Starting phenix.real_space_refine on Tue Aug 26 20:37:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cz1_46056/08_2025/9cz1_46056.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cz1_46056/08_2025/9cz1_46056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cz1_46056/08_2025/9cz1_46056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cz1_46056/08_2025/9cz1_46056.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cz1_46056/08_2025/9cz1_46056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cz1_46056/08_2025/9cz1_46056.map" } resolution = 3.5 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= -0.001 sd= 0.016 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: 5 Type Number sf(0) Gaussians S 82 5.16 5 C 12697 2.51 5 N 3726 2.21 5 O 3978 1.98 5 H 20108 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40591 Number of models: 1 Model: "" Number of chains: 24 Chain: "XA" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1760 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "XB" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1780 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "XC" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1760 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "XD" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1780 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "XE" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1760 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "XF" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1780 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "XG" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1745 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "XH" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1734 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "XI" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1760 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "XJ" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1780 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "XK" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1760 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "XL" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1780 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "XM" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1760 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "XN" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1780 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "XO" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1743 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "XP" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1780 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "XQ" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1745 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "XR" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1724 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "XS" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1655 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "XT" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1580 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "XU" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1449 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "XV" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1339 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "XW" Number of atoms: 1212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1212 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "XX" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1645 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 7.18, per 1000 atoms: 0.18 Number of scatterers: 40591 At special positions: 0 Unit cell: (148.785, 156.96, 132.435, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 O 3978 8.00 N 3726 7.00 C 12697 6.00 H 20108 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 816.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4876 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 9 sheets defined 82.6% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'XA' and resid 246 through 318 Proline residue: XA 277 - end of helix Proline residue: XA 313 - end of helix Processing helix chain 'XA' and resid 318 through 336 Processing helix chain 'XB' and resid 218 through 288 removed outlier: 3.510A pdb=" N ALAXB 233 " --> pdb=" O ALAXB 229 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VALXB 234 " --> pdb=" O GLUXB 230 " (cutoff:3.500A) Processing helix chain 'XB' and resid 290 through 308 Processing helix chain 'XC' and resid 247 through 316 removed outlier: 4.045A pdb=" N GLNXC 262 " --> pdb=" O ARGXC 258 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLNXC 263 " --> pdb=" O GLUXC 259 " (cutoff:3.500A) Proline residue: XC 277 - end of helix Proline residue: XC 313 - end of helix Processing helix chain 'XC' and resid 318 through 338 Processing helix chain 'XD' and resid 218 through 288 removed outlier: 3.531A pdb=" N ASNXD 225 " --> pdb=" O GLUXD 221 " (cutoff:3.500A) Processing helix chain 'XD' and resid 290 through 307 Processing helix chain 'XD' and resid 321 through 325 removed outlier: 4.527A pdb=" N TYRXD 325 " --> pdb=" O PHEXD 322 " (cutoff:3.500A) Processing helix chain 'XE' and resid 247 through 318 removed outlier: 3.561A pdb=" N GLNXE 262 " --> pdb=" O ARGXE 258 " (cutoff:3.500A) Proline residue: XE 277 - end of helix Proline residue: XE 313 - end of helix removed outlier: 3.583A pdb=" N ALAXE 318 " --> pdb=" O GLUXE 314 " (cutoff:3.500A) Processing helix chain 'XE' and resid 318 through 337 removed outlier: 3.641A pdb=" N LYSXE 333 " --> pdb=" O GLUXE 329 " (cutoff:3.500A) Processing helix chain 'XF' and resid 218 through 288 removed outlier: 3.532A pdb=" N VALXF 234 " --> pdb=" O GLUXF 230 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLYXF 275 " --> pdb=" O METXF 271 " (cutoff:3.500A) Processing helix chain 'XF' and resid 290 through 307 Processing helix chain 'XF' and resid 320 through 324 Processing helix chain 'XG' and resid 248 through 318 removed outlier: 3.645A pdb=" N ASPXG 252 " --> pdb=" O LYSXG 248 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASPXG 253 " --> pdb=" O ALAXG 249 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILEXG 265 " --> pdb=" O GLUXG 261 " (cutoff:3.500A) Proline residue: XG 277 - end of helix Proline residue: XG 313 - end of helix Processing helix chain 'XG' and resid 318 through 337 Processing helix chain 'XH' and resid 221 through 288 Processing helix chain 'XH' and resid 290 through 307 Processing helix chain 'XI' and resid 247 through 318 removed outlier: 3.501A pdb=" N TYRXI 271 " --> pdb=" O GLUXI 267 " (cutoff:3.500A) Proline residue: XI 277 - end of helix removed outlier: 3.599A pdb=" N ILEXI 286 " --> pdb=" O GLNXI 282 " (cutoff:3.500A) Proline residue: XI 313 - end of helix removed outlier: 3.649A pdb=" N ALAXI 317 " --> pdb=" O PROXI 313 " (cutoff:3.500A) Processing helix