Starting phenix.real_space_refine on Thu Mar 5 03:32:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xlb_33276/03_2026/7xlb_33276.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xlb_33276/03_2026/7xlb_33276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xlb_33276/03_2026/7xlb_33276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xlb_33276/03_2026/7xlb_33276.map" model { file = "/net/cci-nas-00/data/ceres_data/7xlb_33276/03_2026/7xlb_33276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xlb_33276/03_2026/7xlb_33276.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.088 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 84 5.16 5 C 12404 2.51 5 N 3304 2.21 5 O 3346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19138 Number of models: 1 Model: "" Number of chains: 7 Chain: "E" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2734 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 14, 'TRANS': 321} Chain breaks: 3 Chain: "A" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2734 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 14, 'TRANS': 321} Chain breaks: 3 Chain: "B" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2734 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 14, 'TRANS': 321} Chain breaks: 3 Chain: "C" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2734 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 14, 'TRANS': 321} Chain breaks: 3 Chain: "D" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2734 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 14, 'TRANS': 321} Chain breaks: 3 Chain: "F" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2734 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 14, 'TRANS': 321} Chain breaks: 3 Chain: "G" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2734 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 14, 'TRANS': 321} Chain breaks: 3 Time building chain proxies: 4.50, per 1000 atoms: 0.24 Number of scatterers: 19138 At special positions: 0 Unit cell: (126.96, 126.96, 129.72, 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 84 16.00 O 3346 8.00 N 3304 7.00 C 12404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS E 81 " - pdb=" SG CYS E 279 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 259 " distance=2.03 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 259 " distance=2.03 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 279 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 259 " distance=2.03 Simple disulfide: pdb=" SG CYS D 81 " - pdb=" SG CYS D 279 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 259 " distance=2.03 Simple disulfide: pdb=" SG CYS F 81 " - pdb=" SG CYS F 279 " distance=2.03 Simple disulfide: pdb=" SG CYS F 99 " - pdb=" SG CYS F 259 " distance=2.03 Simple disulfide: pdb=" SG CYS G 81 " - pdb=" SG CYS G 279 " distance=2.03 Simple disulfide: pdb=" SG CYS G 99 " - pdb=" SG CYS G 259 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 770.5 milliseconds 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4564 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 7 sheets defined 60.4% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'E' and resid 48 through 59 Processing helix chain 'E' and resid 59 through 65 removed outlier: 3.808A pdb=" N ILE E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 74 Processing helix chain 'E' and resid 90 through 99 removed outlier: 3.934A pdb=" N TYR E 94 " --> pdb=" O ASP E 90 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA E 95 " --> pdb=" O GLN E 91 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 removed outlier: 4.143A pdb=" N LYS E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 144 removed outlier: 4.375A pdb=" N TRP E 142 " --> pdb=" O PRO E 138 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU E 143 " --> pdb=" O ALA E 139 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 160 removed outlier: 3.681A pdb=" N PHE E 156 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU E 157 " --> pdb=" O GLU E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 172 Processing helix chain 'E' and resid 177 through 182 removed outlier: 3.584A pdb=" N GLN E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER E 182 " --> pdb=" O LYS E 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 177 through 182' Processing helix chain 'E' and resid 191 through 198 removed outlier: 4.143A pdb=" N ASN E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 208 removed outlier: 4.309A pdb=" N ASN E 208 " --> pdb=" O PRO E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 218 Processing helix chain 'E' and resid 223 through 233 removed outlier: 3.764A pdb=" N LEU E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 238 Processing helix chain 'E' and resid 239 through 252 removed outlier: 3.837A pdb=" N LEU E 245 " --> pdb=" O PRO E 241 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS E 246 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR E 247 " --> pdb=" O SER E 243 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR E 248 " --> pdb=" O TYR E 244 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR E 249 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA E 250 " --> pdb=" O CYS E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 292 through 300 removed outlier: 4.027A pdb=" N VAL E 296 " --> pdb=" O GLY E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 315 removed outlier: 3.753A pdb=" N ILE E 304 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE E 305 " --> pdb=" O MET E 301 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU E 306 " --> pdb=" O ASN E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 327 removed outlier: 4.366A pdb=" N LYS E 327 " --> pdb=" O LYS E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 354 removed outlier: 4.120A pdb=" N ILE E 346 " --> pdb=" O CYS E 342 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET E 349 " --> pdb=" O ASN E 345 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE E 350 " --> pdb=" O ILE E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 369 removed outlier: 3.677A pdb=" N ASN E 369 " --> pdb=" O ASP E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 372 No H-bonds generated for 'chain 'E' and resid 370 through 372' Processing helix chain 'E' and resid 378 through 386 removed outlier: 3.734A pdb=" N LEU E 382 " --> pdb=" O VAL E 378 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E 383 " --> pdb=" O VAL E 379 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA E 384 " --> pdb=" O ARG E 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 59 Processing helix chain 'A' and resid 59 through 65 removed outlier: 3.764A pdb=" N ILE A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 74 Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.922A pdb=" N TYR A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA A 95 " --> pdb=" O GLN A 91 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 124 removed outlier: 4.112A pdb=" N LYS A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 removed outlier: 4.370A pdb=" N TRP A 142 " --> pdb=" O PRO A 138 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.682A pdb=" N PHE A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.583A pdb=" N GLN A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER A 182 " --> pdb=" O LYS A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 182' Processing helix chain 'A' and resid 191 through 198 removed outlier: 4.143A pdb=" N ASN A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 removed outlier: 4.307A pdb=" N ASN A 208 " --> pdb=" O PRO A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.712A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 239 through 252 removed outlier: 3.788A pdb=" N LEU A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR A 248 " --> pdb=" O TYR A 244 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 250 " --> pdb=" O CYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 292 through 300 removed outlier: 4.044A pdb=" N VAL A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.758A pdb=" N ILE A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 305 " --> pdb=" O MET A 301 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 removed outlier: 4.305A pdb=" N LYS A 327 " --> pdb=" O LYS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 removed outlier: 4.097A pdb=" N ILE A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 369 removed outlier: 3.630A pdb=" N ASN A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 378 through 386 removed outlier: 3.734A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 383 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 59 Processing helix chain 'B' and resid 59 through 65 removed outlier: 3.776A pdb=" N ILE B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 74 Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.939A pdb=" N TYR B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B 95 " --> pdb=" O GLN B 91 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 removed outlier: 4.138A pdb=" N LYS B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 144 removed outlier: 4.372A pdb=" N TRP B 142 " --> pdb=" O PRO B 138 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 160 removed outlier: 3.711A pdb=" N PHE B 156 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 157 " --> pdb=" O GLU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.584A pdb=" N GLN B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER B 182 " --> pdb=" O LYS B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 182' Processing helix chain 'B' and resid 191 through 198 removed outlier: 4.142A pdb=" N ASN B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 removed outlier: 4.310A pdb=" N ASN B 208 " --> pdb=" O PRO B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 218 Processing helix chain 'B' and resid 223 through 233 removed outlier: 3.718A pdb=" N LEU B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA B 229 " --> pdb=" O LYS B 225 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 239 through 252 removed outlier: 3.839A pdb=" N LEU B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS B 246 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 248 " --> pdb=" O TYR B 244 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 250 " --> pdb=" O CYS B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 292 through 300 removed outlier: 4.057A pdb=" N VAL B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 315 removed outlier: 3.761A pdb=" N ILE B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 305 " --> pdb=" O MET B 301 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 327 removed outlier: 4.283A pdb=" N LYS B 327 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 removed outlier: 4.081A pdb=" N ILE B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET B 349 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 350 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 369 removed outlier: 3.632A pdb=" N ASN B 369 " --> pdb=" O ASP B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 378 through 386 removed outlier: 3.737A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 59 Processing helix chain 'C' and resid 59 through 65 removed outlier: 3.766A pdb=" N ILE C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 74 Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.940A pdb=" N TYR C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA C 95 " --> pdb=" O GLN C 91 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N CYS C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 124 removed outlier: 4.136A pdb=" N LYS C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 144 removed outlier: 4.374A pdb=" N TRP C 142 " --> pdb=" O PRO C 138 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 160 removed outlier: 3.676A pdb=" N PHE C 156 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 177 through 182 removed outlier: 3.585A pdb=" N GLN C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 182' Processing helix chain 'C' and resid 191 through 198 removed outlier: 4.141A pdb=" N ASN C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 208 removed outlier: 4.309A pdb=" N ASN C 208 " --> pdb=" O PRO C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 223 through 233 removed outlier: 3.720A pdb=" N LEU C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA C 229 " --> pdb=" O LYS C 225 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 239 through 252 removed outlier: 3.796A pdb=" N LEU C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS C 246 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR C 248 " --> pdb=" O TYR C 244 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 250 " --> pdb=" O CYS C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 292 through 300 removed outlier: 4.033A pdb=" N VAL C 296 " --> pdb=" O GLY C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 315 removed outlier: 3.731A pdb=" N ILE C 304 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE C 305 " --> pdb=" O MET C 301 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU C 306 " --> pdb=" O ASN C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 327 removed outlier: 4.289A pdb=" N LYS C 327 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 removed outlier: 4.107A pdb=" N ILE C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 350 " --> pdb=" O ILE C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 369 removed outlier: 3.626A pdb=" N ASN C 369 " --> pdb=" O ASP C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 378 through 386 removed outlier: 3.735A pdb=" N LEU C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 383 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA C 384 " --> pdb=" O ARG C 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 59 Processing helix chain 'D' and resid 59 through 65 removed outlier: 3.783A pdb=" N ILE D 63 " --> pdb=" O VAL D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 74 Processing helix chain 'D' and resid 90 through 99 removed outlier: 3.932A pdb=" N TYR D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA D 95 " --> pdb=" O GLN D 91 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N CYS D 99 " --> pdb=" O ALA D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 124 removed outlier: 4.143A pdb=" N LYS D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 144 removed outlier: 4.200A pdb=" N TRP D 142 " --> pdb=" O PRO D 138 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU D 143 " --> pdb=" O ALA D 139 