helix chain 'C3' and resid 26 through 46 Processing helix chain 'C3' and resid 53 through 67 Processing helix chain 'C3' and resid 69 through 88 Processing helix chain 'C3' and resid 88 through 96 Processing helix chain 'C3' and resid 100 through 123 removed outlier: 3.694A pdb=" N THRC3 104 " --> pdb=" O ASNC3 100 " (cutoff:3.500A) Processing helix chain 'C3' and resid 123 through 135 removed outlier: 4.058A pdb=" N VALC3 131 " --> pdb=" O ASPC3 127 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLNC3 132 " --> pdb=" O ARGC3 128 " (cutoff:3.500A) 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: 4.106A pdb=" N GLYC3 194 " --> pdb=" O LEUC3 190 " (cutoff:3.500A) Processing helix chain 'C3' and resid 198 through 205 removed outlier: 3.595A pdb=" N PHEC3 205 " --> pdb=" O TYRC3 201 " (cutoff:3.500A) Processing helix chain 'C3' and resid 205 through 228 Processing helix chain 'C3' and resid 229 through 252 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: 3.966A pdb=" N ILEC3 260 " --> pdb=" O THRC3 256 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYSC3 262 " --> pdb=" O GLUC3 258 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEUC3 268 " --> pdb=" O VALC3 264 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILEC3 269 " --> pdb=" O GLUC3 265 " (cutoff:3.500A) Processing helix chain 'C3' and resid 274 through 278 Processing helix chain 'C3' and resid 283 through 290 removed outlier: 3.750A pdb=" N LYSC3 289 " --> pdb=" O VALC3 285 " (cutoff:3.500A) Processing helix chain 'C3' and resid 292 through 306 removed outlier: 3.943A pdb=" N LEUC3 296 " --> pdb=" O LYSC3 292 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARGC3 305 " --> pdb=" O LYSC3 301 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VALC3 306 " --> pdb=" O LEUC3 302 " (cutoff:3.500A) Processing helix chain 'C3' and resid 308 through 330 removed outlier: 3.565A pdb=" N THRC3 312 " --> pdb=" O ASNC3 308 " (cutoff:3.500A) Processing helix chain 'C3' and resid 343 through 359 Processing helix chain 'C3' and resid 363 through 379 Processing helix chain 'C4' and resid 25 through 47 Processing helix chain 'C4' and resid 53 through 67 removed outlier: 3.625A pdb=" N LEUC4 57 " --> pdb=" O SERC4 53 " (cutoff:3.500A) Processing helix chain 'C4' and resid 69 through 99 removed outlier: 3.980A pdb=" N ARGC4 90 " --> pdb=" O ILEC4 86 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLUC4 91 " --> pdb=" O ASNC4 87 " (cutoff:3.500A) Processing helix chain 'C4' and resid 100 through 123 removed outlier: 3.601A pdb=" N LEUC4 123 " --> pdb=" O ILEC4 119 " (cutoff:3.500A) Processing helix chain 'C4' and resid 124 through 129 removed outlier: 3.591A pdb=" N VALC4 129 " --> pdb=" O TYRC4 125 " (cutoff:3.500A) Processing helix chain 'C4' and resid 129 through 134 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 195 removed outlier: 3.523A pdb=" N ILEC4 183 " --> pdb=" O ASPC4 179 " (cutoff:3.500A) Processing helix chain 'C4' and resid 197 through 205 removed outlier: 4.080A pdb=" N TYRC4 201 " --> pdb=" O GLYC4 197 " (cutoff:3.500A) Processing helix chain 'C4' and resid 205 through 228 Processing helix chain 'C4' and resid 229 through 252 Processing helix chain 'C4' and resid 253 through 269 removed outlier: 3.973A pdb=" N GLUC4 258 " --> pdb=" O LYSC4 254 " (cutoff:3.500A) Proline residue: C4 259 - end of helix Processing helix chain 'C4' and resid 272 through 278 removed outlier: 3.891A pdb=" N VALC4 277 " --> pdb=" O METC4 273 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLUC4 278 " --> pdb=" O LYSC4 274 " (cutoff:3.500A) Processing helix chain 'C4' and resid 283 through 291 removed outlier: 3.574A pdb=" N GLYC4 291 " --> pdb=" O METC4 287 " (cutoff:3.500A) Processing helix chain 'C4' and resid 292 through 306 removed outlier: 3.906A pdb=" N VALC4 306 " --> pdb=" O LEUC4 302 " (cutoff:3.500A) Processing helix chain 'C4' and resid 308 through 330 removed outlier: 3.579A pdb=" N THRC4 312 " --> pdb=" O ASNC4 308 " (cutoff:3.500A) Processing helix chain 'C4' and resid 337 through 361 removed outlier: 3.674A pdb=" N GLUC4 358 " --> pdb=" O ARGC4 354 " (cutoff:3.500A) Processing helix chain 'C4' and resid 363 through 381 removed outlier: 3.636A pdb=" N LYSC4 367 " --> pdb=" O ASPC4 363 " (cutoff:3.500A) Processing helix chain 'C5' and resid 26 through 46 Processing helix chain 'C5' and resid 53 through 67 Processing helix chain 'C5' and resid 69 through 88 Processing helix chain 'C5' and resid 88 through 96 removed outlier: 4.152A pdb=" N SERC5 96 " --> pdb=" O ASPC5 92 " (cutoff:3.500A) Processing helix chain 'C5' and resid 100 through 123 removed outlier: 4.121A pdb=" N METC5 118 " --> pdb=" O THRC5 114 " (cutoff:3.500A) Processing helix chain 'C5' and resid 123 through 134 removed outlier: 3.973A pdb=" N ASPC5 127 " --> pdb=" O LEUC5 123 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARGC5 128 " --> pdb=" O METC5 124 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VALC5 131 " --> pdb=" O ASPC5 127 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLNC5 132 " --> pdb=" O ARGC5 128 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLNC5 133 " --> pdb=" O VALC5 129 " (cutoff:3.500A) Processing helix chain 'C5' and resid 138 through 151 Processing helix chain 'C5' and resid 154 through 174 Processing helix chain 'C5' and resid 179 through 193 removed outlier: 3.770A 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 227 Processing helix chain 'C5' and resid 229 through 251 Processing helix chain 'C5' and resid 253 through 255 No H-bonds generated for 'chain 'C5' and resid 253 through 255' Processing helix chain 'C5' and resid 256 through 269 removed outlier: 3.714A pdb=" N ILEC5 260 " --> pdb=" O THRC5 256 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILEC5 269 " --> pdb=" O GLUC5 265 " (cutoff:3.500A) Processing helix chain 'C5' and resid 272 through 278 Processing helix chain 'C5' and resid 283 through 291 removed outlier: 3.569A pdb=" N ASNC5 290 " --> pdb=" O HISC5 286 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLYC5 291 " --> pdb=" O METC5 287 " (cutoff:3.500A) Processing helix chain 'C5' and resid 292 through 305 removed outlier: 3.717A pdb=" N LEUC5 296 " --> pdb=" O LYSC5 292 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARGC5 305 " --> pdb=" O LYSC5 301 " (cutoff:3.500A) Processing helix chain 'C5' and resid 308 through 330 Processing helix chain 'C5' and resid 337 through 342 Processing helix chain 'C5' and resid 342 through 359 removed outlier: 3.908A pdb=" N LEUC5 346 " --> pdb=" O ILEC5 342 " (cutoff:3.500A) Processing helix chain 'C5' and resid 363 through 380 removed outlier: 4.094A pdb=" N ASPC5 373 " --> pdb=" O THRC5 369 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEUC5 380 " --> pdb=" O TYRC5 376 " (cutoff:3.500A) Processing helix chain 'B1' and resid 3 through 26 Processing helix chain 'B1' and resid 29 through 34 Processing helix chain 'B2' and resid 3 through 26 Processing helix chain 'B2' and resid 29 through 34 removed outlier: 3.572A pdb=" N ILEB2 33 " --> pdb=" O THRB2 29 " (cutoff:3.500A) Processing helix chain 'B3' and resid 3 through 25 Processing helix chain 'B3' and resid 29 through 34 Processing helix chain 'B4' and resid 3 through 25 Processing helix chain 'B4' and resid 29 through 34 removed outlier: 3.744A pdb=" N ILEB4 33 " --> pdb=" O THRB4 29 " (cutoff:3.500A) Processing helix chain 'B5' and resid 3 through 26 removed outlier: 3.527A pdb=" N GLNB5 9 " --> pdb=" O ASPB5 5 " (cutoff:3.500A) Processing helix chain 'B5' and resid 29 through 34 removed outlier: 3.527A pdb=" N ILEB5 33 " --> pdb=" O THRB5 29 " (cutoff:3.500A) Processing helix chain 'G1' and resid 8 through 25 removed outlier: 3.547A pdb=" N ILEG1 25 " --> pdb=" O METG1 21 " (cutoff:3.500A) Processing helix chain 'G1' and resid 29 through 44 Processing helix chain 'G2' and resid 8 through 24 removed outlier: 3.718A pdb=" N ALAG2 12 " --> pdb=" O SERG2 8 " (cutoff:3.500A) Processing helix chain 'G2' and resid 29 through 46 removed outlier: 4.064A pdb=" N LYSG2 46 " --> pdb=" O GLUG2 42 " (cutoff:3.500A) Processing helix chain 'G3' and resid 8 through 24 Processing helix chain 'G3' and resid 29 through 46 removed outlier: 3.682A pdb=" N ALAG3 33 " --> pdb=" O LYSG3 29 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYSG3 46 " --> pdb=" O GLUG3 42 " (cutoff:3.500A) Processing helix chain 'G4' and resid 8 through 25 removed outlier: 3.868A pdb=" N ALAG4 12 " --> pdb=" O SERG4 8 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N METG4 21 " --> pdb=" O GLUG4 17 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLUG4 22 " --> pdb=" O GLNG4 18 " (cutoff:3.500A) Processing helix chain 'G4' and resid 29 through 44 Processing helix chain 'G5' and resid 7 through 25 removed outlier: 4.478A pdb=" N GLNG5 11 " --> pdb=" O ALAG5 7 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N METG5 21 " --> pdb=" O GLUG5 17 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLUG5 22 " --> pdb=" O GLNG5 18 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALAG5 23 " --> pdb=" O LEUG5 19 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASNG5 24 " --> pdb=" O LYSG5 20 " (cutoff:3.500A) Processing helix chain 'G5' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'K1' and resid 53 through 58 removed outlier: 3.522A pdb=" N TYRK1 90 " --> pdb=" O ARGK1 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K1' and resid 157 through 163 removed outlier: 6.555A pdb=" N LEUK1 202 " --> pdb=" O LEUK1 184 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEUK1 184 " --> pdb=" O LEUK1 202 " (cutoff:3.500A) removed outlier: 6.737A 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: 3.813A pdb=" N TYRK2 90 " --> pdb=" O ARGK2 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K2' and resid 155 through 163 removed outlier: 6.694A pdb=" N LEUK2 202 " --> pdb=" O LEUK2 184 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LEUK2 184 " --> pdb=" O LEUK2 202 " (cutoff:3.500A) removed outlier: 7.024A 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 155 through 163 removed outlier: 3.942A pdb=" N LYSK3 155 " --> pdb=" O LEUK3 209 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEUK3 202 " --> pdb=" O LEUK3 184 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEUK3 184 " --> pdb=" O LEUK3 202 " (cutoff:3.500A) removed outlier: 6.891A 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: 7.454A pdb=" N ILEK4 92 " --> pdb=" O ARGK4 47 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASNK4 49 " --> pdb=" O ILEK4 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K4' and resid 157 through 162 removed outlier: 6.437A pdb=" N LEUK4 202 " --> pdb=" O LEUK4 184 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEUK4 184 " --> pdb=" O LEUK4 202 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VALK4 204 " --> pdb=" O GLUK4 182 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K5' and resid 53 through 58 removed outlier: 4.071A pdb=" N TYRK5 90 " --> pdb=" O ARGK5 47 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILEK5 92 " --> pdb=" O ASNK5 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K5' and resid 156 through 163 removed outlier: 3.503A pdb=" N GLNK5 183 " --> pdb=" O VALK5 204 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N SERK5 206 " --> pdb=" O PHEK5 181 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHEK5 181 " --> pdb=" O SERK5 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C1' and resid 278 through 279 Processing sheet with id=AB3, first strand: chain 'C2' and resid 278 through 279 removed outlier: 3.549A pdb=" N METC2 279 " --> pdb=" O SERC2 282 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SERC2 282 " --> pdb=" O METC2 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B1' and resid 47 through 52 removed outlier: 3.757A pdb=" N ARGB1 49 " --> pdb=" O ILEB1 338 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEUB1 336 " --> pdb=" O LEUB1 51 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHEB1 335 " --> pdb=" O SERB1 331 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SERB1 331 " --> pdb=" O PHEB1 335 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYSB1 337 " --> pdb=" O THRB1 329 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYSB1 317 " --> pdb=" O GLYB1 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B1' and resid 58 through 63 removed outlier: 3.938A pdb=" N ALAB1 60 " --> pdb=" O ALAB1 73 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYSB1 78 " --> pdb=" O SERB1 74 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HISB1 91 " --> pdb=" O ILEB1 81 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B1' and resid 100 through 105 removed outlier: 3.680A pdb=" N GLYB1 115 " --> pdb=" O THRB1 102 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ASNB1 125 " --> pdb=" O VALB1 135 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VALB1 135 " --> pdb=" O ASNB1 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B1' and resid 146 through 151 removed outlier: 7.068A pdb=" N SERB1 160 " --> pdb=" O SERB1 147 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N CYSB1 149 " --> pdb=" O VALB1 158 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VALB1 158 " --> pdb=" O CYSB1 149 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N PHEB1 151 " --> pdb=" O GLNB1 156 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLNB1 156 " --> pdb=" O PHEB1 151 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEUB1 168 " --> pdb=" O THRB1 177 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLNB1 175 " --> pdb=" O ASPB1 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B1' and resid 191 through 192 removed outlier: 6.591A pdb=" N ASPB1 212 " --> pdb=" O CYSB1 218 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYSB1 218 " --> pdb=" O ASPB1 212 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B1' and resid 229 through 234 removed outlier: 7.116A pdb=" N GLYB1 244 " --> pdb=" O ASNB1 230 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILEB1 232 " --> pdb=" O ALAB1 242 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALAB1 242 " --> pdb=" O ILEB1 232 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N PHEB1 234 " --> pdb=" O ALAB1 240 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ALAB1 240 " --> pdb=" O PHEB1 234 