chain 'XI' and resid 318 through 338 Processing helix chain 'XJ' and resid 218 through 288 removed outlier: 3.524A pdb=" N ALAXJ 222 " --> pdb=" O GLUXJ 218 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYRXJ 224 " --> pdb=" O SERXJ 220 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASNXJ 225 " --> pdb=" O GLUXJ 221 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLUXJ 230 " --> pdb=" O ARGXJ 226 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARGXJ 231 " --> pdb=" O METXJ 227 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLUXJ 232 " --> pdb=" O ARGXJ 228 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALAXJ 233 " --> pdb=" O ALAXJ 229 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLNXJ 243 " --> pdb=" O ARGXJ 239 " (cutoff:3.500A) Processing helix chain 'XJ' and resid 290 through 307 Processing helix chain 'XJ' and resid 321 through 327 removed outlier: 4.445A pdb=" N TYRXJ 325 " --> pdb=" O PHEXJ 322 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYSXJ 327 " --> pdb=" O ARGXJ 324 " (cutoff:3.500A) Processing helix chain 'XK' and resid 247 through 318 removed outlier: 3.500A pdb=" N ALAXK 254 " --> pdb=" O ALAXK 250 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLUXK 259 " --> pdb=" O ILEXK 255 " (cutoff:3.500A) Proline residue: XK 277 - end of helix Proline residue: XK 313 - end of helix Processing helix chain 'XK' and resid 318 through 338 removed outlier: 3.726A pdb=" N ASNXK 337 " --> pdb=" O LYSXK 333 " (cutoff:3.500A) Processing helix chain 'XL' and resid 219 through 288 Processing helix chain 'XL' and resid 290 through 307 removed outlier: 3.506A pdb=" N TYRXL 294 " --> pdb=" O ASPXL 290 " (cutoff:3.500A) Processing helix chain 'XL' and resid 320 through 327 removed outlier: 4.907A pdb=" N TYRXL 325 " --> pdb=" O PHEXL 322 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYSXL 327 " --> pdb=" O ARGXL 324 " (cutoff:3.500A) Processing helix chain 'XM' and resid 247 through 318 removed outlier: 3.866A pdb=" N ILEXM 255 " --> pdb=" O PHEXM 251 " (cutoff:3.500A) Proline residue: XM 277 - end of helix Proline residue: XM 313 - end of helix Processing helix chain 'XM' and resid 318 through 337 removed outlier: 3.741A pdb=" N LYSXM 333 " --> pdb=" O GLUXM 329 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VALXM 334 " --> pdb=" O THRXM 330 " (cutoff:3.500A) Processing helix chain 'XN' and resid 218 through 288 Processing helix chain 'XN' and resid 290 through 307 Processing helix chain 'XN' and resid 321 through 327 removed outlier: 4.488A pdb=" N TYRXN 325 " --> pdb=" O PHEXN 322 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYSXN 327 " --> pdb=" O ARGXN 324 " (cutoff:3.500A) Processing helix chain 'XO' and resid 248 through 318 removed outlier: 3.690A pdb=" N GLUXO 259 " --> pdb=" O ILEXO 255 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILEXO 265 " --> pdb=" O GLUXO 261 " (cutoff:3.500A) Proline residue: XO 277 - end of helix removed outlier: 3.639A pdb=" N ILEXO 286 " --> pdb=" O GLNXO 282 " (cutoff:3.500A) Proline residue: XO 313 - end of helix removed outlier: 3.632A pdb=" N ALAXO 318 " --> pdb=" O GLUXO 314 " (cutoff:3.500A) Processing helix chain 'XO' and resid 318 through 337 removed outlier: 3.596A pdb=" N ASNXO 337 " --> pdb=" O LYSXO 333 " (cutoff:3.500A) Processing helix chain 'XP' and resid 218 through 289 removed outlier: 3.670A pdb=" N ASNXP 225 " --> pdb=" O GLUXP 221 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALAXP 286 " --> pdb=" O LEUXP 282 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYSXP 289 " --> pdb=" O ASPXP 285 " (cutoff:3.500A) Processing helix chain 'XP' and resid 290 through 307 Processing helix chain 'XP' and resid 320 through 324 Processing helix chain 'XQ' and resid 248 through 318 Proline residue: XQ 277 - end of helix Proline residue: XQ 313 - end of helix Processing helix chain 'XQ' and resid 318 through 336 Processing helix chain 'XR' and resid 222 through 288 removed outlier: 3.637A pdb=" N VALXR 234 " --> pdb=" O GLUXR 230 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALAXR 235 " --> pdb=" O ARGXR 231 " (cutoff:3.500A) Processing helix chain 'XR' and resid 290 through 307 Processing helix chain 'XS' and resid 254 through 318 Proline residue: XS 277 - end of helix Proline residue: XS 313 - end of helix removed outlier: 3.514A pdb=" N ALAXS 317 " --> pdb=" O PROXS 313 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALAXS 318 " --> pdb=" O GLUXS 314 " (cutoff:3.500A) Processing helix chain 'XS' and resid 318 through 338 Processing helix chain 'XT' and resid 230 through 288 Processing helix chain 'XT' and resid 290 through 307 Processing helix chain 'XU' and resid 267 through 312 removed outlier: 3.990A pdb=" N VALXU 275 " --> pdb=" O TYRXU 271 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLNXU 276 " --> pdb=" O THRXU 272 " (cutoff:3.500A) Proline residue: XU 277 - end of helix removed outlier: 3.531A pdb=" N ILEXU 286 " --> pdb=" O GLNXU 282 " (cutoff:3.500A) Processing helix chain 'XU' and resid 312 through 318 removed outlier: 4.117A pdb=" N ALAXU 317 " --> pdb=" O PROXU 313 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALAXU 318 " --> pdb=" O GLUXU 314 " (cutoff:3.500A) Processing helix chain 'XU' and resid 318 through 337 Processing helix chain 'XV' and resid 245 through 289 removed outlier: 3.669A pdb=" N LYSXV 289 " --> pdb=" O ASPXV 285 " (cutoff:3.500A) Processing helix chain 'XV' and resid 290 through 308 Processing helix chain 'XV' and resid 320 through 327 removed outlier: 4.646A pdb=" N TYRXV 325 " --> pdb=" O PHEXV 322 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYSXV 327 " --> pdb=" O ARGXV 324 " (cutoff:3.500A) Processing helix chain 'XW' and resid 283 through 318 removed outlier: 3.728A pdb=" N TYRXW 293 " --> pdb=" O GLUXW 289 " (cutoff:3.500A) Proline residue: XW 313 - end of helix Processing helix chain 'XW' and resid 318 through 338 removed outlier: 3.920A pdb=" N ASNXW 337 " --> pdb=" O LYSXW 333 " (cutoff:3.500A) Processing helix chain 'XX' and resid 226 through 288 removed outlier: 3.585A pdb=" N GLYXX 242 " --> pdb=" O HISXX 238 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASPXX 276 " --> pdb=" O ARGXX 272 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYSXX 281 " --> pdb=" O ALAXX 277 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEUXX 282 " --> pdb=" O GLUXX 278 " (cutoff:3.500A) Processing helix chain 'XX' and resid 290 through 307 Processing helix chain 'XX' and resid 320 through 327 removed outlier: 4.714A pdb=" N TYRXX 325 " --> pdb=" O PHEXX 322 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYSXX 327 " --> pdb=" O ARGXX 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'XC' and resid 339 through 340 removed outlier: 6.423A pdb=" N ARGXC 339 " --> pdb=" O METXD 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'XE' and resid 349 through 350 Processing sheet with id=AA3, first strand: chain 'XG' and resid 339 through 340 removed outlier: 6.545A pdb=" N ARGXG 339 " --> pdb=" O METXH 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'XK' and resid 339 through 340 removed outlier: 6.597A pdb=" N ARGXK 339 " --> pdb=" O METXL 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'XQ' and resid 339 through 340 removed outlier: 6.488A pdb=" N ARGXQ 339 " --> pdb=" O METXR 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'XQ' and resid 350 through 351 removed outlier: 7.227A pdb=" N LEUXQ 350 " --> pdb=" O METXS 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'XS' and resid 339 through 340 removed outlier: 6.123A pdb=" N ARGXS 339 " --> pdb=" O METXT 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'XU' and resid 339 through 340 removed outlier: 6.479A pdb=" N ARGXU 339 " --> pdb=" O METXV 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'XW' and resid 339 through 340 removed outlier: 6.625A pdb=" N ARGXW 339 " --> pdb=" O METXX 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 1760 hydrogen bonds defined for protein. 