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 160 removed outlier: 3.699A pdb=" N PHE D 156 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU D 157 " --> pdb=" O GLU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 172 Processing helix chain 'D' and resid 177 through 182 removed outlier: 3.585A pdb=" N GLN D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER D 182 " --> pdb=" O LYS D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 177 through 182' Processing helix chain 'D' and resid 191 through 198 removed outlier: 4.142A pdb=" N ASN D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 208 removed outlier: 4.309A pdb=" N ASN D 208 " --> pdb=" O PRO D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.730A pdb=" N LEU D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA D 229 " --> pdb=" O LYS D 225 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 239 through 252 removed outlier: 3.816A pdb=" N LEU D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS D 246 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR D 247 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR D 248 " --> pdb=" O TYR D 244 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 250 " --> pdb=" O CYS D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 292 through 300 removed outlier: 4.043A pdb=" N VAL D 296 " --> pdb=" O GLY D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 315 removed outlier: 3.752A pdb=" N ILE D 304 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE D 305 " --> pdb=" O MET D 301 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU D 306 " --> pdb=" O ASN D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 327 removed outlier: 4.352A pdb=" N LYS D 327 " --> pdb=" O LYS D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 354 removed outlier: 4.100A pdb=" N ILE D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE D 350 " --> pdb=" O ILE D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 369 removed outlier: 3.666A pdb=" N ASN D 369 " --> pdb=" O ASP D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 372 No H-bonds generated for 'chain 'D' and resid 370 through 372' Processing helix chain 'D' and resid 378 through 386 removed outlier: 3.731A pdb=" N LEU D 382 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 383 " --> pdb=" O VAL D 379 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA D 384 " --> pdb=" O ARG D 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 59 Processing helix chain 'F' and resid 59 through 65 removed outlier: 3.811A pdb=" N ILE F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 74 Processing helix chain 'F' and resid 90 through 99 removed outlier: 3.936A pdb=" N TYR F 94 " --> pdb=" O ASP F 90 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA F 95 " --> pdb=" O GLN F 91 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS F 99 " --> pdb=" O ALA F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 124 removed outlier: 4.140A pdb=" N LYS F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 144 removed outlier: 4.167A pdb=" N TRP F 142 " --> pdb=" O PRO F 138 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU F 143 " --> pdb=" O ALA F 139 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE F 144 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 160 removed outlier: 3.665A pdb=" N PHE F 156 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU F 157 " --> pdb=" O GLU F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 172 Processing helix chain 'F' and resid 177 through 182 removed outlier: 3.582A pdb=" N GLN F 181 " --> pdb=" O GLU F 177 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER F 182 " --> pdb=" O LYS F 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 177 through 182' Processing helix chain 'F' and resid 191 through 198 removed outlier: 4.143A pdb=" N ASN F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 208 removed outlier: 4.310A pdb=" N ASN F 208 " --> pdb=" O PRO F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 218 Processing helix chain 'F' and resid 223 through 238 removed outlier: 3.672A pdb=" N LEU F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA F 229 " --> pdb=" O LYS F 225 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 233 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE F 234 " --> pdb=" O ARG F 230 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 236 " --> pdb=" O VAL F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 252 removed outlier: 3.808A pdb=" N LEU F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS F 246 " --> pdb=" O ILE F 242 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR F 247 " --> pdb=" O SER F 243 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR F 248 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TYR F 249 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA F 250 " --> pdb=" O CYS F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 292 through 300 removed outlier: 4.043A pdb=" N VAL F 296 " --> pdb=" O GLY F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 315 removed outlier: 3.752A pdb=" N ILE F 304 " --> pdb=" O VAL F 300 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE F 305 " --> pdb=" O MET F 301 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU F 306 " --> pdb=" O ASN F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 327 removed outlier: 4.291A pdb=" N LYS F 327 " --> pdb=" O LYS F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 354 removed outlier: 4.116A pdb=" N ILE F 346 " --> pdb=" O CYS F 342 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET F 349 " --> pdb=" O ASN F 345 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE F 350 " --> pdb=" O ILE F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 369 removed outlier: 3.654A pdb=" N ASN F 369 " --> pdb=" O ASP F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 372 No H-bonds generated for 'chain 'F' and resid 370 through 372' Processing helix chain 'F' and resid 378 through 386 removed outlier: 3.732A pdb=" N LEU F 382 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 383 " --> pdb=" O VAL F 379 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 59 Processing helix chain 'G' and resid 59 through 65 removed outlier: 3.786A pdb=" N ILE G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 74 Processing helix chain 'G' and resid 90 through 99 removed outlier: 3.917A pdb=" N TYR G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA G 95 " --> pdb=" O GLN G 91 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS G 99 " --> pdb=" O ALA G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 124 removed outlier: 4.157A pdb=" N LYS G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 144 removed outlier: 4.223A pdb=" N TRP G 142 " --> pdb=" O PRO G 138 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU G 143 " --> pdb=" O ALA G 139 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE G 144 " --> pdb=" O LEU G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 160 removed outlier: 3.711A pdb=" N PHE G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU G 157 " --> pdb=" O GLU G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 172 Processing helix chain 'G' and resid 177 through 182 removed outlier: 3.582A pdb=" N GLN G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER G 182 " --> pdb=" O LYS G 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 177 through 182' Processing helix chain 'G' and resid 191 through 198 removed outlier: 4.140A pdb=" N ASN G 198 " --> pdb=" O GLU G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 208 removed outlier: 4.310A pdb=" N ASN G 208 " --> pdb=" O PRO G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 218 Processing helix chain 'G' and resid 223 through 233 removed outlier: 3.740A pdb=" N LEU G 228 " --> pdb=" O ALA G 224 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA G 229 " --> pdb=" O LYS G 225 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU G 233 " --> pdb=" O ALA G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 238 Processing helix chain 'G' and resid 239 through 252 removed outlier: 3.848A pdb=" N LEU G 245 " --> pdb=" O PRO G 241 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS G 246 " --> pdb=" O ILE G 242 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR G 247 " --> pdb=" O SER G 243 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR G 248 " --> pdb=" O TYR G 244 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR G 249 " --> pdb=" O LEU G 245 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA G 250 " --> pdb=" O CYS G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 290 Processing helix chain 'G' and resid 292 through 300 removed outlier: 4.037A pdb=" N VAL G 296 " --> pdb=" O GLY G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 315 removed outlier: 3.761A pdb=" N ILE G 304 " --> pdb=" O VAL G 300 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE G 305 " --> pdb=" O MET G 301 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU G 306 " --> pdb=" O ASN G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 327 removed outlier: 4.296A pdb=" N LYS G 327 " --> pdb=" O LYS G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 354 removed outlier: 4.089A pdb=" N ILE G 346 " --> pdb=" O CYS G 342 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET G 349 " --> pdb=" O ASN G 345 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE G 350 " --> pdb=" O ILE G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 369 removed outlier: 3.615A pdb=" N ASN G 369 " --> pdb=" O ASP G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 372 No H-bonds generated for 'chain 'G' and resid 370 through 372' Processing helix chain 'G' and resid 378 through 386 removed outlier: 3.732A pdb=" N LEU G 382 " --> pdb=" O VAL G 378 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU G 383 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA G 384 " --> pdb=" O ARG G 380 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 80 through 81 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA4, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'F' and resid 80 through 81 Processing sheet with id=AA7, first strand: chain 'G' and resid 80 through 81 589 hydrogen bonds defined for protein. 1662 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: 2.85 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6146 1.35 - 1.46: 4421 1.46 - 1.58: 8855 1.58 - 1.70: 3 1.70 - 1.82: 105 Bond restraints: 19530 Sorted by residual: bond pdb=" CB PRO B 125 " pdb=" CG PRO B 125 " ideal model delta sigma weight residual 1.492 1.632 -0.140 5.00e-02 4.00e+02 7.89e+00 bond pdb=" CB PRO C 125 " pdb=" CG PRO C 125 " ideal model delta sigma weight residual 1.492 1.625 -0.133 5.00e-02 4.00e+02 7.09e+00 bond pdb=" CB PRO G 125 " pdb=" CG PRO G 125 " ideal model delta sigma weight residual 1.492 1.604 -0.112 5.00e-02 4.00e+02 5.00e+00 bond pdb=" N PRO B 125 " pdb=" CA PRO B 125 " ideal model delta sigma weight residual 1.471 1.445 0.025 1.32e-02 5.74e+03 3.67e+00 bond pdb=" N PRO C 125 " pdb=" CA PRO C 125 " ideal model delta sigma weight residual 1.472 1.448 0.024 1.32e-02 5.74e+03 3.29e+00 ... (remaining 19525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 26218 2.67 - 5.34: 159 5.34 - 8.01: 30 8.01 - 10.68: 23 10.68 - 13.35: 2 Bond angle restraints: 26432 Sorted by residual: angle pdb=" CA PRO B 125 " pdb=" N PRO B 125 " pdb=" CD PRO B 125 " ideal model delta sigma weight residual 112.00 98.65 13.35 1.40e+00 5.10e-01 9.09e+01 angle pdb=" CA PRO C 125 " pdb=" N PRO C 125 " pdb=" CD PRO C 125 " ideal model delta sigma weight residual 112.00 99.88 12.12 1.40e+00 5.10e-01 7.49e+01 angle pdb=" CA PRO G 125 " pdb=" N PRO G 125 " pdb=" CD PRO G 125 " ideal model delta sigma weight residual 112.00 102.22 9.78 1.40e+00 5.10e-01 4.88e+01 angle pdb=" CA PRO B 62 " pdb=" N PRO B 62 " pdb=" CD PRO B 62 " ideal model delta sigma weight residual 112.00 103.51 8.49 1.40e+00 5.10e-01 3.68e+01 angle pdb=" CA PRO F 62 " pdb=" N PRO F 62 " pdb=" CD PRO F 62 " ideal model delta sigma weight residual 112.00 103.58 8.42 1.40e+00 5.10e-01 3.62e+01 ... (remaining 26427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 9686 17.66 - 35.33: 1547 35.33 - 52.99: 563 52.99 - 70.65: 49 70.65 - 88.31: 41 Dihedral angle restraints: 11886 sinusoidal: 4914 harmonic: 6972 Sorted by residual: dihedral pdb=" CA LEU D 124 " pdb=" C LEU D 124 " pdb=" N PRO D 125 " pdb=" CA PRO D 125 " ideal model delta harmonic sigma weight residual 180.00 139.07 40.93 0 5.00e+00 4.00e-02 6.70e+01 dihedral pdb=" CA LEU F 124 " pdb=" C LEU F 124 " pdb=" N PRO F 125 " pdb=" CA PRO F 125 " ideal model delta harmonic sigma weight residual 180.00 139.81 40.19 0 5.00e+00 4.00e-02 6.46e+01 dihedral pdb=" CA LEU E 124 " pdb=" C LEU E 124 " pdb=" N PRO E 125 " pdb=" CA PRO E 125 " ideal model delta harmonic sigma weight residual 180.00 139.85 40.15 0 5.00e+00 4.00e-02 6.45e+01 ... (remaining 11883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1858 0.030 - 0.060: 883 0.060 - 0.091: 198 0.091 - 0.121: 82 0.121 - 0.151: 24 Chirality restraints: 3045 Sorted by residual: chirality pdb=" CB THR D 151 " pdb=" CA THR D 151 " pdb=" OG1 THR D 151 " pdb=" CG2 THR D 151 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CB THR C 151 " pdb=" CA THR C 151 " pdb=" OG1 THR C 151 " pdb=" CG2 THR C 151 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ILE G 289 " pdb=" N ILE G 289 " pdb=" C ILE G 289 " pdb=" CB ILE G 289 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 3042 not shown) Planarity restraints: 3325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 124 " 0.126 5.00e-02 4.00e+02 1.80e-01 5.20e+01 pdb=" N PRO B 125 " -0.311 5.00e-02 4.00e+02 pdb=" CA PRO B 125 " 0.097 5.00e-02 4.00e+02 pdb=" CD PRO B 125 " 0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 124 " 0.122 5.00e-02 4.00e+02 1.75e-01 4.92e+01 pdb=" N PRO C 125 " -0.303 5.00e-02 4.00e+02 pdb=" CA PRO C 125 " 0.094 5.00e-02 4.00e+02 pdb=" CD PRO C 125 " 0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 124 " -0.116 5.00e-02 4.00e+02 1.69e-01 4.58e+01 pdb=" N PRO G 125 " 0.292 5.00e-02 4.00e+02 pdb=" CA PRO G 125 " -0.092 5.00e-02 4.00e+02 pdb=" CD PRO G 125 " -0.084 5.00e-02 4.00e+02 ... (remaining 3322 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3408 2.77 - 3.30: 17309 3.30 - 3.83: 29189 3.83 - 4.37: 32769 4.37 - 4.90: 56333 Nonbonded interactions: 139008 Sorted by model distance: nonbonded pdb=" OD1 ASP A 365 " pdb=" ND2 ASN A 369 " model vdw 2.236 3.120 nonbonded pdb=" OD1 ASP B 365 " pdb=" ND2 ASN B 369 " model vdw 2.242 