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SERB1 245 " --> pdb=" O THRB1 249 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N THRB1 249 " --> pdb=" O SERB1 245 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N CYSB1 250 " --> pdb=" O THRB1 263 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N THRB1 263 " --> pdb=" O CYSB1 250 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEUB1 252 " --> pdb=" O LEUB1 261 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B1' and resid 273 through 278 removed outlier: 3.629A pdb=" N SERB1 275 " --> pdb=" O GLYB1 288 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYSB1 294 " --> pdb=" O LEUB1 308 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ASPB1 298 " --> pdb=" O ARGB1 304 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARGB1 304 " --> pdb=" O ASPB1 298 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B2' and resid 46 through 52 removed outlier: 5.178A pdb=" N THRB2 47 " --> pdb=" O ASNB2 340 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASNB2 340 " --> pdb=" O THRB2 47 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEUB2 336 " --> pdb=" O LEUB2 51 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHEB2 335 " --> pdb=" O SERB2 331 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SERB2 331 " --> pdb=" O PHEB2 335 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYSB2 337 " --> pdb=" O THRB2 329 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALAB2 328 " --> pdb=" O LEUB2 318 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEUB2 318 " --> pdb=" O ALAB2 328 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLYB2 330 " --> pdb=" O SERB2 316 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B2' and resid 58 through 63 removed outlier: 6.990A pdb=" N ALAB2 73 " --> pdb=" O TYRB2 59 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N METB2 61 " --> pdb=" O VALB2 71 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VALB2 71 " --> pdb=" O METB2 61 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TRPB2 63 " --> pdb=" O LEUB2 69 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEUB2 69 " --> pdb=" O TRPB2 63 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYSB2 78 " --> pdb=" O SERB2 74 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEUB2 79 " --> pdb=" O ALAB2 92 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALAB2 92 " --> pdb=" O LEUB2 79 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILEB2 81 " --> pdb=" O VALB2 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B2' and resid 100 through 105 removed outlier: 5.558A pdb=" N ASNB2 125 " --> pdb=" O VALB2 135 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VALB2 135 " --> pdb=" O ASNB2 125 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B2' and resid 146 through 153 removed outlier: 6.585A pdb=" N SERB2 160 " --> pdb=" O SERB2 147 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N CYSB2 149 " --> pdb=" O VALB2 158 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VALB2 158 " --> pdb=" O CYSB2 149 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N PHEB2 151 " --> pdb=" O GLNB2 156 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLNB2 156 " --> pdb=" O PHEB2 151 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B2' and resid 198 through 202 removed outlier: 4.146A pdb=" N PHEB2 199 " --> pdb=" O TRPB2 211 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ALAB2 208 " --> pdb=" O THRB2 221 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THRB2 221 " --> pdb=" O ALAB2 208 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEUB2 210 " --> pdb=" O ARGB2 219 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N METB2 217 " --> pdb=" O ASPB2 212 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B2' and resid 229 through 234 removed outlier: 6.480A pdb=" N ASPB2 254 " --> pdb=" O GLUB2 260 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLUB2 260 " --> pdb=" O ASPB2 254 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B2' and resid 273 through 278 removed outlier: 3.868A pdb=" N SERB2 275 " --> pdb=" O GLYB2 288 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ASPB2 298 " --> pdb=" O ARGB2 304 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARGB2 304 " --> pdb=" O ASPB2 298 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B3' and resid 47 through 52 removed outlier: 6.303A pdb=" N ILEB3 338 " --> pdb=" O ARGB3 48 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THRB3 50 " --> pdb=" O LEUB3 336 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEUB3 336 " --> pdb=" O THRB3 50 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N PHEB3 335 " --> pdb=" O SERB3 331 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYSB3 337 " --> pdb=" O THRB3 329 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALAB3 328 " --> pdb=" O GLYB3 319 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLYB3 319 " --> pdb=" O ALAB3 328 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B3' and resid 58 through 62 removed outlier: 4.109A pdb=" N ALAB3 60 " --> pdb=" O ALAB3 73 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEUB3 79 " --> pdb=" O ALAB3 92 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALAB3 92 " --> pdb=" O LEUB3 79 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILEB3 81 " --> pdb=" O VALB3 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B3' and resid 100 through 105 removed outlier: 3.503A pdb=" N THRB3 102 " --> pdb=" O GLYB3 115 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLYB3 116 " --> pdb=" O ILEB3 120 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ILEB3 120 " --> pdb=" O GLYB3 116 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N CYSB3 121 " --> pdb=" O GLUB3 138 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLUB3 138 " --> pdb=" O CYSB3 121 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILEB3 123 " --> pdb=" O SERB3 136 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARGB3 134 " --> pdb=" O ASNB3 125 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B3' and resid 149 through 151 Processing sheet with id=AD4, first strand: chain 'B3' and resid 198 through 202 Processing sheet with id=AD5, first strand: chain 'B3' and resid 229 through 234 removed outlier: 7.135A pdb=" N GLYB3 244 " --> pdb=" O ASNB3 230 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ILEB3 232 " --> pdb=" O ALAB3 242 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALAB3 242 " --> pdb=" O ILEB3 232 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N PHEB3 234 " --> pdb=" O ALAB3 240 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ALAB3 240 " --> pdb=" O PHEB3 234 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYSB3 250 " --> pdb=" O THRB3 263 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THRB3 263 " --> pdb=" O CYSB3 250 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEUB3 252 " --> pdb=" O LEUB3 261 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B3' and resid 273 through 278 removed outlier: 3.642A pdb=" N SERB3 275 " --> pdb=" O GLYB3 288 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASPB3 298 " --> pdb=" O ARGB3 304 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ARGB3 304 " --> pdb=" O ASPB3 298 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B4' and resid 46 through 50 removed outlier: 6.048A pdb=" N THRB4 47 " --> pdb=" O ASNB4 340 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASNB4 340 " --> pdb=" O THRB4 47 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARGB4 49 " --> pdb=" O ILEB4 338 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYSB4 337 " --> pdb=" O THRB4 329 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B4' and resid 58 through 62 removed outlier: 3.567A pdb=" N ALAB4 60 " --> pdb=" O ALAB4 73 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEUB4 79 " --> pdb=" O ALAB4 92 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALAB4 92 " --> pdb=" O LEUB4 79 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILEB4 81 " --> pdb=" O VALB4 90 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B4' and resid 102 through 105 removed outlier: 3.618A pdb=" N THRB4 102 " --> pdb=" O GLYB4 115 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N CYSB4 121 " --> pdb=" O GLUB4 138 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLUB4 138 " --> pdb=" O CYSB4 121 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILEB4 123 " --> pdb=" O SERB4 136 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARGB4 134 " --> pdb=" O ASNB4 125 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B4' and resid 146 through 151 removed outlier: 6.835A pdb=" N SERB4 160 " --> pdb=" O SERB4 147 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYSB4 149 " --> pdb=" O VALB4 158 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VALB4 158 " --> pdb=" O CYSB4 149 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N PHEB4 151 " --> pdb=" O GLNB4 156 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLNB4 156 " --> pdb=" O PHEB4 151 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEUB4 168 " --> pdb=" O THRB4 177 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B4' and resid 191 through 192 Processing sheet with id=AE3, first strand: chain 'B4' and resid 229 through 234 removed outlier: 3.835A pdb=" N ALAB4 231 " --> pdb=" O GLYB4 244 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SERB4 245 " --> pdb=" O THRB4 249 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N THRB4 249 " --> pdb=" O SERB4 245 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYSB4 250 " --> pdb=" O THRB4 263 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THRB4 263 " --> pdb=" O CYSB4 250 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEUB4 252 " --> pdb=" O LEUB4 261 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B4' and resid 273 through 278 removed outlier: 3.544A pdb=" N SERB4 277 " --> pdb=" O LEUB4 286 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASPB4 298 " --> pdb=" O ARGB4 304 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ARGB4 304 " --> pdb=" O ASPB4 298 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B5' and resid 46 through 51 removed outlier: 6.540A pdb=" N ILEB5 338 " --> pdb=" O ARGB5 48 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THRB5 50 " --> pdb=" O LEUB5 336 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEUB5 336 " --> pdb=" O THRB5 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYSB5 337 " --> pdb=" O THRB5 329 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B5' and resid 58 through 63 removed outlier: 6.899A pdb=" N ALAB5 73 " --> pdb=" O TYRB5 59 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N METB5 61 " --> pdb=" O VALB5 71 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VALB5 71 " --> pdb=" O METB5 61 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TRPB5 63 " --> pdb=" O LEUB5 69 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEUB5 69 " --> pdb=" O TRPB5 63 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYSB5 78 " --> pdb=" O SERB5 74 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HISB5 91 " --> pdb=" O ILEB5 81 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASPB5 83 " --> pdb=" O LYSB5 89 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LYSB5 89 " --> pdb=" O ASPB5 83 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B5' and resid 100 through 105 removed outlier: 6.822A pdb=" N GLYB5 115 " --> pdb=" O METB5 101 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYSB5 103 " --> pdb=" O ALAB5 113 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALAB5 113 " --> pdb=" O CYSB5 103 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYRB5 105 " --> pdb=" O TYRB5 111 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N TYRB5 111 " --> pdb=" O TYRB5 105 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ASNB5 125 " --> pdb=" O VALB5 135 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VALB5 135 " --> pdb=" O ASNB5 125 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B5' and resid 148 through 151 removed outlier: 3.533A pdb=" N CYSB5 148 " --> pdb=" O SERB5 160 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEUB5 168 " --> pdb=" O THRB5 177 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B5' and resid 187 through 192 removed outlier: 6.090A pdb=" N ASPB5 212 " --> pdb=" O CYSB5 218 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N CYSB5 218 " --> pdb=" O ASPB5 212 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B5' and resid 229 through 234 removed outlier: 3.587A pdb=" N ALAB5 231 " --> pdb=" O GLYB5 244 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N METB5 262 " --> pdb=" O LEUB5 252 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASPB5 254 " --> pdb=" O GLUB5 260 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLUB5 260 " --> pdb=" O ASPB5 254 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B5' and resid 273 through 278 removed outlier: 3.606A pdb=" N SERB5 275 " --> pdb=" O GLYB5 288 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ASPB5 298 " --> pdb=" O ARGB5 304 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARGB5 304 " --> pdb=" O ASPB5 298 " (cutoff:3.500A) 1954 hydrogen bonds defined for protein. 