5226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.42 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20108 1.03 - 1.22: 0 1.22 - 1.42: 8784 1.42 - 1.61: 11824 1.61 - 1.81: 164 Bond restraints: 40880 Sorted by residual: bond pdb=" C LEUXC 312 " pdb=" N PROXC 313 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.87e+00 bond pdb=" C ASPXR 290 " pdb=" N PROXR 291 " ideal model delta sigma weight residual 1.336 1.354 -0.019 1.23e-02 6.61e+03 2.27e+00 bond pdb=" C VALXE 352 " pdb=" N LEUXE 353 " ideal model delta sigma weight residual 1.331 1.361 -0.030 2.07e-02 2.33e+03 2.06e+00 bond pdb=" CB ARGXX 239 " pdb=" CG ARGXX 239 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 2.00e+00 bond pdb=" C GLNXU 276 " pdb=" N PROXU 277 " ideal model delta sigma weight residual 1.334 1.355 -0.021 1.51e-02 4.39e+03 1.85e+00 ... (remaining 40875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 72319 1.98 - 3.97: 1070 3.97 - 5.95: 109 5.95 - 7.94: 11 7.94 - 9.92: 1 Bond angle restraints: 73510 Sorted by residual: angle pdb=" CA LYSXW 346 " pdb=" CB LYSXW 346 " pdb=" CG LYSXW 346 " ideal model delta sigma weight residual 114.10 121.46 -7.36 2.00e+00 2.50e-01 1.35e+01 angle pdb=" N LEUXC 311 " pdb=" CA LEUXC 311 " pdb=" C LEUXC 311 " ideal model delta sigma weight residual 111.02 114.75 -3.73 1.22e+00 6.72e-01 9.33e+00 angle pdb=" CA LEUXW 350 " pdb=" CB LEUXW 350 " pdb=" CG LEUXW 350 " ideal model delta sigma weight residual 116.30 126.22 -9.92 3.50e+00 8.16e-02 8.04e+00 angle pdb=" N LEUXS 312 " pdb=" CA LEUXS 312 " pdb=" C LEUXS 312 " ideal model delta sigma weight residual 109.81 115.82 -6.01 2.21e+00 2.05e-01 7.40e+00 angle pdb=" N ASNXM 349 " pdb=" CA ASNXM 349 " pdb=" C ASNXM 349 " ideal model delta sigma weight residual 110.80 105.09 5.71 2.13e+00 2.20e-01 7.20e+00 ... (remaining 73505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 17662 17.96 - 35.92: 1050 35.92 - 53.88: 287 53.88 - 71.84: 101 71.84 - 89.81: 23 Dihedral angle restraints: 19123 sinusoidal: 10587 harmonic: 8536 Sorted by residual: dihedral pdb=" CB GLUXN 218 " pdb=" CG GLUXN 218 " pdb=" CD GLUXN 218 " pdb=" OE1 GLUXN 218 " ideal model delta sinusoidal sigma weight residual 0.00 89.81 -89.81 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLUXX 247 " pdb=" CG GLUXX 247 " pdb=" CD GLUXX 247 " pdb=" OE1 GLUXX 247 " ideal model delta sinusoidal sigma weight residual 0.00 89.77 -89.77 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLUXH 247 " pdb=" CG GLUXH 247 " pdb=" CD GLUXH 247 " pdb=" OE1 GLUXH 247 " ideal model delta sinusoidal sigma weight residual 0.00 87.20 -87.20 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 19120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2385 0.038 - 0.076: 361 0.076 - 0.115: 180 0.115 - 0.153: 28 0.153 - 0.191: 1 Chirality restraints: 2955 Sorted by residual: chirality pdb=" CA LYSXW 346 " pdb=" N LYSXW 346 " pdb=" C LYSXW 346 " pdb=" CB LYSXW 346 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CA VALXN 313 " pdb=" N VALXN 313 " pdb=" C VALXN 313 " pdb=" CB VALXN 313 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CA GLNXU 276 " pdb=" N GLNXU 276 " pdb=" C GLNXU 276 " pdb=" CB GLNXU 276 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 2952 not shown) Planarity restraints: 6223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASPXW 345 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" C ASPXW 345 " 0.045 2.00e-02 2.50e+03 pdb=" O ASPXW 345 " -0.017 2.00e-02 2.50e+03 pdb=" N LYSXW 346 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEUXS 353 " -0.042 5.00e-02 4.00e+02 6.22e-02 6.20e+00 pdb=" N PROXS 354 " 0.108 5.00e-02 4.00e+02 pdb=" CA PROXS 354 " -0.032 5.00e-02 4.00e+02 pdb=" CD PROXS 354 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEUXE 312 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PROXE 313 " -0.097 5.00e-02 4.00e+02 pdb=" CA PROXE 313 " 0.028 5.00e-02 4.00e+02 pdb=" CD PROXE 313 " 0.032 5.00e-02 4.00e+02 ... (remaining 6220 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 4380 2.26 - 2.85: 92606 2.85 - 3.43: 107283 3.43 - 4.02: 138672 4.02 - 4.60: 216605 Nonbonded interactions: 559546 Sorted by model distance: nonbonded pdb=" OE1 GLNXA 262 " pdb="HH22 ARGXX 226 " model vdw 1.678 2.450 nonbonded pdb=" O LEUXO 335 " pdb=" HZ2 LYSXO 340 " model vdw 1.705 2.450 nonbonded pdb=" O LEUXS 335 " pdb=" HZ2 LYSXS 340 " model vdw 1.720 2.450 nonbonded pdb=" O ASPXV 285 " pdb=" HG SERXV 288 " model vdw 1.721 2.450 nonbonded pdb=" O LEUXA 335 " pdb=" HZ2 LYSXA 340 " model vdw 1.722 2.450 ... (remaining 559541 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'XA' and (resid 253 through 306 or (resid 307 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name NE or name CZ or name N \ H1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name \ HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 308 \ through 355)) selection = (chain 'XC' and (resid 253 through 306 or (resid 307 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name NE or name CZ or name N \ H1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name \ HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 308 \ through 355)) selection = (chain 'XE' and (resid 253 through 306 or (resid 307 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name NE or name CZ or name N \ H1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name \ HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 308 \ through 355)) selection = (chain 'XG' and (resid 253 through 306 or (resid 307 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name NE or name CZ or name N \ H1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name \ HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 308 \ through 355)) selection = (chain 'XI' and (resid 253 through 306 or (resid 307 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name NE or name CZ or name N \ H1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name \ HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 