3.120 nonbonded pdb=" NH1 ARG E 363 " pdb=" OE2 GLU G 160 " model vdw 2.244 3.120 nonbonded pdb=" OD1 ASP C 365 " pdb=" ND2 ASN C 369 " model vdw 2.245 3.120 nonbonded pdb=" OD1 ASP G 365 " pdb=" ND2 ASN G 369 " model vdw 2.245 3.120 ... (remaining 139003 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.790 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 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:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.140 19544 Z= 0.120 Angle : 0.640 13.350 26460 Z= 0.357 Chirality : 0.038 0.151 3045 Planarity : 0.011 0.180 3325 Dihedral : 19.227 88.312 7280 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.19 % Allowed : 37.84 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.16), residues: 2296 helix: -2.54 (0.14), residues: 1281 sheet: -0.54 (0.54), residues: 105 loop : -2.30 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 355 TYR 0.016 0.001 TYR F 165 PHE 0.019 0.001 PHE A 366 TRP 0.003 0.001 TRP F 115 HIS 0.003 0.000 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00333 (19530) covalent geometry : angle 0.64030 (26432) SS BOND : bond 0.00125 ( 14) SS BOND : angle 0.54693 ( 28) hydrogen bonds : bond 0.21366 ( 589) hydrogen bonds : angle 8.52139 ( 1662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.495 Fit side-chains REVERT: A 135 MET cc_start: 0.7532 (mmt) cc_final: 0.6643 (mmt) outliers start: 4 outliers final: 0 residues processed: 128 average time/residue: 0.1225 time to fit residues: 25.3362 Evaluate side-chains 110 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 0.0470 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN E 231 HIS A 155 ASN A 231 HIS B 155 ASN B 231 HIS B 252 GLN C 155 ASN C 231 HIS ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN G 231 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.229531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.209329 restraints weight = 22518.295| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 0.96 r_work: 0.4114 rms_B_bonded: 1.12 restraints_weight: 0.5000 r_work: 0.4032 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work: 0.3950 rms_B_bonded: 4.44 restraints_weight: 0.1250 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19544 Z= 0.113 Angle : 0.599 11.052 26460 Z= 0.307 Chirality : 0.040 0.163 3045 Planarity : 0.007 0.116 3325 Dihedral : 5.011 39.745 2569 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.97 % Allowed : 33.30 % Favored : 61.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.17), residues: 2296 helix: -2.09 (0.15), residues: 1253 sheet: -0.60 (0.53), residues: 105 loop : -2.23 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 363 TYR 0.013 0.002 TYR G 82 PHE 0.011 0.001 PHE C 320 TRP 0.006 0.001 TRP G 100 HIS 0.002 0.000 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00245 (19530) covalent geometry : angle 0.59881 (26432) SS BOND : bond 0.00222 ( 14) SS BOND : angle 0.75205 ( 28) hydrogen bonds : bond 0.04065 ( 589) hydrogen bonds : angle 6.10282 ( 1662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 129 time to evaluate : 0.737 Fit side-chains REVERT: E 311 HIS cc_start: 0.6600 (OUTLIER) cc_final: 0.5719 (p-80) REVERT: G 311 HIS cc_start: 0.6600 (OUTLIER) cc_final: 0.5577 (p-80) outliers start: 104 outliers final: 64 residues processed: 222 average time/residue: 0.1209 time to fit residues: 43.4325 Evaluate side-chains 182 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 116 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 166 HIS Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 311 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 12 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 chunk 145 optimal weight: 9.9990 chunk 190 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 205 optimal weight: 0.6980 chunk 224 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN E 231 HIS E 302 ASN A 231 HIS A 302 ASN B 155 ASN B 231 HIS C 155 ASN C 231 HIS ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C 319 ASN D 155 ASN D 231 HIS ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 ASN F 155 ASN G 155 ASN G 319 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.226841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.206505 restraints weight = 22722.054| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 0.94 r_work: 0.4007 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3852 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19544 Z= 0.137 Angle : 0.625 10.780 26460 Z= 0.316 Chirality : 0.041 0.158 3045 Planarity : 0.007 0.110 3325 Dihedral : 5.094 38.082 2569 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 7.79 % Allowed : 30.29 % Favored : 61.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.17), residues: 2296 helix: -2.12 (0.14), residues: 1295 sheet: -0.69 (0.52), residues: 105 loop : -2.14 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 363 TYR 0.016 0.002 TYR G 82 PHE 0.012 0.001 PHE A 123 TRP 0.009 0.001 TRP G 100 HIS 0.005 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00322 (19530) covalent geometry : angle 0.62426 (26432) SS BOND : bond 0.00277 ( 14) SS BOND : angle 0.95451 ( 28) hydrogen bonds : bond 0.03809 ( 589) hydrogen bonds : angle 5.86916 ( 1662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 121 time to evaluate : 0.568 Fit side-chains REVERT: E 311 HIS cc_start: 0.6591 (OUTLIER) cc_final: 0.5715 (p-80) REVERT: A 234 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7411 (tt) REVERT: C 234 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7222 (tt) REVERT: D 234 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7297 (tt) REVERT: F 234 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7590 (tt) REVERT: F 245 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8121 (pp) REVERT: F 311 HIS cc_start: 0.6511 (OUTLIER) cc_final: 0.5632 (p-80) REVERT: G 234 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7302 (tt) REVERT: G 311 HIS cc_start: 0.6585 (OUTLIER) cc_final: 0.5707 (p-80) outliers start: 163 outliers final: 112 residues processed: 267 average time/residue: 0.1121 time to fit residues: 49.2899 Evaluate side-chains 236 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 115 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 155 ASN Chi-restraints excluded: chain E residue 166 HIS Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 326 HIS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 326 HIS Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 326 HIS Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 326 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 146 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 226 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 203 optimal weight: 0.0000 chunk 8 optimal weight: 0.6980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 231 HIS E 302 ASN A 155 ASN A 231 HIS A 302 ASN B 231 HIS C 231 HIS ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C 319 ASN ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN G 231 HIS G 319 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.228670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.209055 restraints weight = 22574.056| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 0.97 r_work: 0.4066 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.4011 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work: 0.3915 rms_B_bonded: 4.31 restraints_weight: 0.1250 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19544 Z= 0.107 Angle : 0.594 9.371 26460 Z= 0.300 Chirality : 0.039 0.151 3045 Planarity : 0.006 0.102 3325 Dihedral : 4.990 37.777 2569 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 6.35 % Allowed : 31.87 % Favored : 61.