5703 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: 8.13 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10391 1.33 - 1.46: 8202 1.46 - 1.58: 19497 1.58 - 1.71: 0 1.71 - 1.83: 425 Bond restraints: 38515 Sorted by residual: bond pdb=" N VALK1 154 " pdb=" CA VALK1 154 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.84e+00 bond pdb=" N VALK2 154 " pdb=" CA VALK2 154 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.54e+00 bond pdb=" N VALK2 152 " pdb=" CA VALK2 152 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.23e-02 6.61e+03 8.03e+00 bond pdb=" N ILEC2 260 " pdb=" CA ILEC2 260 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.77e+00 bond pdb=" N ILEC1 192 " pdb=" CA ILEC1 192 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 7.11e+00 ... (remaining 38510 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 51023 2.63 - 5.25: 818 5.25 - 7.88: 113 7.88 - 10.50: 24 10.50 - 13.13: 7 Bond angle restraints: 51985 Sorted by residual: angle pdb=" N PROK1 213 " pdb=" CA PROK1 213 " pdb=" C PROK1 213 " ideal model delta sigma weight residual 113.75 106.17 7.58 1.49e+00 4.50e-01 2.59e+01 angle pdb=" N LEUC1 193 " pdb=" CA LEUC1 193 " pdb=" C LEUC1 193 " ideal model delta sigma weight residual 111.71 105.90 5.81 1.15e+00 7.56e-01 2.55e+01 angle pdb=" N ASPB5 323 " pdb=" CA ASPB5 323 " pdb=" C ASPB5 323 " ideal model delta sigma weight residual 114.39 107.45 6.94 1.45e+00 4.76e-01 2.29e+01 angle pdb=" CA METK2 171 " pdb=" CB METK2 171 " pdb=" CG METK2 171 " ideal model delta sigma weight residual 114.10 123.65 -9.55 2.00e+00 2.50e-01 2.28e+01 angle pdb=" N GLUC4 196 " pdb=" CA GLUC4 196 " pdb=" C GLUC4 196 " ideal model delta sigma weight residual 114.16 107.25 6.91 1.48e+00 4.57e-01 2.18e+01 ... (remaining 51980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 20730 17.99 - 35.98: 1959 35.98 - 53.97: 392 53.97 - 71.95: 200 71.95 - 89.94: 99 Dihedral angle restraints: 23380 sinusoidal: 9495 harmonic: 13885 Sorted by residual: dihedral pdb=" CD ARGK3 64 " pdb=" NE ARGK3 64 " pdb=" CZ ARGK3 64 " pdb=" NH1 ARGK3 64 " ideal model delta sinusoidal sigma weight residual 0.00 76.96 -76.96 1 1.00e+01 1.00e-02 7.43e+01 dihedral pdb=" CA SERB4 74 " pdb=" C SERB4 74 " pdb=" N GLNB4 75 " pdb=" CA GLNB4 75 " ideal model delta harmonic sigma weight residual -180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA ASPK3 197 " pdb=" C ASPK3 197 " pdb=" N GLNK3 198 " pdb=" CA GLNK3 198 " ideal model delta harmonic sigma weight residual 180.00 153.88 26.12 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 23377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 5001 0.066 - 0.131: 717 0.131 - 0.197: 54 0.197 - 0.263: 6 0.263 - 0.329: 2 Chirality restraints: 5780 Sorted by residual: chirality pdb=" CG LEUC3 348 " pdb=" CB LEUC3 348 " pdb=" CD1 LEUC3 348 " pdb=" CD2 LEUC3 348 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CB ILEK4 131 " pdb=" CA ILEK4 131 " pdb=" CG1 ILEK4 131 " pdb=" CG2 ILEK4 131 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CG LEUC3 36 " pdb=" CB LEUC3 36 " pdb=" CD1 LEUC3 36 " pdb=" CD2 LEUC3 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 5777 not shown) Planarity restraints: 6775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARGK3 64 " 1.066 9.50e-02 1.11e+02 4.78e-01 1.38e+02 pdb=" NE ARGK3 64 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARGK3 64 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARGK3 64 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARGK3 64 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGC5 184 " -0.405 9.50e-02 1.11e+02 1.82e-01 2.06e+01 pdb=" NE ARGC5 184 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARGC5 184 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARGC5 184 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARGC5 184 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLUC1 258 " 0.066 5.00e-02 4.00e+02 9.89e-02 1.56e+01 pdb=" N PROC1 259 " -0.171 5.00e-02 4.00e+02 pdb=" CA PROC1 259 " 0.050 5.00e-02 4.00e+02 pdb=" CD PROC1 259 " 0.054 5.00e-02 4.00e+02 ... (remaining 6772 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 806 2.68 - 3.24: 40181 3.24 - 3.79: 64283 3.79 - 4.35: 88437 4.35 - 4.90: 138513 Nonbonded interactions: 332220 Sorted by model distance: nonbonded pdb=" OG1 THRC5 293 " pdb=" OG SERC5 359 " model vdw 2.125 3.040 nonbonded pdb=" OG SERC5 221 " pdb=" OE1 GLNC5 222 " model vdw 2.137 3.040 nonbonded pdb=" OH TYRC1 300 " pdb=" OD2 ASPC1 363 " model vdw 2.155 3.040 nonbonded pdb=" O GLUC4 238 " pdb=" ND2 ASNC4 242 " model vdw 2.157 3.120 nonbonded pdb=" O GLUG1 42 " pdb=" NZ LYSG1 46 " model vdw 2.158 3.120 ... (remaining 332215 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.720 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 32.550 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 0.060 38515 Z= 0.189 Angle : 0.838 13.126 51985 Z= 0.474 Chirality : 0.046 0.329 5780 Planarity : 0.008 0.478 6775 Dihedral : 16.816 89.943 14410 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.20 % Favored : 94.55 % Rotamer: Outliers : 0.62 % Allowed : 16.69 % Favored : 82.69 % 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: 0.62 (0.11), residues: 2053 sheet: -1.13 (0.20), residues: 661 loop : -1.71 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGC4 180 TYR 0.040 0.002 TYRC2 62 PHE 0.051 0.002 PHEC4 377 TRP 0.044 0.002 TRPC5 109 HIS 0.018 0.002 HISC5 67 Details of bonding type rmsd covalent geometry : bond 0.00351 (38515) covalent geometry : angle 0.83770 (51985) hydrogen bonds : bond 0.15450 ( 1954) hydrogen bonds : angle 6.59267 ( 5703) *********************** 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 318 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 292 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 69 PHE cc_start: 0.8457 (t80) cc_final: 0.8225 (t80) REVERT: K1 155 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7979 (mptt) REVERT: K1 201 PHE cc_start: 0.8558 (m-80) cc_final: 0.8323 (m-80) REVERT: K2 79 ASP cc_start: 0.4204 (OUTLIER) cc_final: 0.2704 (m-30) REVERT: K2 80 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6890 (pp) REVERT: K3 64 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.6961 (ttp80) REVERT: K3 134 LEU cc_start: 0.9166 (mt) cc_final: 0.8797 (pp) REVERT: K4 129 TYR cc_start: 0.6976 (m-80) cc_final: 0.6242 (m-80) REVERT: C3 64 MET cc_start: 0.2495 (tpt) cc_final: 0.2236 (tpt) REVERT: C3 128 ARG cc_start: 0.8571 (ttt180) cc_final: 0.7538 (ptp-170) REVERT: C4 116 MET cc_start: -0.3436 (ttp) cc_final: -0.4280 (tpp) REVERT: C5 124 MET cc_start: 0.8922 (mtm) cc_final: 0.8517 (mtt) REVERT: C5 317 MET cc_start: 0.5034 (OUTLIER) cc_final: 0.4811 (mmp) REVERT: B1 217 MET cc_start: 0.8839 (ppp) cc_final: 0.8528 (ppp) REVERT: B5 325 MET cc_start: 0.9008 (tpt) cc_final: 0.8533 (tpp) REVERT: G1 1 MET cc_start: 0.7768 (tpp) cc_final: 0.7464 (tpp) outliers start: 26 outliers final: 7 residues processed: 310 average time/residue: 0.2068 time to fit residues: 106.3983 Evaluate side-chains 273 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 261 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 155 LYS Chi-restraints excluded: chain K2 residue 79 ASP Chi-restraints excluded: chain K2 residue 80 LEU Chi-restraints excluded: chain K2 residue 151 GLN Chi-restraints excluded: chain K2 residue 155 LYS Chi-restraints excluded: chain K3 residue 64 ARG Chi-restraints excluded: chain K3 residue 67 LYS Chi-restraints excluded: chain C2 residue 260 ILE Chi-restraints excluded: chain C2 residue 261 VAL Chi-restraints excluded: chain C5 residue 188 GLN Chi-restraints excluded: chain C5 residue 191 MET Chi-restraints excluded: chain C5 residue 317 MET 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: 30.0000 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K1 49 ASN K1 75 GLN ** K1 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1 151 GLN K1 211 ASN K2 75 GLN K2 151 GLN ** K2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K4 162 GLN K5 211 ASN C1 31 ASN C1 42 GLN ** C1 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 106 ASN C1 110 ASN ** C2 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 113 GLN ** C2 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3 188 GLN ** C3 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 188 GLN C5 45 GLN ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 313 ASN ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 237 ASN ** B3 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4 237 ASN ** B4 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5 220 GLN G1 4 ASN G2 11 GLN ** G2 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.065362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.048882 restraints weight = 470412.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.049205 restraints weight = 318190.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.049092 restraints weight = 201818.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.049059 restraints weight = 148067.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.049328 restraints weight = 146080.772| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 38515 Z= 0.264 Angle : 0.761 11.723 51985 Z= 0.408 Chirality : 0.044 0.195 5780 Planarity : 0.005 0.082 6775 Dihedral : 6.494 87.639 5255 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.88 % Favored : 94.00 % Rotamer: Outliers : 2.78 % Allowed : 14.84 % Favored : 82.37 % 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: -0.85 (0.12), residues: 4730 helix: 0.68 (0.11), residues: 2119 sheet: -1.52 (0.18), residues: 758 loop : -1.54 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGC1 120 TYR 0.031 0.002 TYRC4 341 PHE 0.039 0.003 PHEC4 377 TRP 0.033 0.003 TRPC2 109 HIS 0.018 0.002 HISC5 67 Details of bonding type rmsd covalent geometry : bond 0.00538 (38515) covalent geometry : angle 0.76054 (51985) hydrogen bonds : bond 0.05010 ( 1954) hydrogen bonds : angle 5.43023 ( 5703) *********************** 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 383 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 267 time to evaluate : 1.696 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: K1 168 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9300 (tp) REVERT: K2 79 ASP cc_start: 0.4671 (OUTLIER) cc_final: 0.3946 (m-30) REVERT: K5 171 MET cc_start: 0.9252 (ptp) cc_final: 0.8852 (ptp) REVERT: C1 25 MET cc_start: 0.5576 (tpp) cc_final: 0.5251 (tpp) REVERT: C1 254 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.8622 (mmpt) REVERT: C1 299 MET cc_start: 0.5477 (mmt) cc_final: 0.5163 (mmt) REVERT: C3 25 MET cc_start: 0.6370 (ppp) cc_final: 0.5661 (pmm) REVERT: C3 64 MET cc_start: 0.1156 (tpt) cc_final: 0.0911 (tpt) REVERT: C3 99 ASN cc_start: 0.8753 (p0) cc_final: 0.8506 (t0) REVERT: C3 124 MET cc_start: 0.7042 (mtt) cc_final: 0.6384 (mtt) REVERT: C3 128 ARG cc_start: 0.8710 (ttt180) cc_final: 0.7739 (ptm-80) REVERT: C4 64 MET cc_start: 0.5806 (mmt) cc_final: 0.4595 (ttt) REVERT: C4 126 MET cc_start: 0.5941 (ttm) cc_final: 0.5577 (tpp) REVERT: C4 154 TYR cc_start: 0.9315 (t80) cc_final: 0.9094 (m-10) REVERT: C4 287 MET cc_start: -0.0503 (mmt) cc_final: -0.1934 (mmt) REVERT: C4 313 MET cc_start: 0.4692 (mtt) cc_final: 0.4011 (mtt) REVERT: C5 124 MET cc_start: 0.9087 (mtm) cc_final: 0.8653 (mtt) REVERT: C5 317 MET cc_start: 0.6092 (OUTLIER) cc_final: 0.5563 (mmm) REVERT: B1 61 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7545 (ppp) REVERT: B2 45 MET cc_start: 0.8375 (tpt) cc_final: 0.8050 (tpp) REVERT: B3 225 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.7462 (t-90) REVERT: B3 301 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8319 (mttp) REVERT: B4 183 HIS cc_start: 0.6534 (OUTLIER) cc_final: 0.6253 (t-90) REVERT: B4 188 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8381 (ppp) REVERT: B4 262 MET cc_start: 0.8358 (tpp) cc_final: 0.8066 (tpp) REVERT: G1 21 MET cc_start: 0.9348 (mpp) cc_final: 0.9116 (mpp) REVERT: G2 1 MET cc_start: 0.8198 (tpt) cc_final: 0.7276 (tmm) REVERT: G4 1 MET cc_start: 0.8200 (ppp) cc_final: 0.7920 (ppp) outliers start: 116 outliers final: 53 residues processed: 357 average time/residue: 0.2093 time to fit residues: 126.0963 Evaluate side-chains 306 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 244 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 155 LYS Chi-restraints excluded: chain K1 residue 168 LEU Chi-restraints excluded: chain K2 residue 62 LEU Chi-restraints excluded: chain K2 residue 79 ASP Chi-restraints excluded: chain K2 residue 104 ASN Chi-restraints excluded: chain K2 residue 157 VAL Chi-restraints excluded: chain K2 residue 204 VAL Chi-restraints excluded: chain K3 residue 61 THR Chi-restraints excluded: chain K3 residue 67 LYS Chi-restraints excluded: chain K3 residue 92 ILE Chi-restraints excluded: chain K3 residue 152 VAL Chi-restraints excluded: chain K4 residue 104 ASN Chi-restraints excluded: chain K4 residue 202 LEU Chi-restraints excluded: chain K5 residue 134 LEU Chi-restraints excluded: chain K5 residue 187 ILE Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 73 LEU Chi-restraints excluded: chain C1 residue 89 VAL Chi-restraints excluded: chain C1 residue 102 LEU Chi-restraints excluded: chain C1 residue 104 THR Chi-restraints excluded: chain C1 residue 188 GLN Chi-restraints excluded: chain C1 residue 254 LYS Chi-restraints excluded: chain C2 residue 254 LYS Chi-restraints excluded: chain C2 residue 260 ILE Chi-restraints excluded: chain C2 residue 261 VAL Chi-restraints excluded: chain C2 residue 357 LEU Chi-restraints excluded: chain C3 residue 251 CYS Chi-restraints excluded: chain C4 residue 25 MET Chi-restraints excluded: chain C4 residue 69 HIS Chi-restraints excluded: chain C4 residue 82 THR Chi-restraints excluded: chain C4 residue 94 LEU Chi-restraints excluded: chain C4 residue 102 LEU Chi-restraints excluded: chain C4 residue 129 VAL Chi-restraints excluded: chain C4 residue 173 ARG Chi-restraints excluded: chain C4 residue 293 THR Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 300 TYR Chi-restraints excluded: chain C5 residue 317 MET Chi-restraints excluded: chain B1 residue 61 MET Chi-restraints excluded: chain B1 residue 112 VAL Chi-restraints excluded: chain B2 residue 37 ILE Chi-restraints excluded: chain B2 residue 80 ILE Chi-restraints excluded: chain B2 residue 112 VAL Chi-restraints excluded: chain B2 residue 321 THR Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 225 HIS Chi-restraints excluded: chain B3 residue 286 LEU Chi-restraints excluded: chain B3 residue 301 LYS Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 183 HIS Chi-restraints excluded: chain B4 residue 187 VAL Chi-restraints excluded: chain B4 residue 188 MET Chi-restraints excluded: chain B4 residue 266 HIS Chi-restraints excluded: chain B4 residue 267 ASP Chi-restraints excluded: chain B4 residue 320 VAL Chi-restraints excluded: chain B5 residue 200 VAL Chi-restraints excluded: chain B5 residue 234 PHE Chi-restraints excluded: chain B5 residue 296 VAL Chi-restraints excluded: chain G1 residue 38 MET Chi-restraints excluded: chain G4 residue 38 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 435 optimal weight: 10.0000 chunk 273 optimal weight: 6.9990 chunk 245 optimal weight: 0.8980 chunk 124 optimal weight: 30.0000 chunk 42 optimal weight: 50.0000 chunk 63 optimal weight: 30.0000 chunk 447 optimal weight: 10.0000 chunk 268 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 309 optimal weight: 2.