308 \ through 355)) selection = (chain 'XK' and (resid 253 through 306 or (resid 307 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name NE or name CZ or name N \ H1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name \ HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 308 \ through 355)) selection = (chain 'XM' and (resid 253 through 306 or (resid 307 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name NE or name CZ or name N \ H1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name \ HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 308 \ through 355)) selection = (chain 'XO' and resid 253 through 355) selection = (chain 'XQ' and (resid 253 through 306 or (resid 307 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name NE or name CZ or name N \ H1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name \ HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 308 \ through 355)) selection = (chain 'XS' and (resid 253 through 306 or (resid 307 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name NE or name CZ or name N \ H1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name \ HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 308 \ through 355)) } ncs_group { reference = (chain 'XB' and (resid 229 through 266 or (resid 267 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21)) or \ resid 268 through 277 or (resid 278 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 279 through 291 or (resid 292 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 293 through 329)) selection = (chain 'XD' and (resid 229 through 266 or (resid 267 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21)) or \ resid 268 through 277 or (resid 278 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 279 through 291 or (resid 292 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 293 through 329)) selection = (chain 'XF' and (resid 229 through 266 or (resid 267 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21)) or \ resid 268 through 277 or (resid 278 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 279 through 291 or (resid 292 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 293 through 329)) selection = (chain 'XH' and (resid 229 through 277 or (resid 278 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 279 through 291 or ( \ resid 292 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 293 through 329)) selection = (chain 'XJ' and (resid 229 through 266 or (resid 267 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21)) or \ resid 268 through 277 or (resid 278 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 279 through 291 or (resid 292 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 293 through 329)) selection = (chain 'XL' and (resid 229 through 266 or (resid 267 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21)) or \ resid 268 through 277 or (resid 278 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 279 through 291 or (resid 292 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 293 through 329)) selection = (chain 'XN' and (resid 229 through 266 or (resid 267 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21)) or \ resid 268 through 277 or (resid 278 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 279 through 291 or (resid 292 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 293 through 329)) selection = (chain 'XP' and (resid 229 through 266 or (resid 267 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21)) or \ resid 268 through 277 or (resid 278 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 279 through 291 or (resid 292 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 293 through 329)) selection = (chain 'XR' and (resid 229 through 266 or (resid 267 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21)) or \ resid 268 through 277 or (resid 278 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 279 through 291 or (resid 292 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 293 through 329)) selection = (chain 'XT' and (resid 229 through 266 or (resid 267 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21)) or \ resid 268 through 277 or (resid 278 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 279 through 291 or (resid 292 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 293 through 329)) selection = (chain 'XX' and (resid 229 through 266 or (resid 267 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21)) or \ resid 268 through 329)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.680 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: 0.220 Extract box with map and model: 0.540 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 32.960 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5521 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20772 Z= 0.181 Angle : 0.667 9.925 27904 Z= 0.385 Chirality : 0.036 0.191 2955 Planarity : 0.005 0.062 3774 Dihedral : 12.131 89.805 8081 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.15), residues: 2508 helix: -0.52 (0.10), residues: 1976 sheet: None (None), residues: 0 loop : -2.70 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGXX 239 TYR 0.008 0.001 TYRXK 271 PHE 0.016 0.001 PHEXX 307 HIS 0.001 0.000 HISXL 238 Details of bonding type rmsd covalent geometry : bond 0.00361 (20772) covalent geometry : angle 0.66717 (27904) hydrogen bonds : bond 0.22206 ( 1760) hydrogen bonds : angle 5.72078 ( 5226) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 310 is missing expected H atoms. Skipping. Evaluate side-chains 1014 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1014 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: XA 253 ASP cc_start: 0.8143 (m-30) cc_final: 0.7893 (m-30) REVERT: XA 338 THR cc_start: 0.3773 (p) cc_final: 0.3487 (p) REVERT: XB 258 THR cc_start: 0.6997 (m) cc_final: 0.6596 (m) REVERT: XB 293 PHE cc_start: 0.6054 (t80) cc_final: 0.5767 (t80) REVERT: XB 314 MET cc_start: 0.6637 (mtp) cc_final: 0.6430 (mtp) REVERT: XC 315 TYR cc_start: 0.4618 (t80) cc_final: 0.4345 (t80) REVERT: XD 314 MET cc_start: 0.6796 (mtp) cc_final: 0.6273 (mtp) REVERT: XD 315 VAL cc_start: 0.6709 (t) cc_final: 0.6223 (t) REVERT: XE 293 TYR cc_start: 0.4525 (t80) cc_final: 0.4196 (t80) REVERT: XE 320 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7601 (pm20) REVERT: XE 324 GLU cc_start: 0.7693 (tp30) cc_final: 0.7077 (mt-10) REVERT: XE 328 ILE cc_start: 0.7939 (mt) cc_final: 0.7616 (mt) REVERT: XF 241 GLN cc_start: 0.5959 (mt0) cc_final: 0.5757 (tm-30) REVERT: XF 315 VAL cc_start: 0.7578 (t) cc_final: 0.7223 (t) REVERT: XG 260 ASN cc_start: 0.7719 (m-40) cc_final: 0.7300 (m110) REVERT: XG 324 GLU cc_start: 0.7361 (tp30) cc_final: 0.7012 (mt-10) REVERT: XG 328 ILE cc_start: 0.7418 (mt) cc_final: 0.7083 (mt) REVERT: XI 288 GLU cc_start: 0.4236 (mm-30) cc_final: 0.3575 (tp30) REVERT: XI 324 GLU cc_start: 0.6032 (tp30) cc_final: 0.5480 (mm-30) REVERT: XI 328 ILE cc_start: 0.6483 (mt) cc_final: 0.6161 (mt) REVERT: XI 330 