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.17), residues: 2296 helix: -2.02 (0.15), residues: 1274 sheet: -0.94 (0.52), residues: 112 loop : -2.23 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 363 TYR 0.012 0.001 TYR G 82 PHE 0.008 0.001 PHE F 366 TRP 0.006 0.001 TRP G 100 HIS 0.002 0.000 HIS G 231 Details of bonding type rmsd covalent geometry : bond 0.00254 (19530) covalent geometry : angle 0.59342 (26432) SS BOND : bond 0.00217 ( 14) SS BOND : angle 0.72439 ( 28) hydrogen bonds : bond 0.03250 ( 589) hydrogen bonds : angle 5.69276 ( 1662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 125 time to evaluate : 0.747 Fit side-chains REVERT: E 311 HIS cc_start: 0.6758 (OUTLIER) cc_final: 0.5775 (p-80) REVERT: C 234 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7312 (tt) REVERT: C 349 MET cc_start: 0.7331 (mtt) cc_final: 0.6617 (mtt) REVERT: D 234 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7415 (tt) REVERT: F 245 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8072 (pp) REVERT: F 311 HIS cc_start: 0.6676 (OUTLIER) cc_final: 0.5844 (p-80) REVERT: G 234 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7338 (tt) REVERT: G 311 HIS cc_start: 0.6747 (OUTLIER) cc_final: 0.5675 (p-80) outliers start: 133 outliers final: 94 residues processed: 245 average time/residue: 0.1168 time to fit residues: 47.2219 Evaluate side-chains 215 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 114 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 166 HIS Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 326 HIS Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 326 HIS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 326 HIS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 326 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 25 optimal weight: 4.9990 chunk 222 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 131 optimal weight: 30.0000 chunk 185 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 157 optimal weight: 0.4980 chunk 113 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN A 231 HIS A 302 ASN B 155 ASN B 231 HIS C 155 ASN C 231 HIS ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C 319 ASN D 155 ASN ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN G 155 ASN G 231 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.225543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.205110 restraints weight = 22468.710| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 0.93 r_work: 0.3999 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19544 Z= 0.154 Angle : 0.657 11.773 26460 Z= 0.327 Chirality : 0.042 0.185 3045 Planarity : 0.006 0.103 3325 Dihedral : 5.142 36.771 2569 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 8.27 % Allowed : 30.15 % Favored : 61.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.17), residues: 2296 helix: -2.10 (0.14), residues: 1330 sheet: -1.18 (0.51), residues: 112 loop : -2.24 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 230 TYR 0.017 0.002 TYR G 82 PHE 0.016 0.001 PHE E 320 TRP 0.010 0.001 TRP A 100 HIS 0.013 0.001 HIS G 231 Details of bonding type rmsd covalent geometry : bond 0.00381 (19530) covalent geometry : angle 0.65637 (26432) SS BOND : bond 0.00293 ( 14) SS BOND : angle 1.01572 ( 28) hydrogen bonds : bond 0.03591 ( 589) hydrogen bonds : angle 5.59754 ( 1662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 116 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: E 311 HIS cc_start: 0.6664 (OUTLIER) cc_final: 0.5751 (p-80) REVERT: A 234 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7436 (tt) REVERT: C 234 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7167 (tt) REVERT: C 349 MET cc_start: 0.7366 (mtt) cc_final: 0.6675 (mtt) REVERT: D 234 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7368 (tt) REVERT: F 234 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7558 (tt) REVERT: G 311 HIS cc_start: 0.6748 (OUTLIER) cc_final: 0.5960 (p-80) outliers start: 173 outliers final: 140 residues processed: 273 average time/residue: 0.1055 time to fit residues: 48.2265 Evaluate side-chains 259 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 113 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 164 CYS Chi-restraints excluded: chain E residue 166 HIS Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 326 HIS Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 326 HIS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 TYR Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 326 HIS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 326 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 1 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 193 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 0.0270 chunk 72 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 231 HIS A 155 ASN A 302 ASN B 155 ASN C 155 ASN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C 319 ASN D 155 ASN ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN G 155 ASN G 231 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.228338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.208098 restraints weight = 22379.197| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 0.94 r_work: 0.4026 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3882 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19544 Z= 0.105 Angle : 0.605 13.854 26460 Z= 0.302 Chirality : 0.040 0.160 3045 Planarity : 0.006 0.094 3325 Dihedral : 4.999 37.309 2569 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 6.98 % Allowed : 31.25 % Favored : 61.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.17), residues: 2296 helix: -2.03 (0.14), residues: 1316 sheet: -0.97 (0.51), residues: 112 loop : -2.33 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 363 TYR 0.011 0.001 TYR G 82 PHE 0.018 0.001 PHE G 320 TRP 0.005 0.001 TRP G 100 HIS 0.005 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00256 (19530) covalent geometry : angle 0.60507 (26432) SS BOND : bond 0.00199 ( 14) SS BOND : angle 0.66166 ( 28) hydrogen bonds : bond 0.03058 ( 589) hydrogen bonds : angle 5.54815 ( 1662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 123 time to evaluate : 0.499 Fit side-chains REVERT: E 311 HIS cc_start: 0.6673 (OUTLIER) cc_final: 0.5728 (p-80) REVERT: A 234 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7252 (tt) REVERT: C 234 ILE cc_start: 0.7367 (OUTLIER) cc_final: 0.7066 (tt) REVERT: C 349 MET cc_start: 0.7342 (mtt) cc_final: 0.6657 (mtt) REVERT: D 234 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7235 (tt) REVERT: F 234 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7482 (tt) REVERT: F 245 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8017 (pp) REVERT: F 311 HIS cc_start: 0.6368 (OUTLIER) cc_final: 0.5448 (p-80) REVERT: G 234 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7129 (tt) REVERT: G 311 HIS cc_start: 0.6682 (OUTLIER) cc_final: 0.5624 (p-80) outliers start: 146 outliers final: 103 residues processed: 253 average time/residue: 0.1065 time to fit residues: 44.5332 Evaluate side-chains 233 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 121 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 TYR Chi-restraints excluded: chain E residue 166 HIS Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 326 HIS Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 326 HIS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 TYR Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 326 HIS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 326 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 112 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 221 optimal weight: 0.8980 chunk 214 optimal weight: 7.9990 chunk 190 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 17 optimal weight: 0.0870 chunk 89 optimal weight: 0.