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K1 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 192 ASN ** K2 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 103 GLN C1 106 ASN C1 110 ASN ** C2 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 132 GLN ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 250 HIS C4 324 GLN C5 45 GLN ** C5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 75 GLN B3 237 ASN B4 237 ASN B4 259 GLN ** B4 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.066135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.049426 restraints weight = 467684.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.049071 restraints weight = 293186.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.049477 restraints weight = 198805.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.049533 restraints weight = 155500.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.049510 restraints weight = 138577.412| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 38515 Z= 0.189 Angle : 0.654 11.032 51985 Z= 0.352 Chirality : 0.042 0.348 5780 Planarity : 0.004 0.052 6775 Dihedral : 5.918 89.693 5236 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.41 % Favored : 94.46 % Rotamer: Outliers : 2.37 % Allowed : 15.97 % Favored : 81.65 % 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: 0.89 (0.11), residues: 2120 sheet: -1.49 (0.18), residues: 763 loop : -1.37 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGC1 120 TYR 0.026 0.002 TYRC4 341 PHE 0.037 0.002 PHEC4 377 TRP 0.027 0.002 TRPC1 109 HIS 0.016 0.001 HISC5 67 Details of bonding type rmsd covalent geometry : bond 0.00385 (38515) covalent geometry : angle 0.65380 (51985) hydrogen bonds : bond 0.04414 ( 1954) hydrogen bonds : angle 5.18041 ( 5703) *********************** 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 355 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 256 time to evaluate : 1.615 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 162 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: K1 167 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8734 (pm20) REVERT: K2 79 ASP cc_start: 0.4677 (OUTLIER) cc_final: 0.3796 (m-30) REVERT: K4 129 TYR cc_start: 0.7282 (m-80) cc_final: 0.6610 (m-80) REVERT: K5 171 MET cc_start: 0.9154 (ptp) cc_final: 0.8695 (ptp) REVERT: C1 109 TRP cc_start: 0.8384 (t60) cc_final: 0.7834 (t60) REVERT: C1 189 MET cc_start: 0.9354 (mtt) cc_final: 0.8694 (mtt) REVERT: C2 64 MET cc_start: 0.5530 (OUTLIER) cc_final: 0.4975 (tpp) REVERT: C3 25 MET cc_start: 0.6473 (ppp) cc_final: 0.5918 (pmm) REVERT: C3 64 MET cc_start: 0.0582 (tpt) cc_final: 0.0326 (tpt) REVERT: C4 64 MET cc_start: 0.5678 (mmt) cc_final: 0.5367 (mtp) REVERT: C4 126 MET cc_start: 0.5988 (ttm) cc_final: 0.5624 (tpp) REVERT: C4 287 MET cc_start: -0.0966 (mmt) cc_final: -0.1613 (mmt) REVERT: C5 116 MET cc_start: 0.1007 (ttt) cc_final: 0.0479 (ttm) REVERT: C5 124 MET cc_start: 0.9018 (mtm) cc_final: 0.8642 (mtt) REVERT: C5 317 MET cc_start: 0.6542 (OUTLIER) cc_final: 0.6191 (mmm) REVERT: B5 325 MET cc_start: 0.8814 (tpt) cc_final: 0.8560 (tpt) REVERT: G1 46 LYS cc_start: 0.9176 (mmtm) cc_final: 0.8870 (mmmt) REVERT: G2 1 MET cc_start: 0.7972 (tpt) cc_final: 0.6937 (tmm) REVERT: G4 1 MET cc_start: 0.8286 (ppp) cc_final: 0.8025 (ppp) outliers start: 99 outliers final: 59 residues processed: 331 average time/residue: 0.2370 time to fit residues: 131.6574 Evaluate side-chains 307 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 243 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 162 GLN Chi-restraints excluded: chain K1 residue 167 GLU Chi-restraints excluded: chain K1 residue 214 TYR Chi-restraints excluded: chain K2 residue 79 ASP Chi-restraints excluded: chain K2 residue 104 ASN Chi-restraints excluded: chain K2 residue 155 LYS Chi-restraints excluded: chain K3 residue 67 LYS Chi-restraints excluded: chain K3 residue 92 ILE Chi-restraints excluded: chain K3 residue 152 VAL Chi-restraints excluded: chain K3 residue 169 THR Chi-restraints excluded: chain K4 residue 104 ASN Chi-restraints excluded: chain K4 residue 187 ILE Chi-restraints excluded: chain K4 residue 202 LEU Chi-restraints excluded: chain K5 residue 187 ILE Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 73 LEU Chi-restraints excluded: chain C1 residue 89 VAL Chi-restraints excluded: chain C1 residue 102 LEU Chi-restraints excluded: chain C1 residue 104 THR Chi-restraints excluded: chain C1 residue 152 VAL Chi-restraints excluded: chain C1 residue 188 GLN Chi-restraints excluded: chain C1 residue 240 ARG Chi-restraints excluded: chain C1 residue 287 MET Chi-restraints excluded: chain C2 residue 64 MET Chi-restraints excluded: chain C2 residue 73 LEU Chi-restraints excluded: chain C2 residue 254 LYS Chi-restraints excluded: chain C2 residue 260 ILE Chi-restraints excluded: chain C2 residue 357 LEU Chi-restraints excluded: chain C3 residue 37 LEU Chi-restraints excluded: chain C3 residue 251 CYS Chi-restraints excluded: chain C4 residue 25 MET Chi-restraints excluded: chain C4 residue 69 HIS Chi-restraints excluded: chain C4 residue 85 LEU Chi-restraints excluded: chain C4 residue 94 LEU Chi-restraints excluded: chain C4 residue 102 LEU Chi-restraints excluded: chain C4 residue 129 VAL Chi-restraints excluded: chain C4 residue 293 THR Chi-restraints excluded: chain C5 residue 25 MET Chi-restraints excluded: chain C5 residue 138 ASN Chi-restraints excluded: chain C5 residue 163 GLN Chi-restraints excluded: chain C5 residue 191 MET Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 300 TYR Chi-restraints excluded: chain C5 residue 306 VAL Chi-restraints excluded: chain C5 residue 310 LEU Chi-restraints excluded: chain C5 residue 317 MET Chi-restraints excluded: chain B2 residue 29 THR Chi-restraints excluded: chain B2 residue 37 ILE Chi-restraints excluded: chain B2 residue 112 VAL Chi-restraints excluded: chain B2 residue 128 THR Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 74 SER Chi-restraints excluded: chain B3 residue 263 THR Chi-restraints excluded: chain B3 residue 286 LEU Chi-restraints excluded: chain B4 residue 71 VAL Chi-restraints excluded: chain B4 residue 74 SER Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 266 HIS Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 200 VAL Chi-restraints excluded: chain B5 residue 234 PHE Chi-restraints excluded: chain B5 residue 296 VAL Chi-restraints excluded: chain G4 residue 38 MET Chi-restraints excluded: chain G5 residue 58 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 190 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 420 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 329 optimal weight: 20.0000 chunk 254 optimal weight: 30.0000 chunk 352 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 240 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 381 optimal weight: 8.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K1 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1 183 GLN ** K2 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 130 ASN ** K3 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K4 49 ASN K4 75 GLN ** K4 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 156 HIS ** C1 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 141 ASN ** C2 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3 106 ASN ** C3 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 250 HIS C4 324 GLN C5 31 ASN C5 48 ASN ** C5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 361 ASN ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 142 HIS B2 32 GLN ** B2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 237 ASN ** B4 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4 340 ASN ** B5 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 17 GLN ** B5 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.064466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.048007 restraints weight = 477446.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.048188 restraints weight = 330383.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.048135 restraints weight = 212032.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.048155 restraints weight = 150489.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.048174 restraints weight = 153551.035| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 38515 Z= 0.240 Angle : 0.702 12.058 51985 Z= 0.375 Chirality : 0.043 0.255 5780 Planarity : 0.004 0.052 6775 Dihedral : 5.885 85.870 5231 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.15 % Favored : 93.72 % Rotamer: Outliers : 3.29 % Allowed : 16.14 % Favored : 80.58 % 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: -0.66 (0.12), residues: 4730 helix: 0.79 (0.11), residues: 2125 sheet: -1.50 (0.18), residues: 773 loop : -1.35 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGC1 120 TYR 0.025 0.002 TYRC4 341 PHE 0.036 0.003 PHEC4 377 TRP 0.028 0.002 TRPB5 211 HIS 0.018 0.002 HISC5 67 Details of bonding type rmsd covalent geometry : bond 0.00493 (38515) covalent geometry : angle 0.70156 (51985) hydrogen bonds : bond 0.04380 ( 1954) hydrogen bonds : angle 5.23188 ( 5703) *********************** 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 391 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 254 time to evaluate : 1.571 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 162 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6976 (tm-30) REVERT: K2 79 ASP cc_start: 0.4129 (OUTLIER) cc_final: 0.3499 (m-30) REVERT: K4 129 TYR cc_start: 0.7397 (m-80) cc_final: 0.6628 (m-80) REVERT: K5 171 MET cc_start: 0.9185 (ptp) cc_final: 0.8733 (ptp) REVERT: C1 109 TRP cc_start: 0.8401 (t60) cc_final: 0.7098 (t60) REVERT: C1 254 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8522 (mmpt) REVERT: C1 299 MET cc_start: 0.5651 (mmt) cc_final: 0.5185 (mmt) REVERT: C2 100 ASN cc_start: 0.9001 (m-40) cc_final: 0.8577 (t0) REVERT: C3 25 MET cc_start: 0.6756 (ppp) cc_final: 0.6300 (pmm) REVERT: C3 64 MET cc_start: 0.0647 (tpt) cc_final: 0.0352 (tpt) REVERT: C3 124 MET cc_start: 0.7454 (mtt) cc_final: 0.7245 (mtt) REVERT: C3 128 ARG cc_start: 0.8906 (ttt180) cc_final: 0.8219 (ptm-80) REVERT: C4 126 MET cc_start: 0.6270 (ttm) cc_final: 0.5872 (tpp) REVERT: C4 287 MET cc_start: -0.0264 (mmt) cc_final: -0.1065 (mmt) REVERT: C5 124 MET cc_start: 0.9076 (mtm) cc_final: 0.8621 (mtp) REVERT: C5 317 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6502 (mmm) REVERT: B1 61 MET cc_start: 0.7662 (ppp) cc_final: 0.7360 (ppp) REVERT: B4 183 HIS cc_start: 0.6676 (OUTLIER) cc_final: 0.6281 (t-90) REVERT: B4 262 MET cc_start: 0.8171 (tpp) cc_final: 0.7853 (tpp) REVERT: G1 46 LYS cc_start: 0.9187 (mmtm) cc_final: 0.8983 (mmmt) REVERT: G2 1 MET cc_start: 0.8654 (tpt) cc_final: 0.7658 (tmm) REVERT: G3 21 MET cc_start: 0.9288 (mpp) cc_final: 0.9082 (mpp) REVERT: G4 1 MET cc_start: 0.8385 (ppp) cc_final: 0.7982 (ppp) outliers start: 137 outliers final: 83 residues processed: 360 average time/residue: 0.2327 time to fit residues: 141.3187 Evaluate side-chains 325 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 237 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 162 GLN Chi-restraints excluded: chain K1 residue 214 TYR Chi-restraints excluded: chain K2 residue 79 ASP Chi-restraints excluded: chain K2 residue 104 ASN Chi-restraints excluded: chain K2 residue 155 LYS Chi-restraints excluded: chain K3 residue 61 THR Chi-restraints excluded: chain K3 residue 67 LYS Chi-restraints excluded: chain K3 residue 92 ILE Chi-restraints excluded: chain K3 residue 152 VAL Chi-restraints excluded: chain K3 residue 169 THR Chi-restraints excluded: chain K4 residue 104 ASN Chi-restraints excluded: chain K4 residue 187 ILE Chi-restraints excluded: chain K4 residue 202 LEU Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 134 LEU Chi-restraints excluded: chain K5 residue 187 ILE Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 73 LEU Chi-restraints excluded: chain C1 residue 89 VAL Chi-restraints excluded: chain C1 residue 104 THR Chi-restraints excluded: chain C1 residue 188 GLN Chi-restraints excluded: chain C1 residue 240 ARG Chi-restraints excluded: chain C1 residue 254 LYS Chi-restraints excluded: chain C1 residue 256 THR Chi-restraints excluded: chain C1 residue 287 MET Chi-restraints excluded: chain C2 residue 73 LEU Chi-restraints excluded: chain C2 residue 125 TYR Chi-restraints excluded: chain C2 residue 254 LYS Chi-restraints excluded: chain C2 residue 260 ILE Chi-restraints excluded: chain C2 residue 357 LEU Chi-restraints excluded: chain C3 residue 37 LEU Chi-restraints excluded: chain C3 residue 177 VAL Chi-restraints excluded: chain C3 residue 251 CYS Chi-restraints excluded: chain C3 residue 254 LYS Chi-restraints excluded: chain C3 residue 257 GLU Chi-restraints excluded: chain C4 residue 25 MET Chi-restraints excluded: chain C4 residue 69 HIS Chi-restraints excluded: chain C4 residue 82 THR Chi-restraints excluded: chain C4 residue 85 LEU Chi-restraints excluded: chain C4 residue 94 LEU Chi-restraints excluded: chain C4 residue 127 ASP Chi-restraints excluded: chain C4 residue 129 VAL Chi-restraints excluded: chain C4 residue 173 ARG Chi-restraints excluded: chain C4 residue 293 THR Chi-restraints excluded: chain C5 residue 25 MET Chi-restraints excluded: chain C5 residue 138 ASN Chi-restraints excluded: chain C5 residue 154 TYR Chi-restraints excluded: chain C5 residue 191 MET Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 300 TYR Chi-restraints excluded: chain C5 residue 306 VAL Chi-restraints excluded: chain C5 residue 310 LEU Chi-restraints excluded: chain C5 residue 317 MET Chi-restraints excluded: chain B1 residue 45 MET Chi-restraints excluded: chain B1 residue 112 VAL Chi-restraints excluded: chain B1 residue 181 THR Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B2 residue 29 THR Chi-restraints excluded: chain B2 residue 37 ILE Chi-restraints excluded: chain B2 residue 80 ILE Chi-restraints excluded: chain B2 residue 101 MET Chi-restraints excluded: chain B2 residue 112 VAL Chi-restraints excluded: chain B2 residue 128 THR Chi-restraints excluded: chain B2 residue 223 THR Chi-restraints excluded: chain B2 residue 285 LEU Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 225 HIS Chi-restraints excluded: chain B3 residue 263 THR Chi-restraints excluded: chain B3 residue 286 LEU Chi-restraints excluded: chain B4 residue 71 VAL Chi-restraints excluded: chain B4 residue 74 SER Chi-restraints excluded: chain B4 residue 101 MET Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 183 HIS Chi-restraints excluded: chain B4 residue 187 VAL Chi-restraints excluded: chain B4 residue 267 ASP Chi-restraints excluded: chain B5 residue 101 MET Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 200 VAL Chi-restraints excluded: chain B5 residue 234 PHE Chi-restraints excluded: chain B5 residue 290 ASP Chi-restraints excluded: chain B5 residue 296 VAL Chi-restraints excluded: chain G3 residue 26 ASP Chi-restraints excluded: chain G4 residue 38 MET Chi-restraints excluded: chain G5 residue 58 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 300 optimal weight: 10.0000 chunk 177 optimal weight: 0.0040 chunk 200 optimal weight: 7.9990 chunk 191 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 chunk 411 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 154 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 263 optimal weight: 8.9990 chunk 245 optimal weight: 3.9990 overall best weight: 2.3398 ------------------------------------------------------------------------------- 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** ** K4 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3 188 GLN ** C3 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3 381 ASN ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 250 HIS ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 324 GLN ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 259 GLN ** B3 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5 259 GLN G4 18 GLN G5 5 ASN ** G5 11 GLN ** 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 = 0.4129 r_free = 0.4129 target = 0.065931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.049509 restraints weight = 461324.