THR cc_start: 0.7204 (m) cc_final: 0.6843 (m) REVERT: XK 251 PHE cc_start: 0.7295 (m-10) cc_final: 0.6947 (m-10) REVERT: XK 344 ASN cc_start: 0.7382 (m-40) cc_final: 0.7126 (p0) REVERT: XK 350 LEU cc_start: 0.8447 (mp) cc_final: 0.8158 (mt) REVERT: XL 265 GLU cc_start: 0.6757 (tp30) cc_final: 0.5384 (tm-30) REVERT: XL 292 ASP cc_start: 0.7498 (m-30) cc_final: 0.7192 (p0) REVERT: XM 323 ARG cc_start: 0.7296 (ttt90) cc_final: 0.6947 (mmt90) REVERT: XM 338 THR cc_start: 0.5389 (p) cc_final: 0.4086 (p) REVERT: XN 312 ASP cc_start: 0.5240 (m-30) cc_final: 0.5027 (m-30) REVERT: XP 248 LYS cc_start: 0.7028 (mttt) cc_final: 0.6632 (mttm) REVERT: XQ 265 ILE cc_start: 0.8556 (mt) cc_final: 0.8333 (mm) REVERT: XQ 275 VAL cc_start: 0.8250 (t) cc_final: 0.8034 (t) REVERT: XQ 321 ILE cc_start: 0.6725 (mm) cc_final: 0.6215 (mt) REVERT: XQ 331 MET cc_start: 0.5162 (tpp) cc_final: 0.4860 (mmt) REVERT: XQ 350 LEU cc_start: 0.9083 (mt) cc_final: 0.8847 (mp) REVERT: XR 244 GLU cc_start: 0.8192 (tt0) cc_final: 0.7938 (tt0) REVERT: XR 265 GLU cc_start: 0.7437 (tp30) cc_final: 0.6966 (tm-30) REVERT: XR 313 VAL cc_start: 0.6037 (t) cc_final: 0.5768 (m) REVERT: XS 335 LEU cc_start: 0.6487 (mt) cc_final: 0.6286 (mt) REVERT: XT 265 GLU cc_start: 0.8502 (tp30) cc_final: 0.7837 (tp30) REVERT: XT 299 SER cc_start: 0.8794 (t) cc_final: 0.8131 (p) REVERT: XV 247 GLU cc_start: 0.6295 (mm-30) cc_final: 0.5626 (tm-30) REVERT: XW 288 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6572 (mm-30) REVERT: XW 321 ILE cc_start: 0.7647 (mm) cc_final: 0.7271 (mt) REVERT: XW 345 ASP cc_start: 0.7384 (m-30) cc_final: 0.7117 (m-30) REVERT: XX 227 MET cc_start: 0.4337 (mtt) cc_final: 0.3991 (mmp) REVERT: XX 293 PHE cc_start: 0.5743 (t80) cc_final: 0.4924 (t80) outliers start: 0 outliers final: 0 residues processed: 1014 average time/residue: 0.4777 time to fit residues: 663.4430 Evaluate side-chains 642 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 642 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.2980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 247 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: XA 302 GLN XA 337 ASN XB 225 ASN XB 305 ASN XB 310 ASN XC 263 GLN XC 280 ASN XE 276 GLN XI 344 ASN XK 349 ASN XM 280 ASN ** XO 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XO 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** XQ 262 GLN XQ 296 GLN XR 243 GLN ** XS 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** XU 282 GLN ** XU 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.109602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.088263 restraints weight = 149523.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.092449 restraints weight = 44918.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.094946 restraints weight = 22365.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.096378 restraints weight = 15358.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.097167 restraints weight = 12570.116| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6008 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20772 Z= 0.217 Angle : 0.637 6.152 27904 Z= 0.357 Chirality : 0.035 0.147 2955 Planarity : 0.006 0.103 3774 Dihedral : 2.899 17.196 2910 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.18 % Allowed : 14.85 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.16), residues: 2508 helix: 1.65 (0.10), residues: 1959 sheet: None (None), residues: 0 loop : -2.29 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARGXE 258 TYR 0.025 0.002 TYRXH 294 PHE 0.028 0.002 PHEXD 296 HIS 0.018 0.002 HISXL 238 Details of bonding type rmsd covalent geometry : bond 0.00409 (20772) covalent geometry : angle 0.63684 (27904) hydrogen bonds : bond 0.08411 ( 1760) hydrogen bonds : angle 4.92824 ( 5226) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 310 is missing expected H atoms. Skipping. Evaluate side-chains 758 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 713 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: XA 324 GLU cc_start: 0.8083 (tp30) cc_final: 0.7007 (mm-30) REVERT: XC 324 GLU cc_start: 0.7981 (tp30) cc_final: 0.7620 (tp30) REVERT: XD 314 MET cc_start: 0.6823 (mtp) cc_final: 0.6370 (mtp) REVERT: XD 315 VAL cc_start: 0.6921 (t) cc_final: 0.6446 (t) REVERT: XE 320 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7558 (pm20) REVERT: XE 324 GLU cc_start: 0.7722 (tp30) cc_final: 0.7059 (mt-10) REVERT: XE 328 ILE cc_start: 0.7810 (mt) cc_final: 0.7486 (mt) REVERT: XF 307 PHE cc_start: 0.7925 (m-80) cc_final: 0.7567 (m-80) REVERT: XF 315 VAL cc_start: 0.7646 (t) cc_final: 0.7377 (t) REVERT: XG 324 GLU cc_start: 0.7708 (tp30) cc_final: 0.7243 (mt-10) REVERT: XG 328 ILE cc_start: 0.7418 (mt) cc_final: 0.7164 (mt) REVERT: XG 331 MET cc_start: 0.5523 (mmt) cc_final: 0.5237 (mmt) REVERT: XI 324 GLU cc_start: 0.6303 (tp30) cc_final: 0.5665 (mm-30) REVERT: XI 328 ILE cc_start: 0.6727 (mt) cc_final: 0.6445 (mt) REVERT: XK 293 TYR cc_start: 0.7802 (t80) cc_final: 0.7590 (t80) REVERT: XK 300 GLU cc_start: 0.6622 (mt-10) cc_final: 0.6339 (mt-10) REVERT: XK 326 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6784 (mt) REVERT: XK 344 ASN cc_start: 0.7558 (m-40) cc_final: 0.6946 (p0) REVERT: XL 265 GLU cc_start: 0.6496 (tp30) cc_final: 0.5231 (tm-30) REVERT: XM 293 TYR cc_start: 0.6723 (t80) cc_final: 0.6520 (t80) REVERT: XM 331 MET cc_start: 0.7399 (mmm) cc_final: 0.6696 (mmm) REVERT: XN 312 ASP cc_start: 0.6053 (m-30) cc_final: 0.5630 (m-30) REVERT: XO 308 PHE cc_start: 0.7367 (t80) cc_final: 0.7166 (t80) REVERT: XQ 265 ILE cc_start: 0.8921 (mt) cc_final: 0.8690 (mm) REVERT: XR 314 MET cc_start: 0.3755 (ptm) cc_final: 0.3269 (ptm) REVERT: XT 265 GLU cc_start: 0.8550 (tp30) cc_final: 0.7893 (tp30) REVERT: XT 301 ARG cc_start: 0.8109 (tpp80) cc_final: 0.7763 (mmm-85) REVERT: XT 314 MET cc_start: 0.4099 (ptp) cc_final: 0.3886 (ptm) REVERT: XU 297 THR cc_start: 0.8066 (m) cc_final: 0.7772 (p) REVERT: XU 331 MET cc_start: 0.6894 (tpp) cc_final: 0.6544 (tpp) REVERT: XV 247 GLU cc_start: 0.5690 (mm-30) cc_final: 0.4857 (tm-30) REVERT: XW 345 ASP cc_start: 0.7524 (m-30) cc_final: 0.7253 (m-30) outliers start: 45 outliers final: 37 residues processed: 740 average time/residue: 0.4438 time to fit residues: 453.1339 Evaluate side-chains 659 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 621 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain XA residue 351 MET Chi-restraints excluded: chain XD residue 313 VAL Chi-restraints excluded: chain XD residue 317 SER Chi-restraints excluded: chain XE residue 276 GLN Chi-restraints excluded: chain XE residue 326 LEU Chi-restraints excluded: chain XE residue 349 ASN Chi-restraints excluded: chain XF residue 327 LYS Chi-restraints excluded: chain XH residue 232 GLU Chi-restraints excluded: chain XH residue 263 GLU Chi-restraints excluded: chain XH residue 317 SER Chi-restraints excluded: chain XJ residue 297 ILE Chi-restraints excluded: chain XK residue 326 LEU Chi-restraints excluded: chain XL