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN E 231 HIS A 155 ASN A 231 HIS ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 231 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.228308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.208281 restraints weight = 22597.910| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 0.90 r_work: 0.4041 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3905 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19544 Z= 0.107 Angle : 0.606 14.076 26460 Z= 0.299 Chirality : 0.039 0.143 3045 Planarity : 0.005 0.091 3325 Dihedral : 4.935 37.307 2569 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 6.59 % Allowed : 31.63 % Favored : 61.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.17), residues: 2296 helix: -1.98 (0.14), residues: 1316 sheet: -0.95 (0.51), residues: 112 loop : -2.32 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 230 TYR 0.011 0.001 TYR A 82 PHE 0.015 0.001 PHE G 320 TRP 0.006 0.001 TRP G 100 HIS 0.005 0.000 HIS G 231 Details of bonding type rmsd covalent geometry : bond 0.00264 (19530) covalent geometry : angle 0.60612 (26432) SS BOND : bond 0.00211 ( 14) SS BOND : angle 0.68245 ( 28) hydrogen bonds : bond 0.03024 ( 589) hydrogen bonds : angle 5.51023 ( 1662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 124 time to evaluate : 0.664 Fit side-chains REVERT: E 311 HIS cc_start: 0.6700 (OUTLIER) cc_final: 0.5754 (p-80) REVERT: A 234 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7293 (tt) REVERT: C 349 MET cc_start: 0.7382 (mtt) cc_final: 0.6684 (mtt) REVERT: D 234 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7227 (tt) REVERT: F 234 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7429 (tt) REVERT: F 245 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8062 (pp) REVERT: F 311 HIS cc_start: 0.6430 (OUTLIER) cc_final: 0.5422 (p-80) REVERT: G 234 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7093 (tt) REVERT: G 311 HIS cc_start: 0.6662 (OUTLIER) cc_final: 0.5600 (p-80) outliers start: 138 outliers final: 109 residues processed: 251 average time/residue: 0.1109 time to fit residues: 46.3303 Evaluate side-chains 238 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 121 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 TYR Chi-restraints excluded: chain E residue 155 ASN Chi-restraints excluded: chain E residue 164 CYS Chi-restraints excluded: chain E residue 166 HIS Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 326 HIS Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 326 HIS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 TYR Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 326 HIS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 326 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 77 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 216 optimal weight: 0.9980 chunk 156 optimal weight: 0.5980 chunk 152 optimal weight: 0.0870 chunk 184 optimal weight: 0.8980 chunk 108 optimal weight: 0.4980 chunk 22 optimal weight: 0.0970 chunk 8 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN E 231 HIS C 155 ASN C 231 HIS ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN G 155 ASN G 231 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.229660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.209624 restraints weight = 22647.523| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 0.93 r_work: 0.4048 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3920 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 19544 Z= 0.101 Angle : 0.603 14.985 26460 Z= 0.295 Chirality : 0.039 0.146 3045 Planarity : 0.005 0.088 3325 Dihedral : 4.848 37.126 2569 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 6.12 % Allowed : 32.25 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.17), residues: 2296 helix: -1.85 (0.15), residues: 1274 sheet: -0.85 (0.51), residues: 112 loop : -2.26 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 363 TYR 0.009 0.001 TYR A 82 PHE 0.017 0.001 PHE E 320 TRP 0.004 0.001 TRP G 100 HIS 0.009 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00247 (19530) covalent geometry : angle 0.60296 (26432) SS BOND : bond 0.00181 ( 14) SS BOND : angle 0.57722 ( 28) hydrogen bonds : bond 0.02908 ( 589) hydrogen bonds : angle 5.46980 ( 1662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 121 time to evaluate : 0.699 Fit side-chains REVERT: E 311 HIS cc_start: 0.6709 (OUTLIER) cc_final: 0.5702 (p-80) REVERT: A 234 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7200 (tt) REVERT: C 349 MET cc_start: 0.7338 (mtt) cc_final: 0.6653 (mtt) REVERT: D 128 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.7878 (mp) REVERT: D 223 LEU cc_start: 0.5894 (OUTLIER) cc_final: 0.5546 (mp) REVERT: F 234 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7297 (tt) REVERT: F 245 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7972 (pp) REVERT: F 311 HIS cc_start: 0.6402 (OUTLIER) cc_final: 0.5259 (p-80) REVERT: G 234 ILE cc_start: 0.7386 (OUTLIER) cc_final: 0.6992 (tt) REVERT: G 311 HIS cc_start: 0.6681 (OUTLIER) cc_final: 0.5593 (p-80) outliers start: 128 outliers final: 103 residues processed: 236 average time/residue: 0.1126 time to fit residues: 44.0315 Evaluate side-chains 233 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 121 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 TYR Chi-restraints excluded: chain E residue 164 CYS Chi-restraints excluded: chain E residue 166 HIS Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 326 HIS Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 326 HIS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 TYR Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 326 HIS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 326 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 154 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 147 optimal weight: 0.3980 chunk 83 optimal weight: 0.6980 chunk 96 optimal weight: 8.9990 chunk 185 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 152 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 231 HIS B 155 ASN C 155 ASN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN F 155 ASN G 155 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.229624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.209826 restraints weight = 22528.197| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 0.93 r_work: 0.4046 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3887 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19544 Z= 0.101 Angle : 0.609 15.199 26460 Z= 0.296 Chirality : 0.039 0.147 3045 Planarity : 0.005 0.087 3325 Dihedral : 4.805 36.821 2569 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 6.21 % Allowed : 32.11 % Favored : 61.