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.048867 restraints weight = 301961.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.049039 restraints weight = 203508.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.048891 restraints weight = 156847.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.049066 restraints weight = 135656.511| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 38515 Z= 0.138 Angle : 0.634 11.680 51985 Z= 0.334 Chirality : 0.042 0.210 5780 Planarity : 0.004 0.054 6775 Dihedral : 5.538 84.052 5231 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.69 % Favored : 95.20 % Rotamer: Outliers : 2.40 % Allowed : 17.55 % Favored : 80.05 % 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: -0.41 (0.12), residues: 4730 helix: 1.01 (0.11), residues: 2146 sheet: -1.40 (0.18), residues: 768 loop : -1.24 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGC1 120 TYR 0.033 0.001 TYRB3 85 PHE 0.039 0.002 PHEC4 377 TRP 0.020 0.002 TRPB5 211 HIS 0.019 0.001 HISC5 67 Details of bonding type rmsd covalent geometry : bond 0.00286 (38515) covalent geometry : angle 0.63370 (51985) hydrogen bonds : bond 0.03909 ( 1954) hydrogen bonds : angle 5.00264 ( 5703) *********************** 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 362 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 262 time to evaluate : 1.672 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: K1 162 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: K2 79 ASP cc_start: 0.3997 (OUTLIER) cc_final: 0.3357 (m-30) REVERT: K4 129 TYR cc_start: 0.7072 (m-80) cc_final: 0.6482 (m-80) REVERT: K5 171 MET cc_start: 0.9118 (ptp) cc_final: 0.8623 (ptp) REVERT: C1 25 MET cc_start: 0.5280 (tpp) cc_final: 0.5003 (tmm) REVERT: C1 109 TRP cc_start: 0.8350 (t60) cc_final: 0.7432 (t60) REVERT: C1 299 MET cc_start: 0.5466 (mmt) cc_final: 0.5174 (mmt) REVERT: C2 64 MET cc_start: 0.5605 (ttt) cc_final: 0.4840 (tpp) REVERT: C2 100 ASN cc_start: 0.9017 (m-40) cc_final: 0.8557 (t0) REVERT: C2 191 MET cc_start: 0.8347 (mmm) cc_final: 0.7805 (mmt) REVERT: C3 25 MET cc_start: 0.4516 (ppp) cc_final: 0.3550 (pmm) REVERT: C3 64 MET cc_start: 0.1386 (tpt) cc_final: 0.0991 (tpt) REVERT: C3 128 ARG cc_start: 0.8853 (ttt180) cc_final: 0.8152 (ptm-80) REVERT: C4 64 MET cc_start: 0.5721 (mmt) cc_final: 0.4935 (mmm) REVERT: C4 126 MET cc_start: 0.6623 (ttm) cc_final: 0.6194 (tpp) REVERT: C4 287 MET cc_start: 0.0267 (mmt) cc_final: -0.0604 (mmt) REVERT: C5 124 MET cc_start: 0.8964 (mtm) cc_final: 0.8499 (mtp) REVERT: C5 168 MET cc_start: 0.8646 (ttt) cc_final: 0.8365 (ttt) REVERT: C5 317 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.6284 (mmt) REVERT: B1 61 MET cc_start: 0.7423 (ppp) cc_final: 0.7179 (ppp) REVERT: B1 325 MET cc_start: 0.8228 (ppp) cc_final: 0.6700 (ppp) REVERT: B2 188 MET cc_start: 0.9052 (ppp) cc_final: 0.8694 (tmm) REVERT: B3 188 MET cc_start: 0.7762 (pmm) cc_final: 0.6446 (ppp) REVERT: B4 188 MET cc_start: 0.8782 (ptm) cc_final: 0.7979 (ppp) REVERT: B4 200 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7855 (p) REVERT: B4 325 MET cc_start: 0.7728 (ttt) cc_final: 0.7352 (ptm) REVERT: B5 61 MET cc_start: 0.7509 (ptp) cc_final: 0.6965 (mpp) REVERT: B5 146 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7732 (mt) REVERT: G1 46 LYS cc_start: 0.9259 (mmtm) cc_final: 0.9051 (mmmt) REVERT: G2 1 MET cc_start: 0.8378 (tpt) cc_final: 0.7227 (tmm) REVERT: G4 1 MET cc_start: 0.8490 (ppp) cc_final: 0.8040 (ppp) outliers start: 100 outliers final: 72 residues processed: 340 average time/residue: 0.2371 time to fit residues: 136.9869 Evaluate side-chains 320 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 243 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 162 GLN Chi-restraints excluded: chain K1 residue 214 TYR Chi-restraints excluded: chain K2 residue 79 ASP Chi-restraints excluded: chain K2 residue 104 ASN Chi-restraints excluded: chain K3 residue 67 LYS Chi-restraints excluded: chain K3 residue 92 ILE Chi-restraints excluded: chain K3 residue 169 THR Chi-restraints excluded: chain K4 residue 104 ASN Chi-restraints excluded: chain K4 residue 187 ILE Chi-restraints excluded: chain K4 residue 202 LEU Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 187 ILE Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 73 LEU Chi-restraints excluded: chain C1 residue 89 VAL Chi-restraints excluded: chain C1 residue 102 LEU Chi-restraints excluded: chain C1 residue 104 THR Chi-restraints excluded: chain C1 residue 188 GLN Chi-restraints excluded: chain C1 residue 240 ARG Chi-restraints excluded: chain C1 residue 256 THR Chi-restraints excluded: chain C1 residue 287 MET Chi-restraints excluded: chain C1 residue 293 THR Chi-restraints excluded: chain C2 residue 73 LEU Chi-restraints excluded: chain C2 residue 125 TYR Chi-restraints excluded: chain C2 residue 260 ILE Chi-restraints excluded: chain C2 residue 357 LEU Chi-restraints excluded: chain C3 residue 37 LEU Chi-restraints excluded: chain C3 residue 177 VAL Chi-restraints excluded: chain C3 residue 251 CYS Chi-restraints excluded: chain C3 residue 254 LYS Chi-restraints excluded: chain C3 residue 257 GLU Chi-restraints excluded: chain C4 residue 25 MET Chi-restraints excluded: chain C4 residue 69 HIS Chi-restraints excluded: chain C4 residue 85 LEU Chi-restraints excluded: chain C4 residue 94 LEU Chi-restraints excluded: chain C4 residue 102 LEU Chi-restraints excluded: chain C4 residue 129 VAL Chi-restraints excluded: chain C4 residue 185 ASN Chi-restraints excluded: chain C4 residue 293 THR Chi-restraints excluded: chain C4 residue 302 LEU Chi-restraints excluded: chain C4 residue 347 ASP Chi-restraints excluded: chain C5 residue 25 MET Chi-restraints excluded: chain C5 residue 74 TYR Chi-restraints excluded: chain C5 residue 138 ASN Chi-restraints excluded: chain C5 residue 154 TYR Chi-restraints excluded: chain C5 residue 191 MET Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 300 TYR Chi-restraints excluded: chain C5 residue 306 VAL Chi-restraints excluded: chain C5 residue 310 LEU Chi-restraints excluded: chain C5 residue 317 MET Chi-restraints excluded: chain B1 residue 45 MET Chi-restraints excluded: chain B1 residue 112 VAL Chi-restraints excluded: chain B1 residue 190 LEU Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B2 residue 29 THR Chi-restraints excluded: chain B2 residue 37 ILE Chi-restraints excluded: chain B2 residue 80 ILE Chi-restraints excluded: chain B2 residue 112 VAL Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 112 VAL Chi-restraints excluded: chain B3 residue 225 HIS Chi-restraints excluded: chain B3 residue 286 LEU Chi-restraints excluded: chain B3 residue 317 CYS Chi-restraints excluded: chain B4 residue 74 SER Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 200 VAL Chi-restraints excluded: chain B4 residue 271 CYS Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 136 SER Chi-restraints excluded: chain B5 residue 146 LEU Chi-restraints excluded: chain B5 residue 234 PHE Chi-restraints excluded: chain B5 residue 296 VAL Chi-restraints excluded: chain G3 residue 54 VAL Chi-restraints excluded: chain G4 residue 38 MET Chi-restraints excluded: chain G5 residue 58 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 294 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 chunk 460 optimal weight: 20.0000 chunk 164 optimal weight: 50.0000 chunk 356 optimal weight: 20.0000 chunk 384 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 36 optimal weight: 0.0070 chunk 162 optimal weight: 40.0000 chunk 194 optimal weight: 40.0000 chunk 165 optimal weight: 8.9990 overall best weight: 7.6010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K1 104 ASN ** K2 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3 151 GLN ** C1 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5 340 ASN ** G5 11 GLN ** 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 = 0.4043 r_free = 0.4043 target = 0.063253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.047048 restraints weight = 477589.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.046861 restraints weight = 323109.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.046722 restraints weight = 209755.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.046832 restraints weight = 160532.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.046902 restraints weight = 137696.736| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 38515 Z= 0.278 Angle : 0.757 12.206 51985 Z= 0.400 Chirality : 0.044 0.273 5780 Planarity : 0.005 0.052 6775 Dihedral : 5.830 77.827 5231 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 25.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.68 % Favored : 93.21 % Rotamer: Outliers : 3.62 % Allowed : 17.72 % Favored : 78.66 % 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: 0.71 (0.11), residues: 2130 sheet: -1.68 (0.18), residues: 769 loop : -1.29 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARGC4 173 TYR 0.028 0.002 TYRB3 85 PHE 0.041 0.003 PHEC4 377 TRP 0.028 0.003 TRPC3 109 HIS 0.021 0.002 HISC5 67 Details of bonding type rmsd covalent geometry : bond 0.00570 (38515) covalent geometry : angle 0.75725 (51985) hydrogen bonds : bond 0.04465 ( 1954) hydrogen bonds : angle 5.32177 ( 5703) *********************** 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 398 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 247 time to evaluate : 1.694 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: K1 162 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6918 (tm-30) REVERT: K1 167 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8840 (pm20) REVERT: K2 79 ASP cc_start: 0.4713 (OUTLIER) cc_final: 0.4332 (m-30) REVERT: K3 168 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9419 (mt) REVERT: C1 299 MET cc_start: 0.5231 (mmt) cc_final: 0.4806 (mmt) REVERT: C2 64 MET cc_start: 0.5935 (ttt) cc_final: 0.5298 (tpp) REVERT: C2 100 ASN cc_start: 0.8981 (m-40) cc_final: 0.8466 (t0) REVERT: C3 25 MET cc_start: 0.5511 (ppp) cc_final: 0.4565 (pmm) REVERT: C3 64 MET cc_start: 0.1663 (tpt) cc_final: 0.1381 (tpt) REVERT: C3 124 MET cc_start: 0.7371 (mtt) cc_final: 0.7093 (mtt) REVERT: C3 126 MET cc_start: 0.8454 (ppp) cc_final: 0.8220 (ppp) REVERT: C4 64 MET cc_start: 0.5844 (mmt) cc_final: 0.5026 (mmm) REVERT: C4 287 MET cc_start: 0.0657 (mmt) cc_final: -0.0335 (mmt) REVERT: C5 124 MET cc_start: 0.9140 (mtm) cc_final: 0.8696 (mtp) REVERT: C5 317 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6834 (mmm) REVERT: B1 325 MET cc_start: 0.8465 (ppp) cc_final: 0.7377 (ppp) REVERT: B2 125 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8078 (p0) REVERT: B2 188 MET cc_start: 0.9152 (ppp) cc_final: 0.8600 (ppp) REVERT: B4 105 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7280 (t80) REVERT: B4 183 HIS cc_start: 0.6763 (OUTLIER) cc_final: 0.6380 (t-90) REVERT: B4 188 MET cc_start: 0.8781 (ptm) cc_final: 0.8267 (ppp) REVERT: B4 200 VAL cc_start: 0.8121 (OUTLIER) cc_final: 0.7885 (p) REVERT: B4 262 MET cc_start: 0.8250 (tpp) cc_final: 0.7997 (tpp) REVERT: B5 146 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7868 (mt) REVERT: B5 325 MET cc_start: 0.8791 (tpt) cc_final: 0.8549 (tpp) REVERT: G4 1 MET cc_start: 0.8544 (ppp) cc_final: 0.8013 (ppp) outliers start: 151 outliers final: 102 residues processed: 367 average time/residue: 0.2333 time to fit residues: 144.4765 Evaluate side-chains 345 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 233 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 111 LEU Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 162 GLN Chi-restraints excluded: chain K1 residue 167 GLU Chi-restraints excluded: chain K1 residue 191 TYR Chi-restraints excluded: chain K1 residue 214 TYR Chi-restraints excluded: chain K2 residue 58 THR Chi-restraints excluded: chain K2 residue 79 ASP Chi-restraints excluded: chain K2 residue 104 ASN Chi-restraints excluded: chain K3 residue 92 ILE Chi-restraints excluded: chain K3 residue 152 VAL Chi-restraints excluded: chain K3 residue 168 LEU Chi-restraints excluded: chain K3 residue 169 THR Chi-restraints excluded: chain K4 residue 104 ASN Chi-restraints excluded: chain K4 residue 187 ILE Chi-restraints excluded: chain K5 residue 48 