residue 232 GLU Chi-restraints excluded: chain XL residue 263 GLU Chi-restraints excluded: chain XL residue 271 MET Chi-restraints excluded: chain XM residue 267 GLU Chi-restraints excluded: chain XM residue 289 GLU Chi-restraints excluded: chain XN residue 223 ILE Chi-restraints excluded: chain XN residue 231 ARG Chi-restraints excluded: chain XN residue 285 ASP Chi-restraints excluded: chain XO residue 248 LYS Chi-restraints excluded: chain XO residue 267 GLU Chi-restraints excluded: chain XO residue 282 GLN Chi-restraints excluded: chain XO residue 289 GLU Chi-restraints excluded: chain XP residue 232 GLU Chi-restraints excluded: chain XP residue 263 GLU Chi-restraints excluded: chain XQ residue 289 GLU Chi-restraints excluded: chain XQ residue 300 GLU Chi-restraints excluded: chain XQ residue 302 GLN Chi-restraints excluded: chain XQ residue 322 THR Chi-restraints excluded: chain XQ residue 333 LYS Chi-restraints excluded: chain XR residue 282 LEU Chi-restraints excluded: chain XR residue 285 ASP Chi-restraints excluded: chain XS residue 302 GLN Chi-restraints excluded: chain XS residue 349 ASN Chi-restraints excluded: chain XU residue 330 THR Chi-restraints excluded: chain XU residue 341 VAL Chi-restraints excluded: chain XW residue 341 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 49 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: XB 225 ASN XC 337 ASN XF 241 GLN XH 225 ASN XI 276 GLN XJ 243 GLN XK 260 ASN XM 276 GLN XM 302 GLN XO 263 GLN XR 243 GLN ** XS 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XS 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** XS 282 GLN ** XU 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** XV 310 ASN XX 310 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.114491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.091770 restraints weight = 156644.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.095935 restraints weight = 51122.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.098435 restraints weight = 26633.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.099854 restraints weight = 18761.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.100626 restraints weight = 15591.381| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.7755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.225 20772 Z= 0.340 Angle : 0.870 16.350 27904 Z= 0.476 Chirality : 0.043 0.332 2955 Planarity : 0.007 0.107 3774 Dihedral : 3.726 20.241 2910 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.88 % Allowed : 15.62 % Favored : 80.49 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.15), residues: 2508 helix: 1.54 (0.10), residues: 1945 sheet: None (None), residues: 0 loop : -2.62 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGXC 258 TYR 0.069 0.003 TYRXR 294 PHE 0.035 0.003 PHEXK 251 HIS 0.016 0.002 HISXT 238 Details of bonding type rmsd covalent geometry : bond 0.00710 (20772) covalent geometry : angle 0.87040 (27904) hydrogen bonds : bond 0.07184 ( 1760) hydrogen bonds : angle 5.06062 ( 5226) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 310 is missing expected H atoms. Skipping. Evaluate side-chains 792 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 712 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: XA 324 GLU cc_start: 0.8255 (tp30) cc_final: 0.7878 (mm-30) REVERT: XC 258 ARG cc_start: 0.6511 (ttm-80) cc_final: 0.6137 (ttm-80) REVERT: XC 324 GLU cc_start: 0.8326 (tp30) cc_final: 0.7638 (tp30) REVERT: XC 325 ARG cc_start: 0.8572 (tmm-80) cc_final: 0.8343 (tmm160) REVERT: XC 345 ASP cc_start: 0.6932 (t70) cc_final: 0.6729 (t0) REVERT: XD 312 ASP cc_start: 0.7144 (m-30) cc_final: 0.6690 (m-30) REVERT: XE 324 GLU cc_start: 0.8450 (tp30) cc_final: 0.7951 (mt-10) REVERT: XE 344 ASN cc_start: 0.7286 (t0) cc_final: 0.6632 (t0) REVERT: XF 232 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8235 (tm-30) REVERT: XF 315 VAL cc_start: 0.7943 (t) cc_final: 0.7607 (t) REVERT: XG 324 GLU cc_start: 0.8343 (tp30) cc_final: 0.7820 (tt0) REVERT: XG 328 ILE cc_start: 0.8146 (mt) cc_final: 0.7865 (mt) REVERT: XG 343 VAL cc_start: 0.6326 (t) cc_final: 0.6114 (t) REVERT: XI 263 GLN cc_start: 0.8953 (mt0) cc_final: 0.8682 (tt0) REVERT: XI 278 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7855 (mtp85) REVERT: XI 328 ILE cc_start: 0.8143 (mt) cc_final: 0.7918 (mt) REVERT: XI 330 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8394 (m) REVERT: XJ 314 MET cc_start: 0.8066 (mtp) cc_final: 0.7778 (mtp) REVERT: XK 293 TYR cc_start: 0.7973 (t80) cc_final: 0.7690 (t80) REVERT: XK 300 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6900 (mt-10) REVERT: XL 265 GLU cc_start: 0.7481 (tp30) cc_final: 0.6622 (tp30) REVERT: XM 262 GLN cc_start: 0.7070 (pt0) cc_final: 0.6762 (mm-40) REVERT: XM 285 ARG cc_start: 0.7346 (mtp180) cc_final: 0.7139 (ttm-80) REVERT: XM 331 MET cc_start: 0.8281 (mmm) cc_final: 0.7916 (mmm) REVERT: XO 323 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.8245 (mtp85) REVERT: XP 276 ASP cc_start: 0.7443 (m-30) cc_final: 0.7229 (m-30) REVERT: XQ 265 ILE cc_start: 0.9197 (mt) cc_final: 0.8913 (mm) REVERT: XQ 331 MET cc_start: 0.6633 (tpp) cc_final: 0.5665 (tpp) REVERT: XR 243 GLN cc_start: 0.8963 (mm110) cc_final: 0.8726 (mm110) REVERT: XR 276 ASP cc_start: 0.8172 (m-30) cc_final: 0.7909 (m-30) REVERT: XS 327 TYR cc_start: 0.7391 (t80) cc_final: 0.6966 (t80) REVERT: XT 250 ARG cc_start: 0.8483 (ttm110) cc_final: 0.8280 (mtp180) REVERT: XT 265 GLU cc_start: 0.8328 (tp30) cc_final: 0.7491 (tp30) REVERT: XU 297 THR cc_start: 0.8354 (m) cc_final: 0.8104 (p) REVERT: XU 299 LEU cc_start: 0.7784 (mt) cc_final: 0.7577 (mt) REVERT: XU 300 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7286 (mm-30) REVERT: XU 331 MET cc_start: 0.8003 (tpp) cc_final: 0.7159 (tpp) REVERT: XV 271 MET cc_start: 0.7052 (mmm) cc_final: 0.6746 (mmm) REVERT: XV 274 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7307 (mt-10) REVERT: XV 292 ASP cc_start: 0.8598 (t0) cc_final: 0.8363 (m-30) REVERT: XW 328 ILE cc_start: 0.8848 (tp) cc_final: 0.8618 (tt) REVERT: XW 345 ASP cc_start: 0.7372 (m-30) cc_final: 0.7074 (m-30) outliers start: 80 outliers final: 52 residues processed: 753 average time/residue: 0.4407 time to fit residues: 455.7433 Evaluate side-chains 676 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 622 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain XA residue 321 ILE Chi-restraints excluded: chain XA residue 351 MET Chi-restraints excluded: chain XB residue 221 GLU Chi-restraints excluded: chain XB residue 230 GLU Chi-restraints excluded: chain XD residue 230 GLU Chi-restraints excluded: chain XD residue 255 TYR Chi-restraints excluded: chain XD residue 313 VAL Chi-restraints excluded: chain XD residue 317 SER Chi-restraints excluded: chain XE residue 276 GLN Chi-restraints excluded: chain XE residue 280 ASN Chi-restraints excluded: chain XE residue 349 ASN Chi-restraints excluded: chain XF residue 217 THR Chi-restraints excluded: chain XG residue 