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.17), residues: 2296 helix: -1.84 (0.15), residues: 1316 sheet: -0.47 (0.52), residues: 105 loop : -2.31 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 363 TYR 0.009 0.001 TYR A 82 PHE 0.015 0.001 PHE E 320 TRP 0.005 0.001 TRP G 100 HIS 0.006 0.000 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00252 (19530) covalent geometry : angle 0.60900 (26432) SS BOND : bond 0.00189 ( 14) SS BOND : angle 0.59840 ( 28) hydrogen bonds : bond 0.02872 ( 589) hydrogen bonds : angle 5.42060 ( 1662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 123 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: E 311 HIS cc_start: 0.6615 (OUTLIER) cc_final: 0.5604 (p-80) REVERT: A 234 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7231 (tt) REVERT: C 234 ILE cc_start: 0.7367 (OUTLIER) cc_final: 0.7055 (tt) REVERT: C 349 MET cc_start: 0.7355 (mtt) cc_final: 0.7140 (mtt) REVERT: D 128 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7884 (mp) REVERT: F 234 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7337 (tt) REVERT: F 245 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8029 (pp) REVERT: F 311 HIS cc_start: 0.6319 (OUTLIER) cc_final: 0.5178 (p-80) REVERT: G 234 ILE cc_start: 0.7391 (OUTLIER) cc_final: 0.6976 (tt) REVERT: G 311 HIS cc_start: 0.6620 (OUTLIER) cc_final: 0.5516 (p-80) outliers start: 130 outliers final: 108 residues processed: 239 average time/residue: 0.1083 time to fit residues: 42.9100 Evaluate side-chains 238 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 121 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 TYR Chi-restraints excluded: chain E residue 164 CYS Chi-restraints excluded: chain E residue 166 HIS Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 326 HIS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 TYR Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 326 HIS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 326 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 130 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 48 optimal weight: 0.0020 chunk 102 optimal weight: 0.0010 chunk 38 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 178 optimal weight: 8.9990 chunk 170 optimal weight: 1.9990 chunk 8 optimal weight: 0.0670 chunk 125 optimal weight: 4.9990 overall best weight: 0.3732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 155 ASN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN G 155 ASN G 231 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.229961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.210660 restraints weight = 22718.838| |-----------------------------------------------------------------------------| r_work (start): 0.4329 rms_B_bonded: 0.95 r_work: 0.4057 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work: 0.3881 rms_B_bonded: 4.76 restraints_weight: 0.1250 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 19544 Z= 0.099 Angle : 0.609 15.690 26460 Z= 0.293 Chirality : 0.039 0.148 3045 Planarity : 0.005 0.088 3325 Dihedral : 4.745 36.871 2569 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 5.73 % Allowed : 32.35 % Favored : 61.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.17), residues: 2296 helix: -1.76 (0.15), residues: 1316 sheet: -0.42 (0.52), residues: 105 loop : -2.29 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 363 TYR 0.008 0.001 TYR A 82 PHE 0.013 0.001 PHE E 320 TRP 0.003 0.001 TRP G 100 HIS 0.010 0.000 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00242 (19530) covalent geometry : angle 0.60912 (26432) SS BOND : bond 0.00171 ( 14) SS BOND : angle 0.54708 ( 28) hydrogen bonds : bond 0.02764 ( 589) hydrogen bonds : angle 5.39317 ( 1662) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 127 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: E 311 HIS cc_start: 0.6735 (OUTLIER) cc_final: 0.5734 (p-80) REVERT: A 234 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7367 (tt) REVERT: B 251 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8382 (t) REVERT: C 349 MET cc_start: 0.7376 (mtt) cc_final: 0.7151 (mtt) REVERT: D 128 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.7923 (mp) REVERT: F 234 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7373 (tt) REVERT: F 311 HIS cc_start: 0.6466 (OUTLIER) cc_final: 0.5332 (p-80) REVERT: G 234 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7080 (tt) REVERT: G 311 HIS cc_start: 0.6761 (OUTLIER) cc_final: 0.5678 (p-80) outliers start: 120 outliers final: 100 residues processed: 234 average time/residue: 0.1126 time to fit residues: 43.3713 Evaluate side-chains 229 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 121 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 TYR Chi-restraints excluded: chain E residue 164 CYS Chi-restraints excluded: chain E residue 166 HIS Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 326 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 326 HIS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 TYR Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 326 HIS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 326 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 115 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 197 optimal weight: 20.0000 chunk 67 optimal weight: 0.0670 chunk 69 optimal weight: 0.5980 chunk 192 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 170 optimal weight: 0.6980 chunk 219 optimal weight: 0.0770 chunk 168 optimal weight: 0.6980 chunk 148 optimal weight: 6.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN C 155 ASN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 ASN G 231 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.230934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.211278 restraints weight = 22659.535| |-----------------------------------------------------------------------------| r_work (start): 0.4331 rms_B_bonded: 1.00 r_work: 0.4055 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3923 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 19544 Z= 0.099 Angle : 0.617 15.584 26460 Z= 0.294 Chirality : 0.039 0.206 3045 Planarity : 0.005 0.087 3325 Dihedral : 4.699 36.518 2569 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 5.69 % Allowed : 32.58 % Favored : 61.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.17), residues: 2296 helix: -1.70 (0.15), residues: 1316 sheet: -0.45 (0.52), residues: 105 loop : -2.28 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 230 TYR 0.008 0.001 TYR A 82 PHE 0.017 0.001 PHE F 320 TRP 0.004 0.001 TRP G 100 HIS 0.005 0.000 HIS G 231 Details of bonding type rmsd covalent geometry : bond 0.00243 (19530) covalent geometry : angle 0.61741 (26432) SS BOND : bond 0.00171 ( 14) SS BOND : angle 0.54032 ( 28) hydrogen bonds : bond 0.02692 ( 589) hydrogen bonds : angle 5.36075 ( 1662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4045.75 seconds wall clock time: 70 minutes 34.77 seconds (4234.77 seconds total)