LEU Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 134 LEU Chi-restraints excluded: chain K5 residue 187 ILE Chi-restraints excluded: chain C1 residue 34 TRP Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 73 LEU Chi-restraints excluded: chain C1 residue 89 VAL Chi-restraints excluded: chain C1 residue 102 LEU Chi-restraints excluded: chain C1 residue 104 THR Chi-restraints excluded: chain C1 residue 139 VAL Chi-restraints excluded: chain C1 residue 152 VAL Chi-restraints excluded: chain C1 residue 188 GLN Chi-restraints excluded: chain C1 residue 240 ARG Chi-restraints excluded: chain C1 residue 254 LYS Chi-restraints excluded: chain C1 residue 256 THR Chi-restraints excluded: chain C1 residue 293 THR Chi-restraints excluded: chain C2 residue 67 HIS Chi-restraints excluded: chain C2 residue 73 LEU Chi-restraints excluded: chain C2 residue 125 TYR Chi-restraints excluded: chain C2 residue 192 ILE Chi-restraints excluded: chain C2 residue 212 MET Chi-restraints excluded: chain C2 residue 357 LEU Chi-restraints excluded: chain C2 residue 369 THR Chi-restraints excluded: chain C3 residue 37 LEU Chi-restraints excluded: chain C3 residue 62 TYR Chi-restraints excluded: chain C3 residue 120 ARG Chi-restraints excluded: chain C3 residue 177 VAL Chi-restraints excluded: chain C3 residue 251 CYS Chi-restraints excluded: chain C3 residue 254 LYS Chi-restraints excluded: chain C4 residue 25 MET Chi-restraints excluded: chain C4 residue 69 HIS Chi-restraints excluded: chain C4 residue 85 LEU Chi-restraints excluded: chain C4 residue 94 LEU Chi-restraints excluded: chain C4 residue 102 LEU Chi-restraints excluded: chain C4 residue 127 ASP Chi-restraints excluded: chain C4 residue 129 VAL Chi-restraints excluded: chain C4 residue 185 ASN Chi-restraints excluded: chain C4 residue 293 THR Chi-restraints excluded: chain C4 residue 302 LEU Chi-restraints excluded: chain C4 residue 347 ASP Chi-restraints excluded: chain C5 residue 67 HIS Chi-restraints excluded: chain C5 residue 74 TYR Chi-restraints excluded: chain C5 residue 138 ASN Chi-restraints excluded: chain C5 residue 191 MET Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 300 TYR Chi-restraints excluded: chain C5 residue 306 VAL Chi-restraints excluded: chain C5 residue 310 LEU Chi-restraints excluded: chain C5 residue 317 MET Chi-restraints excluded: chain B1 residue 45 MET Chi-restraints excluded: chain B1 residue 112 VAL Chi-restraints excluded: chain B1 residue 190 LEU Chi-restraints excluded: chain B1 residue 273 ILE Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B2 residue 29 THR Chi-restraints excluded: chain B2 residue 37 ILE Chi-restraints excluded: chain B2 residue 80 ILE Chi-restraints excluded: chain B2 residue 101 MET Chi-restraints excluded: chain B2 residue 112 VAL Chi-restraints excluded: chain B2 residue 125 ASN Chi-restraints excluded: chain B2 residue 128 THR Chi-restraints excluded: chain B2 residue 214 ARG Chi-restraints excluded: chain B2 residue 223 THR Chi-restraints excluded: chain B2 residue 285 LEU Chi-restraints excluded: chain B3 residue 44 GLN Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 85 TYR Chi-restraints excluded: chain B3 residue 101 MET Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 112 VAL Chi-restraints excluded: chain B3 residue 225 HIS Chi-restraints excluded: chain B3 residue 263 THR Chi-restraints excluded: chain B3 residue 286 LEU Chi-restraints excluded: chain B3 residue 317 CYS Chi-restraints excluded: chain B3 residue 338 ILE Chi-restraints excluded: chain B4 residue 74 SER Chi-restraints excluded: chain B4 residue 101 MET Chi-restraints excluded: chain B4 residue 105 TYR Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 183 HIS Chi-restraints excluded: chain B4 residue 187 VAL Chi-restraints excluded: chain B4 residue 200 VAL Chi-restraints excluded: chain B4 residue 271 CYS Chi-restraints excluded: chain B5 residue 101 MET Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 136 SER Chi-restraints excluded: chain B5 residue 146 LEU Chi-restraints excluded: chain B5 residue 200 VAL Chi-restraints excluded: chain B5 residue 234 PHE Chi-restraints excluded: chain B5 residue 290 ASP Chi-restraints excluded: chain B5 residue 296 VAL Chi-restraints excluded: chain G2 residue 9 ILE Chi-restraints excluded: chain G3 residue 26 ASP Chi-restraints excluded: chain G4 residue 38 MET Chi-restraints excluded: chain G5 residue 58 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 279 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 122 optimal weight: 30.0000 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 337 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 313 optimal weight: 5.9990 chunk 355 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K2 162 GLN ** K2 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3 151 GLN ** C1 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3 188 GLN C3 218 GLN ** C3 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1 4 ASN ** G5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.064607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.046787 restraints weight = 467351.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.045546 restraints weight = 278403.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.045756 restraints weight = 202028.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.046024 restraints weight = 166254.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.046010 restraints weight = 151601.354| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 38515 Z= 0.147 Angle : 0.664 14.005 51985 Z= 0.347 Chirality : 0.042 0.190 5780 Planarity : 0.004 0.070 6775 Dihedral : 5.502 74.773 5225 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.84 % Favored : 95.07 % Rotamer: Outliers : 2.73 % Allowed : 18.85 % 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: -0.51 (0.12), residues: 4730 helix: 0.92 (0.11), residues: 2147 sheet: -1.53 (0.17), residues: 798 loop : -1.23 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGC1 120 TYR 0.033 0.002 TYRB3 85 PHE 0.042 0.002 PHEC4 377 TRP 0.020 0.002 TRPC3 109 HIS 0.020 0.001 HISC5 67 Details of bonding type rmsd covalent geometry : bond 0.00308 (38515) covalent geometry : angle 0.66414 (51985) hydrogen bonds : bond 0.03897 ( 1954) hydrogen bonds : angle 5.05153 ( 5703) *********************** 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 371 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 257 time to evaluate : 1.497 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 162 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.6932 (tm-30) REVERT: K1 167 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8766 (pm20) REVERT: K2 79 ASP cc_start: 0.4945 (OUTLIER) cc_final: 0.4513 (m-30) REVERT: K2 162 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: K4 71 TYR cc_start: 0.8988 (t80) cc_final: 0.8647 (m-80) REVERT: K4 129 TYR cc_start: 0.7213 (m-80) cc_final: 0.6510 (m-80) REVERT: K5 164 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8650 (pm20) REVERT: K5 171 MET cc_start: 0.9122 (ptp) cc_final: 0.8707 (ptp) REVERT: C1 25 MET cc_start: 0.5702 (tpp) cc_final: 0.4520 (tmm) REVERT: C1 254 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8684 (mmpt) REVERT: C1 299 MET cc_start: 0.5198 (mmt) cc_final: 0.4695 (mmt) REVERT: C2 64 MET cc_start: 0.5704 (ttt) cc_final: 0.5250 (tpp) REVERT: C2 100 ASN cc_start: 0.8858 (m-40) cc_final: 0.8383 (t0) REVERT: C3 25 MET cc_start: 0.5051 (OUTLIER) cc_final: 0.4181 (pmm) REVERT: C3 64 MET cc_start: 0.1222 (tpt) cc_final: 0.0831 (tpt) REVERT: C4 64 MET cc_start: 0.5943 (mmt) cc_final: 0.4451 (tpp) REVERT: C4 126 MET cc_start: 0.6449 (tpp) cc_final: 0.6064 (tpp) REVERT: C4 287 MET cc_start: 0.0834 (mmt) cc_final: -0.0171 (mmt) REVERT: C5 116 MET cc_start: 0.1738 (ttt) cc_final: 0.1153 (ttm) REVERT: C5 124 MET cc_start: 0.9009 (mtm) cc_final: 0.8534 (mtp) REVERT: C5 128 ARG cc_start: 0.9182 (ttt180) cc_final: 0.8918 (ttm170) REVERT: C5 168 MET cc_start: 0.8354 (ttt) cc_final: 0.8137 (ttt) REVERT: C5 317 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6747 (mmm) REVERT: B1 61 MET cc_start: 0.7547 (ppp) cc_final: 0.7343 (ppp) REVERT: B1 217 MET cc_start: 0.9008 (ppp) cc_final: 0.8758 (ppp) REVERT: B1 325 MET cc_start: 0.8324 (ppp) cc_final: 0.6994 (ppp) REVERT: B2 188 MET cc_start: 0.9059 (ppp) cc_final: 0.8645 (tmm) REVERT: B4 105 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7341 (t80) REVERT: B4 188 MET cc_start: 0.8769 (ptm) cc_final: 0.8199 (ppp) REVERT: B4 200 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7830 (p) REVERT: B4 262 MET cc_start: 0.8070 (tpp) cc_final: 0.7832 (tpp) REVERT: B5 146 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7740 (mt) REVERT: G4 1 MET cc_start: 0.8806 (ppp) cc_final: 0.8429 (ppp) outliers start: 114 outliers final: 82 residues processed: 342 average time/residue: 0.2202 time to fit residues: 127.1738 Evaluate side-chains 332 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 239 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 162 GLN Chi-restraints excluded: chain K1 residue 167 GLU Chi-restraints excluded: chain K1 residue 214 TYR Chi-restraints excluded: chain K2 residue 79 ASP Chi-restraints excluded: chain K2 residue 104 ASN Chi-restraints excluded: chain K2 residue 162 GLN Chi-restraints excluded: chain K3 residue 92 ILE Chi-restraints excluded: chain K3 residue 151 GLN Chi-restraints excluded: chain K3 residue 169 THR Chi-restraints excluded: chain K4 residue 104 ASN Chi-restraints excluded: chain K4 residue 187 ILE Chi-restraints excluded: chain K4 residue 202 LEU Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 164 GLN Chi-restraints excluded: chain K5 residue 185 VAL Chi-restraints excluded: chain K5 residue 187 ILE Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 73 LEU Chi-restraints excluded: chain C1 residue 89 VAL Chi-restraints excluded: chain C1 residue 102 LEU Chi-restraints excluded: chain C1 residue 104 THR Chi-restraints excluded: chain C1 residue 123 LEU Chi-restraints excluded: chain C1 residue 139 VAL Chi-restraints excluded: chain C1 residue 152 VAL Chi-restraints excluded: chain C1 residue 240 ARG Chi-restraints excluded: chain C1 residue 254 LYS Chi-restraints excluded: chain C1 residue 256 THR Chi-restraints excluded: chain C1 residue 293 THR Chi-restraints excluded: chain C2 residue 73 LEU Chi-restraints excluded: chain C2 residue 125 TYR Chi-restraints excluded: chain C2 residue 212 MET Chi-restraints excluded: chain C2 residue 357 LEU Chi-restraints excluded: chain C3 residue 25 MET Chi-restraints excluded: chain C3 residue 37 LEU Chi-restraints excluded: chain C3 residue 62 TYR Chi-restraints excluded: chain C3 residue 120 ARG Chi-restraints excluded: chain C3 residue 177 VAL Chi-restraints excluded: chain C3 residue 188 GLN Chi-restraints excluded: chain C3 residue 251 CYS Chi-restraints excluded: chain C3 residue 254 LYS Chi-restraints excluded: chain C3 residue 257 GLU Chi-restraints excluded: chain C4 residue 25 MET Chi-restraints excluded: chain C4 residue 69 HIS Chi-restraints excluded: chain C4 residue 82 THR Chi-restraints excluded: chain C4 residue 85 LEU Chi-restraints excluded: chain C4 residue 129 VAL Chi-restraints excluded: chain C4 residue 185 ASN Chi-restraints excluded: chain C4 residue 275 THR Chi-restraints excluded: chain C4 residue 293 THR Chi-restraints excluded: chain C4 residue 302 LEU Chi-restraints excluded: chain C4 residue 347 ASP Chi-restraints excluded: chain C5 residue 25 MET Chi-restraints excluded: chain C5 residue 74 TYR Chi-restraints excluded: chain C5 residue 138 ASN Chi-restraints excluded: chain C5 residue 191 MET Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 273 MET Chi-restraints excluded: chain C5 residue 300 TYR Chi-restraints excluded: chain C5 residue 310 LEU Chi-restraints excluded: chain C5 residue 317 MET Chi-restraints excluded: chain B1 residue 45 MET Chi-restraints excluded: chain B1 residue 112 VAL Chi-restraints excluded: chain B1 residue 157 ILE Chi-restraints excluded: chain B1 residue 190 LEU Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B2 residue 29 THR Chi-restraints excluded: chain B2 residue 37 ILE Chi-restraints excluded: chain B2 residue 80 ILE Chi-restraints excluded: chain B2 residue 112 VAL Chi-restraints excluded: chain B2 residue 128 THR Chi-restraints excluded: chain B2 residue 223 THR Chi-restraints excluded: chain B2 residue 285 LEU Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 85 TYR Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 112 VAL Chi-restraints excluded: chain B3 residue 181 THR Chi-restraints excluded: chain B3 residue 225 HIS Chi-restraints excluded: chain B3 residue 286 LEU Chi-restraints excluded: chain B3 residue 317 CYS Chi-restraints excluded: chain B4 residue 74 SER Chi-restraints excluded: chain B4 residue 105 TYR Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 187 VAL Chi-restraints excluded: chain B4 residue 200 VAL Chi-restraints excluded: chain B4 residue 271 CYS Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 136 SER Chi-restraints excluded: chain B5 residue 146 LEU Chi-restraints excluded: chain B5 residue 200 VAL Chi-restraints excluded: chain B5 residue 234 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 310 optimal weight: 20.0000 chunk 297 optimal weight: 20.0000 chunk 380 optimal weight: 9.9990 chunk 214 optimal weight: 5.9990 chunk 390 optimal weight: 7.9990 chunk 314 optimal weight: 5.9990 chunk 442 optimal weight: 6.9990 chunk 371 optimal weight: 20.0000 chunk 247 optimal weight: 7.9990 chunk 346 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K2 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 103 GLN C1 290 ASN ** C3 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4 362 ASN ** C5 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5 340 ASN ** G5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.063182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.046075 restraints weight = 471858.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.045737 restraints weight = 291479.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.045986 restraints weight = 206385.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.046179 restraints weight = 167906.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.045383 restraints weight = 151880.317| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 38515 Z= 0.256 Angle : 0.745 12.049 51985 Z= 0.392 Chirality : 0.043 0.332 5780 Planarity : 0.005 0.050 6775 Dihedral : 5.697 69.758 5225 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 23.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.02 % Favored : 92.92 % Rotamer: Outliers : 2.90 % Allowed : 19.04 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.12), residues: 4730 helix: 0.71 (0.11), residues: 2146 sheet: -1.66 (0.17), residues: 794 loop : -1.33 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGC3 120 TYR 0.029 0.002 TYRC5 62 PHE 0.045 0.003 PHEC4 377 TRP 0.051 0.003 TRPC3 109 HIS 0.021 0.002 HISC5 67 Details of bonding type rmsd covalent geometry : bond 0.00525 (38515) covalent geometry : angle 0.74491 (51985) hydrogen bonds : bond 0.04294 ( 1954) hydrogen bonds : angle 5.23056 ( 5703) *********************** 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 361 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 240 time to evaluate : 1.575 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: K1 162 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7097 (tm-30) REVERT: K1 167 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8728 (pm20) REVERT: K2 162 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7995 (tm-30) REVERT: K3 71 TYR cc_start: 0.8988 (t80) cc_final: 0.8750 (t80) REVERT: K4 71 TYR cc_start: 0.8905 (t80) cc_final: 0.8509 (m-80) REVERT: K5 164 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8641 (pt0) REVERT: K5 171 MET cc_start: 0.9220 (ptp) cc_final: 0.8858 (ptp) REVERT: C1 25 MET cc_start: 0.5907 (tpp) cc_final: 0.4727 (tmm) REVERT: C1 220 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: C1 240 ARG cc_start: 0.5393 (OUTLIER) cc_final: 0.4936 (tpt170) REVERT: C1 254 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.8705 (mmpt) REVERT: C1 299 MET cc_start: 0.5641 (mmt) cc_final: 0.5104 (mmt) REVERT: C2 64 MET cc_start: 0.5922 (ttt) cc_final: 0.5344 (tpp) REVERT: C2 100 ASN cc_start: 0.8926 (m-40) cc_final: 0.8453 (t0) REVERT: C2 180 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8277 (mpt180) REVERT: C3 25 MET cc_start: 0.3375 (OUTLIER) cc_final: 0.2423 (pmm) REVERT: C3 64 MET cc_start: 0.2228 (tpt) cc_final: 0.1954 (tpt) REVERT: C3 126 MET cc_start: 0.8372 (ppp) cc_final: 0.8141 (ppp) REVERT: C4 64 MET cc_start: 0.6529 (mmt) cc_final: 0.4750 (tpp) REVERT: C4 287 MET cc_start: 0.1127 (mmt) cc_final: 0.0106 (mmp) REVERT: C5 116 MET cc_start: 0.2748 (OUTLIER) cc_final: 0.2310 (ttm) REVERT: C5 124 MET cc_start: 0.9137 (mtm) cc_final: 0.8743 (mtp) REVERT: C5 128 ARG cc_start: 0.9249 (ttt180) cc_final: 0.8964 (ttm170) REVERT: C5 168 MET cc_start: 0.8548 (ttt) cc_final: 0.8337 (ttt) REVERT: C5 317 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7062 (mmm) REVERT: B1 217 MET cc_start: 0.9003 (ppp) cc_final: 0.8749 (ppp) REVERT: B1 325 MET cc_start: 0.8485 (ppp) cc_final: 0.7358 (ppp) REVERT: B2 188 MET cc_start: 0.9131 (ppp) cc_final: 0.8626 (ppp) REVERT: B4 105 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7308 (t80) REVERT: B4 188 MET cc_start: 0.8654 (ptm) cc_final: 0.8231 (ppp) REVERT: B4 200 VAL cc_start: 0.8086 (OUTLIER) cc_final: 0.7846 (p) REVERT: B5 146 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7897 (mt) REVERT: B5 325 MET cc_start: 0.8805 (tpt) cc_final: 0.8388 (tpp) REVERT: G1 1 MET cc_start: 0.8449 (tpp) cc_final: 0.7854 (tpp) REVERT: G4 1 MET cc_start: 0.8843 (ppp) cc_final: 0.8389 (ppp) outliers start: 121 outliers final: 90 residues processed: 333 average time/residue: 0.2244 time to fit residues: 126.6583 Evaluate side-chains 339 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 235 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 162 GLN Chi-restraints excluded: chain K1 residue 167 GLU Chi-restraints excluded: chain K1 residue 191 TYR Chi-restraints excluded: chain K1 residue 214 TYR Chi-restraints excluded: chain K2 residue 58 THR Chi-restraints excluded: chain K2 residue 104 ASN Chi-restraints excluded: chain K2 residue 162 GLN Chi-restraints excluded: chain K3 residue 80 LEU Chi-restraints excluded: chain K3 residue 92 ILE Chi-restraints excluded: chain K3 residue 152 VAL Chi-restraints excluded: chain K3 residue 169 THR Chi-restraints excluded: chain K4 residue 104 ASN Chi-restraints excluded: chain K4 residue 187 ILE Chi-restraints excluded: chain K5 residue 48 LEU Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 134 LEU Chi-restraints excluded: chain K5 residue 164 GLN Chi-restraints excluded: chain K5 residue 185 VAL Chi-restraints excluded: chain K5 residue 187 ILE Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 66 LEU Chi-restraints excluded: chain C1 residue 73 LEU Chi-restraints excluded: chain C1 residue 89 VAL Chi-restraints excluded: chain C1 residue 102 LEU Chi-restraints excluded: chain C1 residue 104 THR Chi-restraints excluded: chain C1 residue 123 LEU Chi-restraints excluded: chain C1 residue 139 VAL Chi-restraints excluded: chain C1 residue 220 GLU Chi-restraints excluded: chain C1 residue 240 ARG Chi-restraints excluded: chain C1 residue 254 LYS Chi-restraints excluded: chain C1 residue 256 THR Chi-restraints excluded: chain C2 residue 67 HIS Chi-restraints excluded: chain C2 residue 73 LEU Chi-restraints excluded: chain C2 residue 125 TYR Chi-restraints excluded: chain C2 residue 180 ARG Chi-restraints excluded: chain C2 residue 212 MET Chi-restraints excluded: chain C2 residue 369 THR Chi-restraints excluded: chain C3 residue 25 MET Chi-restraints excluded: chain C3 residue 37 LEU Chi-restraints excluded: chain C3 residue 62 TYR Chi-restraints excluded: chain C3 residue 120 ARG Chi-restraints excluded: chain C3 residue 177 VAL Chi-restraints excluded: chain C3 residue 251 CYS Chi-restraints excluded: chain C3 residue 254 LYS Chi-restraints excluded: chain C4 residue 25 MET Chi-restraints excluded: chain C4 residue 69 HIS Chi-restraints excluded: chain C4 residue 85 LEU Chi-restraints excluded: chain C4 residue 127 ASP Chi-restraints excluded: chain C4 residue 129 VAL Chi-restraints excluded: chain C4 residue 185 ASN Chi-restraints excluded: chain C4 residue 275 THR Chi-restraints excluded: chain C4 residue 293 THR Chi-restraints excluded: chain C4 residue 302 LEU Chi-restraints excluded: chain C4 residue 347 ASP Chi-restraints excluded: chain C5 residue 25 MET Chi-restraints excluded: chain C5 residue 74 TYR Chi-restraints excluded: chain C5 residue 116 MET Chi-restraints excluded: chain C5 residue 138 ASN Chi-restraints excluded: chain C5 residue 191 MET Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 300 TYR Chi-restraints excluded: chain C5 residue 310 LEU Chi-restraints excluded: chain C5 residue 317 MET Chi-restraints excluded: chain B1 residue 45 MET Chi-restraints excluded: chain B1 residue 112 VAL Chi-restraints excluded: chain B1 residue 190 LEU Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B2 residue 29 THR Chi-restraints excluded: chain B2 residue 37 ILE Chi-restraints excluded: chain B2 residue 80 ILE Chi-restraints excluded: chain B2 residue 101 MET Chi-restraints excluded: chain B2 residue 112 VAL Chi-restraints excluded: chain B2 residue 128 THR Chi-restraints excluded: chain B2 residue 214 ARG Chi-restraints excluded: chain B2 residue 223 THR Chi-restraints excluded: chain B2 residue 262 MET Chi-restraints excluded: chain B2 residue 285 LEU Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 85 TYR Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 112 VAL Chi-restraints excluded: chain B3 residue 181 THR Chi-restraints excluded: chain B3 residue 225 HIS Chi-restraints excluded: chain B3 residue 286 LEU Chi-restraints excluded: chain B3 residue 317 CYS Chi-restraints excluded: chain B4 residue 74 SER Chi-restraints excluded: chain B4 residue 101 MET Chi-restraints excluded: chain B4 residue 105 TYR Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 187 VAL Chi-restraints excluded: chain B4 residue 200 VAL Chi-restraints excluded: chain B4 residue 213 VAL Chi-restraints excluded: chain B4 residue 271 CYS Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 136 SER Chi-restraints excluded: chain B5 residue 146 LEU Chi-restraints excluded: chain B5 residue 200 VAL Chi-restraints excluded: chain B5 residue 234 PHE Chi-restraints excluded: chain B5 residue 290 ASP Chi-restraints excluded: chain B5 residue 296 VAL Chi-restraints excluded: chain G3 residue 26 ASP 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 73 optimal weight: 0.9990 chunk 330 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 437 optimal weight: 9.9990 chunk 409 optimal weight: 2.9990 chunk 406 optimal weight: 5.9990 chunk 454 optimal weight: 6.9990 chunk 392 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 146 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K2 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3 151 GLN K3 162 GLN ** C1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 290 ASN ** C2 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C5 60 ASN ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.064350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.047102 restraints weight = 474961.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.046927 restraints weight = 283352.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.047191 restraints weight = 198006.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.047522 restraints weight = 161777.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.047334 restraints weight = 143014.568| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 38515 Z= 0.151 Angle : 0.683 11.507 51985 Z= 0.354 Chirality : 0.043 0.274 5780 Planarity : 0.004 0.052 6775 Dihedral : 5.406 65.549 5223 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.03 % Favored : 94.90 % Rotamer: Outliers : 2.61 % Allowed : 19.45 % Favored : 77.94 % 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: -0.54 (0.12), residues: 4730 helix: 0.87 (0.11), residues: 2146 sheet: -1.58 (0.17), residues: 808 loop : -1.17 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGC1 120 TYR 0.028 0.002 TYRB3 85 PHE 0.047 0.002 PHEC4 377 TRP 0.038 0.002 TRPC3 109 HIS 0.022 0.001 HISC5 67 Details of bonding type rmsd covalent geometry : bond 0.00320 (38515) covalent geometry : angle 0.68252 (51985) hydrogen bonds : bond 0.03886 ( 1954) hydrogen bonds : angle 5.04655 ( 5703) *********************** 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 355 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 246 time to evaluate : 1.641 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 162 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6482 (tm-30) REVERT: K1 167 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8734 (pm20) REVERT: K4 71 TYR cc_start: 0.9100 (t80) cc_final: 0.8879 (m-80) REVERT: K5 60 GLN cc_start: 0.9009 (mp10) cc_final: 0.8550 (mp10) REVERT: K5 164 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8543 (pm20) REVERT: K5 171 MET cc_start: 0.9166 (ptp) cc_final: 0.8716 (ptp) REVERT: C1 240 ARG cc_start: 0.5335 (OUTLIER) cc_final: 0.4978 (tpt170) REVERT: C1 254 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.8709 (mmpt) REVERT: C1 299 MET cc_start: 0.5635 (mmt) cc_final: 0.5009 (mmt) REVERT: C2 64 MET cc_start: 0.5564 (ttt) cc_final: 0.5102 (tpp) REVERT: C2 100 ASN cc_start: 0.8833 (m-40) cc_final: 0.8366 (t0) REVERT: C3 25 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.6055 (pmm) REVERT: C3 219 MET cc_start: 0.8893 (tmm) cc_final: 0.8644 (tmm) REVERT: C4 64 MET cc_start: 0.5938 (mmt) cc_final: 0.4349 (tpp) REVERT: C4 126 MET cc_start: 0.5909 (tpp) cc_final: 0.5620 (tpp) REVERT: C4 287 MET cc_start: 0.1629 (mmt) cc_final: 0.0280 (mmp) REVERT: C5 116 MET cc_start: 0.2259 (OUTLIER) cc_final: 0.1746 (ttm) REVERT: C5 124 MET cc_start: 0.8996 (mtm) cc_final: 0.8507 (mtp) REVERT: C5 128 ARG cc_start: 0.9172 (ttt180) cc_final: 0.8934 (ttm170) REVERT: C5 317 MET cc_start: 0.7256 (OUTLIER) cc_final: 0.6764 (mmm) REVERT: B1 266 HIS cc_start: 0.8399 (OUTLIER) cc_final: 0.7936 (m170) REVERT: B1 325 MET cc_start: 0.8362 (ppp) cc_final: 0.7062 (ppp) REVERT: B2 188 MET cc_start: 0.9037 (ppp) cc_final: 0.8626 (tmm) REVERT: B4 105 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.7425 (t80) REVERT: B4 188 MET cc_start: 0.8667 (ptm) cc_final: 0.8202 (ppp) REVERT: B4 200 VAL cc_start: 0.8040 (OUTLIER) cc_final: 0.7820 (p) REVERT: B4 262 MET cc_start: 0.8023 (tpp) cc_final: 0.7397 (tpp) REVERT: B5 146 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7787 (mt) REVERT: B5 325 MET cc_start: 0.8618 (tpt) cc_final: 0.8198 (tpp) REVERT: G1 1 MET cc_start: 0.8473 (tpp) cc_final: 0.7770 (tpp) REVERT: G4 1 MET cc_start: 0.8735 (ppp) cc_final: 0.8275 (ppp) outliers start: 109 outliers final: 84 residues processed: 328 average time/residue: 0.2284 time to fit residues: 126.7671 Evaluate side-chains 336 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 240 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 162 GLN Chi-restraints excluded: chain K1 residue 167 GLU Chi-restraints excluded: chain K1 residue 191 TYR Chi-restraints excluded: chain K1 residue 214 TYR Chi-restraints excluded: chain K2 residue 104 ASN Chi-restraints excluded: chain K2 residue 157 VAL Chi-restraints excluded: chain K3 residue 80 LEU Chi-restraints excluded: chain K3 residue 92 ILE Chi-restraints excluded: chain K3 residue 151 GLN Chi-restraints excluded: chain K3 residue 169 THR Chi-restraints excluded: chain K4 residue 104 ASN Chi-restraints excluded: chain K4 residue 187 ILE Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 164 GLN Chi-restraints excluded: chain K5 residue 185 VAL Chi-restraints excluded: chain K5 residue 187 ILE Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 73 LEU Chi-restraints excluded: chain C1 residue 87 ASN Chi-restraints excluded: chain C1 residue 89 VAL Chi-restraints excluded: chain C1 residue 102 LEU Chi-restraints excluded: chain C1 residue 104 THR Chi-restraints excluded: chain C1 residue 123 LEU Chi-restraints excluded: chain C1 residue 139 VAL Chi-restraints excluded: chain C1 residue 152 VAL Chi-restraints excluded: chain C1 residue 240 ARG Chi-restraints excluded: chain C1 residue 254 LYS Chi-restraints excluded: chain C2 residue 73 LEU Chi-restraints excluded: chain C2 residue 125 TYR Chi-restraints excluded: chain C2 residue 180 ARG Chi-restraints excluded: chain C2 residue 212 MET Chi-restraints excluded: chain C3 residue 25 MET Chi-restraints excluded: chain C3 residue 37 LEU Chi-restraints excluded: chain C3 residue 62 TYR Chi-restraints excluded: chain C3 residue 120 ARG Chi-restraints excluded: chain C3 residue 177 VAL Chi-restraints excluded: chain C3 residue 251 CYS Chi-restraints excluded: chain C3 residue 254 LYS Chi-restraints excluded: chain C3 residue 257 GLU Chi-restraints excluded: chain C4 residue 25 MET Chi-restraints excluded: chain C4 residue 69 HIS Chi-restraints excluded: chain C4 residue 85 LEU Chi-restraints excluded: chain C4 residue 129 VAL Chi-restraints excluded: chain C4 residue 275 THR Chi-restraints excluded: chain C4 residue 293 THR Chi-restraints excluded: chain C4 residue 302 LEU Chi-restraints excluded: chain C4 residue 347 ASP Chi-restraints excluded: chain C5 residue 25 MET Chi-restraints excluded: chain C5 residue 74 TYR Chi-restraints excluded: chain C5 residue 116 MET Chi-restraints excluded: chain C5 residue 120 ARG Chi-restraints excluded: chain C5 residue 138 ASN Chi-restraints excluded: chain C5 residue 191 MET Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 252 LEU Chi-restraints excluded: chain C5 residue 273 MET Chi-restraints excluded: chain C5 residue 300 TYR Chi-restraints excluded: chain C5 residue 310 LEU Chi-restraints excluded: chain C5 residue 317 MET Chi-restraints excluded: chain B1 residue 45 MET Chi-restraints excluded: chain B1 residue 112 VAL Chi-restraints excluded: chain B1 residue 190 LEU Chi-restraints excluded: chain B1 residue 266 HIS Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B2 residue 29 THR Chi-restraints excluded: chain B2 residue 37 ILE Chi-restraints excluded: chain B2 residue 80 ILE Chi-restraints excluded: chain B2 residue 112 VAL Chi-restraints excluded: chain B2 residue 147 SER Chi-restraints excluded: chain B2 residue 223 THR Chi-restraints excluded: chain B2 residue 262 MET Chi-restraints excluded: chain B2 residue 285 LEU Chi-restraints excluded: chain B3 residue 61 MET Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 85 TYR Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 112 VAL Chi-restraints excluded: chain B3 residue 181 THR Chi-restraints excluded: chain B3 residue 225 HIS Chi-restraints excluded: chain B3 residue 286 LEU Chi-restraints excluded: chain B3 residue 317 CYS Chi-restraints excluded: chain B4 residue 74 SER Chi-restraints excluded: chain B4 residue 105 TYR Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 187 VAL Chi-restraints excluded: chain B4 residue 200 VAL Chi-restraints excluded: chain B4 residue 213 VAL Chi-restraints excluded: chain B4 residue 271 CYS Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 136 SER Chi-restraints excluded: chain B5 residue 146 LEU Chi-restraints excluded: chain B5 residue 200 VAL Chi-restraints excluded: chain B5 residue 234 PHE Chi-restraints excluded: chain B5 residue 340 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 168 optimal weight: 9.9990 chunk 330 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 196 optimal weight: 0.5980 chunk 70 optimal weight: 10.0000 chunk 400 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 176 optimal weight: 0.0000 chunk 83 optimal weight: 8.9990 chunk 343 optimal weight: 3.9990 chunk 401 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K2 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3 106 ASN ** C3 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.065078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.048669 restraints weight = 471339.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.048072 restraints weight = 285439.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.048442 restraints weight = 193032.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.048573 restraints weight = 151149.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.048582 restraints weight = 131329.813| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.211 38515 Z= 0.199 Angle : 0.772 59.085 51985 Z= 0.418 Chirality : 0.043 0.436 5780 Planarity : 0.004 0.060 6775 Dihedral : 5.396 65.515 5223 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.20 % Favored : 94.74 % Rotamer: Outliers : 2.40 % Allowed : 19.62 % Favored : 77.99 % Cbeta Deviations : 0.02 % 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: -0.52 (0.12), residues: 4730 helix: 0.87 (0.11), residues: 2145 sheet: -1.57 (0.17), residues: 808 loop : -1.16 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.000 ARGB2 214 TYR 0.031 0.002 TYRC2 201 PHE 0.046 0.002 PHEC4 377 TRP 0.140 0.003 TRPC3 109 HIS 0.020 0.001 HISC5 67 Details of bonding type rmsd covalent geometry : bond 0.00425 (38515) covalent geometry : angle 0.77234 (51985) hydrogen bonds : bond 0.03907 ( 1954) hydrogen bonds : angle 5.06104 ( 5703) ********************** 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 342 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 242 time to evaluate : 1.622 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: K1 162 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6467 (tm-30) REVERT: K1 167 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8719 (pm20) REVERT: K3 151 GLN cc_start: 0.5871 (OUTLIER) cc_final: 0.5636 (tp-100) REVERT: K4 71 TYR cc_start: 0.9054 (t80) cc_final: 0.8742 (m-80) REVERT: K5 60 GLN cc_start: 0.9110 (mp10) cc_final: 0.8616 (mp10) REVERT: K5 164 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8537 (pm20) REVERT: K5 171 MET cc_start: 0.9165 (ptp) cc_final: 0.8711 (ptp) REVERT: C1 240 ARG cc_start: 0.5730 (OUTLIER) cc_final: 0.5338 (tpt170) REVERT: C1 254 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8629 (mmpt) REVERT: C1 299 MET cc_start: 0.5115 (mmt) cc_final: 0.4601 (mmt) REVERT: C2 64 MET cc_start: 0.5558 (ttt) cc_final: 0.5095 (tpp) REVERT: C2 100 ASN cc_start: 0.8914 (m-40) cc_final: 0.8425 (t0) REVERT: C3 25 MET cc_start: 0.4927 (OUTLIER) cc_final: 0.4007 (pmm) REVERT: C4 64 MET cc_start: 0.6269 (mmt) cc_final: 0.4573 (tpp) REVERT: C4 126 MET cc_start: 0.6169 (tpp) cc_final: 0.5890 (tpp) REVERT: C4 287 MET cc_start: 0.1052 (mmt) cc_final: 0.0219 (mmt) REVERT: C5 116 MET cc_start: 0.2257 (OUTLIER) cc_final: 0.1716 (ttm) REVERT: C5 124 MET cc_start: 0.9007 (mtm) cc_final: 0.8519 (mtp) REVERT: C5 128 ARG cc_start: 0.9196 (ttt180) cc_final: 0.8918 (ttm170) REVERT: C5 317 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6741 (mmm) REVERT: B1 266 HIS cc_start: 0.8383 (OUTLIER) cc_final: 0.7925 (m170) REVERT: B1 325 MET cc_start: 0.8350 (ppp) cc_final: 0.7058 (ppp) REVERT: B2 188 MET cc_start: 0.9012 (ppp) cc_final: 0.8608 (tmm) REVERT: B3 325 MET cc_start: 0.8837 (tpt) cc_final: 0.8494 (tpt) REVERT: B4 105 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.7416 (t80) REVERT: B4 188 MET cc_start: 0.8658 (ptm) cc_final: 0.8178 (ppp) REVERT: B4 200 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7825 (p) REVERT: B4 262 MET cc_start: 0.8022 (tpp) cc_final: 0.7399 (tpp) REVERT: B5 146 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7772 (mt) REVERT: B5 325 MET cc_start: 0.8643 (tpt) cc_final: 0.8225 (tpp) REVERT: G1 1 MET cc_start: 0.8454 (tpp) cc_final: 0.7723 (tpp) REVERT: G4 1 MET cc_start: 0.8679 (ppp) cc_final: 0.8168 (ppp) outliers start: 100 outliers final: 85 residues processed: 316 average time/residue: 0.2288 time to fit residues: 122.7086 Evaluate side-chains 339 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 241 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K1 residue 92 ILE Chi-restraints excluded: chain K1 residue 112 VAL Chi-restraints excluded: chain K1 residue 162 GLN Chi-restraints excluded: chain K1 residue 167 GLU Chi-restraints excluded: chain K1 residue 191 TYR Chi-restraints excluded: chain K1 residue 214 TYR Chi-restraints excluded: chain K2 residue 104 ASN Chi-restraints excluded: chain K3 residue 80 LEU Chi-restraints excluded: chain K3 residue 92 ILE Chi-restraints excluded: chain K3 residue 151 GLN Chi-restraints excluded: chain K3 residue 152 VAL Chi-restraints excluded: chain K3 residue 169 THR Chi-restraints excluded: chain K4 residue 104 ASN Chi-restraints excluded: chain K4 residue 187 ILE Chi-restraints excluded: chain K5 residue 97 THR Chi-restraints excluded: chain K5 residue 164 GLN Chi-restraints excluded: chain K5 residue 185 VAL Chi-restraints excluded: chain K5 residue 187 ILE Chi-restraints excluded: chain C1 residue 57 LEU Chi-restraints excluded: chain C1 residue 73 LEU Chi-restraints excluded: chain C1 residue 87 ASN Chi-restraints excluded: chain C1 residue 89 VAL Chi-restraints excluded: chain C1 residue 102 LEU Chi-restraints excluded: chain C1 residue 104 THR Chi-restraints excluded: chain C1 residue 123 LEU Chi-restraints excluded: chain C1 residue 139 VAL Chi-restraints excluded: chain C1 residue 152 VAL Chi-restraints excluded: chain C1 residue 240 ARG Chi-restraints excluded: chain C1 residue 254 LYS Chi-restraints excluded: chain C2 residue 73 LEU Chi-restraints excluded: chain C2 residue 125 TYR Chi-restraints excluded: chain C2 residue 180 ARG Chi-restraints excluded: chain C2 residue 212 MET Chi-restraints excluded: chain C3 residue 25 MET Chi-restraints excluded: chain C3 residue 37 LEU Chi-restraints excluded: chain C3 residue 62 TYR Chi-restraints excluded: chain C3 residue 120 ARG Chi-restraints excluded: chain C3 residue 177 VAL Chi-restraints excluded: chain C3 residue 251 CYS Chi-restraints excluded: chain C3 residue 254 LYS Chi-restraints excluded: chain C3 residue 257 GLU Chi-restraints excluded: chain C4 residue 25 MET Chi-restraints excluded: chain C4 residue 69 HIS Chi-restraints excluded: chain C4 residue 85 LEU Chi-restraints excluded: chain C4 residue 129 VAL Chi-restraints excluded: chain C4 residue 275 THR Chi-restraints excluded: chain C4 residue 293 THR Chi-restraints excluded: chain C4 residue 302 LEU Chi-restraints excluded: chain C4 residue 347 ASP Chi-restraints excluded: chain C5 residue 25 MET Chi-restraints excluded: chain C5 residue 74 TYR Chi-restraints excluded: chain C5 residue 116 MET Chi-restraints excluded: chain C5 residue 120 ARG Chi-restraints excluded: chain C5 residue 138 ASN Chi-restraints excluded: chain C5 residue 191 MET Chi-restraints excluded: chain C5 residue 242 ASN Chi-restraints excluded: chain C5 residue 252 LEU Chi-restraints excluded: chain C5 residue 273 MET Chi-restraints excluded: chain C5 residue 300 TYR Chi-restraints excluded: chain C5 residue 310 LEU Chi-restraints excluded: chain C5 residue 317 MET Chi-restraints excluded: chain B1 residue 45 MET Chi-restraints excluded: chain B1 residue 112 VAL Chi-restraints excluded: chain B1 residue 157 ILE Chi-restraints excluded: chain B1 residue 190 LEU Chi-restraints excluded: chain B1 residue 266 HIS Chi-restraints excluded: chain B1 residue 296 VAL Chi-restraints excluded: chain B2 residue 29 THR Chi-restraints excluded: chain B2 residue 37 ILE Chi-restraints excluded: chain B2 residue 80 ILE Chi-restraints excluded: chain B2 residue 112 VAL Chi-restraints excluded: chain B2 residue 147 SER Chi-restraints excluded: chain B2 residue 223 THR Chi-restraints excluded: chain B2 residue 262 MET Chi-restraints excluded: chain B2 residue 285 LEU Chi-restraints excluded: chain B3 residue 61 MET Chi-restraints excluded: chain B3 residue 71 VAL Chi-restraints excluded: chain B3 residue 85 TYR Chi-restraints excluded: chain B3 residue 102 THR Chi-restraints excluded: chain B3 residue 112 VAL Chi-restraints excluded: chain B3 residue 181 THR Chi-restraints excluded: chain B3 residue 225 HIS Chi-restraints excluded: chain B3 residue 286 LEU Chi-restraints excluded: chain B3 residue 317 CYS Chi-restraints excluded: chain B4 residue 74 SER Chi-restraints excluded: chain B4 residue 105 TYR Chi-restraints excluded: chain B4 residue 135 VAL Chi-restraints excluded: chain B4 residue 165 THR Chi-restraints excluded: chain B4 residue 187 VAL Chi-restraints excluded: chain B4 residue 200 VAL Chi-restraints excluded: chain B4 residue 213 VAL Chi-restraints excluded: chain B4 residue 271 CYS Chi-restraints excluded: chain B5 residue 102 THR Chi-restraints excluded: chain B5 residue 136 SER Chi-restraints excluded: chain B5 residue 146 LEU Chi-restraints excluded: chain B5 residue 200 VAL Chi-restraints excluded: chain B5 residue 234 PHE Chi-restraints excluded: chain B5 residue 340 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 412 optimal weight: 10.0000 chunk 462 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 157 optimal weight: 30.0000 chunk 444 optimal weight: 4.9990 chunk 398 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 458 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K2 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.065109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.049052 restraints weight = 474968.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.049276 restraints weight = 314141.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.049157 restraints weight = 197520.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.049265 restraints weight = 142496.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.049173 restraints weight = 145003.026| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 38515 Z= 0.195 Angle : 0.772 59.200 51985 Z= 0.418 Chirality : 0.043 0.415 5780 Planarity : 0.004 0.060 6775 Dihedral : 5.395 65.513 5223 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.20 % Favored : 94.74 % Rotamer: Outliers : 2.35 % Allowed : 19.66 % Favored : 77.99 % Cbeta Deviations : 0.02 % 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: -0.52 (0.12), residues: 4730 helix: 0.87 (0.11), residues: 2145 sheet: -1.57 (0.17), residues: 808 loop : -1.16 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.000 ARGB2 214 TYR 0.031 0.002 TYRC2 201 PHE 0.046 0.002 PHEC4 377 TRP 0.141 0.003 TRPC3 109 HIS 0.020 0.001 HISC5 67 Details of bonding type rmsd covalent geometry : bond 0.00423 (38515) covalent geometry : angle 0.77169 (51985) hydrogen bonds : bond 0.03906 ( 1954) hydrogen bonds : angle 5.06095 ( 5703) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13443.49 seconds wall clock time: 231 minutes 9.75 seconds (13869.75 seconds total)