269 GLU Chi-restraints excluded: chain XG residue 274 GLU Chi-restraints excluded: chain XG residue 338 THR Chi-restraints excluded: chain XG residue 352 VAL Chi-restraints excluded: chain XH residue 232 GLU Chi-restraints excluded: chain XH residue 263 GLU Chi-restraints excluded: chain XH residue 317 SER Chi-restraints excluded: chain XI residue 330 THR Chi-restraints excluded: chain XI residue 352 VAL Chi-restraints excluded: chain XJ residue 290 ASP Chi-restraints excluded: chain XK residue 349 ASN Chi-restraints excluded: chain XL residue 232 GLU Chi-restraints excluded: chain XL residue 263 GLU Chi-restraints excluded: chain XL residue 271 MET Chi-restraints excluded: chain XL residue 317 SER Chi-restraints excluded: chain XM residue 267 GLU Chi-restraints excluded: chain XM residue 289 GLU Chi-restraints excluded: chain XM residue 321 ILE Chi-restraints excluded: chain XN residue 285 ASP Chi-restraints excluded: chain XO residue 289 GLU Chi-restraints excluded: chain XO residue 322 THR Chi-restraints excluded: chain XO residue 350 LEU Chi-restraints excluded: chain XP residue 232 GLU Chi-restraints excluded: chain XP residue 263 GLU Chi-restraints excluded: chain XQ residue 255 ILE Chi-restraints excluded: chain XQ residue 289 GLU Chi-restraints excluded: chain XQ residue 322 THR Chi-restraints excluded: chain XQ residue 333 LYS Chi-restraints excluded: chain XR residue 255 TYR Chi-restraints excluded: chain XR residue 282 LEU Chi-restraints excluded: chain XR residue 285 ASP Chi-restraints excluded: chain XS residue 255 ILE Chi-restraints excluded: chain XS residue 269 GLU Chi-restraints excluded: chain XS residue 353 LEU Chi-restraints excluded: chain XT residue 256 GLU Chi-restraints excluded: chain XT residue 292 ASP Chi-restraints excluded: chain XT residue 298 ARG Chi-restraints excluded: chain XU residue 300 GLU Chi-restraints excluded: chain XU residue 330 THR Chi-restraints excluded: chain XV residue 263 GLU Chi-restraints excluded: chain XX residue 227 MET Chi-restraints excluded: chain XX residue 314 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 83 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** XA 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XE 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** XE 263 GLN XF 241 GLN XG 280 ASN XH 241 GLN XQ 302 GLN ** XS 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XU 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.114154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.091478 restraints weight = 156370.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.095618 restraints weight = 50521.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.098072 restraints weight = 26286.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.099465 restraints weight = 18558.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.100243 restraints weight = 15462.814| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.9115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 20772 Z= 0.214 Angle : 0.657 8.955 27904 Z= 0.359 Chirality : 0.037 0.161 2955 Planarity : 0.005 0.067 3774 Dihedral : 3.438 26.254 2910 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.40 % Allowed : 18.92 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.16), residues: 2508 helix: 2.41 (0.10), residues: 1959 sheet: None (None), residues: 0 loop : -2.18 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGXR 228 TYR 0.034 0.002 TYRXT 294 PHE 0.033 0.002 PHEXV 296 HIS 0.007 0.001 HISXL 238 Details of bonding type rmsd covalent geometry : bond 0.00426 (20772) covalent geometry : angle 0.65674 (27904) hydrogen bonds : bond 0.06439 ( 1760) hydrogen bonds : angle 4.50421 ( 5226) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 310 is missing expected H atoms. Skipping. Evaluate side-chains 748 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 678 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: XA 285 ARG cc_start: 0.7944 (mtp85) cc_final: 0.7523 (mtp85) REVERT: XA 324 GLU cc_start: 0.8257 (tp30) cc_final: 0.7933 (mm-30) REVERT: XC 324 GLU cc_start: 0.8402 (tp30) cc_final: 0.7681 (tp30) REVERT: XC 345 ASP cc_start: 0.7293 (t70) cc_final: 0.6993 (t0) REVERT: XD 305 ASN cc_start: 0.9294 (OUTLIER) cc_final: 0.8823 (m-40) REVERT: XD 315 VAL cc_start: 0.7119 (t) cc_final: 0.6707 (t) REVERT: XE 324 GLU cc_start: 0.8707 (tp30) cc_final: 0.8269 (mt-10) REVERT: XE 344 ASN cc_start: 0.7087 (t0) cc_final: 0.6768 (t0) REVERT: XE 346 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6408 (mmmt) REVERT: XF 232 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8384 (tm-30) REVERT: XF 292 ASP cc_start: 0.8309 (m-30) cc_final: 0.8097 (m-30) REVERT: XF 307 PHE cc_start: 0.9007 (m-80) cc_final: 0.8750 (m-80) REVERT: XF 310 ASN cc_start: 0.6609 (p0) cc_final: 0.5796 (m-40) REVERT: XF 315 VAL cc_start: 0.8019 (t) cc_final: 0.7672 (t) REVERT: XF 326 MET cc_start: 0.7607 (tpp) cc_final: 0.7076 (tpp) REVERT: XG 267 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8385 (mm-30) REVERT: XG 324 GLU cc_start: 0.8332 (tp30) cc_final: 0.7792 (tt0) REVERT: XG 328 ILE cc_start: 0.8382 (mt) cc_final: 0.8065 (mt) REVERT: XG 329 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7920 (tm-30) REVERT: XG 342 LEU cc_start: 0.6694 (mm) cc_final: 0.5611 (tp) REVERT: XG 343 VAL cc_start: 0.6476 (t) cc_final: 0.6230 (t) REVERT: XI 266 ARG cc_start: 0.8491 (mmt-90) cc_final: 0.8258 (mmt-90) REVERT: XI 278 ARG cc_start: 0.8349 (mmm-85) cc_final: 0.7998 (mtp85) REVERT: XI 324 GLU cc_start: 0.6873 (tp30) cc_final: 0.6390 (mm-30) REVERT: XI 328 ILE cc_start: 0.8258 (mt) cc_final: 0.7987 (mt) REVERT: XK 331 MET cc_start: 0.7585 (mmt) cc_final: 0.7355 (mmt) REVERT: XK 334 VAL cc_start: 0.9277 (t) cc_final: 0.9022 (m) REVERT: XL 265 GLU cc_start: 0.7684 (tp30) cc_final: 0.7165 (tp30) REVERT: XL 292 ASP cc_start: 0.8211 (p0) cc_final: 0.7842 (p0) REVERT: XN 254 ASP cc_start: 0.7861 (m-30) cc_final: 0.7500 (m-30) REVERT: XN 312 ASP cc_start: 0.8549 (m-30) cc_final: 0.8187 (m-30) REVERT: XO 300 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7536 (mm-30) REVERT: XP 247 GLU cc_start: 0.7400 (tp30) cc_final: 0.6710 (tt0) REVERT: XP 250 ARG cc_start: 0.7898 (mpp80) cc_final: 0.7638 (mtm110) REVERT: XQ 302 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6811 (mt0) REVERT: XQ 331 MET cc_start: 0.7324 (tpp) cc_final: 0.6132 (tpp) REVERT: XR 276 ASP cc_start: 0.8407 (m-30) cc_final: 0.8040 (m-30) REVERT: XS 326 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7140 (mm) REVERT: XT 241 GLN cc_start: 0.7526 (tm-30) cc_final: 0.7252 (tm-30) REVERT: XT 255 TYR cc_start: 0.8292 (t80) cc_final: 0.7555 (t80) REVERT: XT 265 GLU cc_start: 0.8472 (tp30) cc_final: 0.7990 (tp30) REVERT: XU 331 MET cc_start: 0.8065 (tpp) cc_final: 0.7645 (tpp) REVERT: XV 271 MET cc_start: 0.7310 (mmm) cc_final: 0.7015 (mmm) REVERT: XW 307 ARG cc_start: 0.8319 (mtm180) cc_final: 0.8010 (mtp180) REVERT: XW 333 LYS cc_start: 0.8928 (ttpt) cc_final: 0.8725 (ttpt) REVERT: XW 345 ASP cc_start: 0.7706 (m-30) cc_final: 0.7399 (m-30) outliers start: 70 outliers final: 54 residues processed: 717 average time/residue: 0.4130 time to fit residues: 409.7055 Evaluate side-chains 675 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 615 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain XA residue 351 MET Chi-restraints excluded: chain XB residue 221 GLU Chi-restraints excluded: chain XB residue 230 GLU Chi-restraints excluded: chain XB residue 247 GLU Chi-restraints excluded: chain XB residue 317 SER Chi-restraints excluded: chain XD residue 243 GLN Chi-restraints excluded: chain XD residue 305 ASN Chi-restraints excluded: chain XD residue 313 VAL Chi-restraints excluded: chain XD residue 317 SER Chi-restraints excluded: chain XE residue 267 GLU Chi-restraints excluded: chain XE residue 346 LYS Chi-restraints excluded: chain XE residue 350 LEU Chi-restraints excluded: chain XF residue 241 GLN Chi-restraints excluded: chain XF residue 257 VAL Chi-restraints excluded: chain XF residue 261 LEU Chi-restraints excluded: chain XF residue 313 VAL Chi-restraints excluded: chain XG residue 267 GLU Chi-restraints excluded: chain XG residue 269 GLU Chi-restraints excluded: chain XG residue 274 GLU Chi-restraints excluded: chain XG residue 300 GLU Chi-restraints excluded: chain XG residue 350 LEU Chi-restraints excluded: chain XH residue 232 GLU Chi-restraints excluded: chain XI residue 300 GLU Chi-restraints excluded: chain XJ residue 274 GLU Chi-restraints excluded: chain XJ residue 290 ASP Chi-restraints excluded: chain XL residue 224 TYR Chi-restraints excluded: chain XL residue 232 GLU Chi-restraints excluded: chain XL residue 263 GLU Chi-restraints excluded: chain XL residue 271 MET Chi-restraints excluded: chain XM residue 267 GLU Chi-restraints excluded: chain XM residue 289 GLU Chi-restraints excluded: chain XM residue 296 GLN Chi-restraints excluded: chain XM residue 349 ASN Chi-restraints excluded: chain XN residue 285 ASP Chi-restraints excluded: chain XO residue 267 GLU Chi-restraints excluded: chain XO residue 282 GLN Chi-restraints excluded: chain XO residue 289 GLU Chi-restraints excluded: chain XO residue 300 GLU Chi-restraints excluded: chain XO residue 328 ILE Chi-restraints excluded: chain XO residue 334 VAL Chi-restraints excluded: chain XP residue 232 GLU Chi-restraints excluded: chain XP residue 263 GLU Chi-restraints excluded: chain XQ residue 255 ILE Chi-restraints excluded: chain XQ residue 289 GLU Chi-restraints excluded: chain XQ residue 300 GLU Chi-restraints excluded: chain XQ residue 302 GLN Chi-restraints excluded: chain XQ residue 322 THR Chi-restraints excluded: chain XQ residue 333 LYS Chi-restraints excluded: chain XR residue 282 LEU Chi-restraints excluded: chain XR residue 285 ASP Chi-restraints excluded: chain XS residue 326 LEU Chi-restraints excluded: chain XS residue 349 ASN Chi-restraints excluded: chain XS residue 353 LEU Chi-restraints excluded: chain XT residue 256 GLU Chi-restraints excluded: chain XT residue 292 ASP Chi-restraints excluded: chain XU residue 353 LEU Chi-restraints excluded: chain XV residue 263 GLU Chi-restraints excluded: chain XV residue 317 SER Chi-restraints excluded: chain XW residue 341 VAL Chi-restraints excluded: chain XX residue 227 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 111 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 chunk 219 optimal weight: 0.2980 chunk 180 optimal weight: 0.5980 chunk 18 optimal weight: 0.0870 chunk 21 optimal weight: 0.0570 chunk 144 optimal weight: 2.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: XJ 241 GLN ** XL 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** XL 243 GLN XN 241 GLN XQ 262 GLN XS 280 ASN ** XU 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.114430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.091684 restraints weight = 154756.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.095838 restraints weight = 50042.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.098312 restraints weight = 26078.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.099709 restraints weight = 18439.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.100453 restraints weight = 15359.790| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.9500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20772 Z= 0.165 Angle : 0.590 7.614 27904 Z= 0.318 Chirality : 0.034 0.179 2955 Planarity : 0.004 0.061 3774 Dihedral : 3.273 24.115 2910 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.01 % Allowed : 21.06 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.98 (0.16), residues: 2508 helix: 2.92 (0.10), residues: 1960 sheet: None (None), residues: 0 loop : -1.87 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGXO 323 TYR 0.019 0.001 TYRXM 264 PHE 0.026 0.001 PHEXD 296 HIS 0.006 0.001 HISXT 238 Details of bonding type rmsd covalent geometry : bond 0.00303 (20772) covalent geometry : angle 0.58966 (27904) hydrogen bonds : bond 0.06228 ( 1760) hydrogen bonds : angle 4.20816 ( 5226) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 310 is missing expected H atoms. Skipping. Evaluate side-chains 719 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 657 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: XA 324 GLU cc_start: 0.8097 (tp30) cc_final: 0.7716 (mm-30) REVERT: XB 310 ASN cc_start: 0.6255 (p0) cc_final: 0.5037 (t0) REVERT: XB 314 MET cc_start: 0.7388 (mtp) cc_final: 0.7089 (mtp) REVERT: XC 324 GLU cc_start: 0.8351 (tp30) cc_final: 0.7532 (tp30) REVERT: XC 345 ASP cc_start: 0.7392 (t70) cc_final: 0.7137 (t0) REVERT: XD 315 VAL cc_start: 0.7198 (t) cc_final: 0.6891 (t) REVERT: XE 324 GLU cc_start: 0.8671 (tp30) cc_final: 0.8263 (mt-10) REVERT: XE 344 ASN cc_start: 0.7127 (t0) cc_final: 0.6846 (t0) REVERT: XE 346 LYS cc_start: 0.6858 (mmmt) cc_final: 0.6454 (mmmt) REVERT: XF 292 ASP cc_start: 0.8253 (m-30) cc_final: 0.8035 (m-30) REVERT: XF 310 ASN cc_start: 0.6582 (p0) cc_final: 0.5851 (m-40) REVERT: XF 315 VAL cc_start: 0.8062 (t) cc_final: 0.7712 (t) REVERT: XF 321 ASP cc_start: 0.6386 (p0) cc_final: 0.6155 (p0) REVERT: XF 326 MET cc_start: 0.7783 (tpp) cc_final: 0.7532 (tpp) REVERT: XG 329 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8236 (tm-30) REVERT: XI 278 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7771 (mtp85) REVERT: XI 300 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8116 (mm-30) REVERT: XI 328 ILE cc_start: 0.8191 (mt) cc_final: 0.7930 (mt) REVERT: XI 344 ASN cc_start: 0.7924 (p0) cc_final: 0.7694 (p0) REVERT: XI 351 MET cc_start: 0.5972 (mmt) cc_final: 0.5724 (mmp) REVERT: XL 265 GLU cc_start: 0.7715 (tp30) cc_final: 0.7001 (tp30) REVERT: XL 292 ASP cc_start: 0.8318 (p0) cc_final: 0.7889 (p0) REVERT: XL 314 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7253 (mtp) REVERT: XM 263 GLN cc_start: 0.7106 (tm-30) cc_final: 0.6781 (tm-30) REVERT: XM 267 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: XM 331 MET cc_start: 0.9092 (tpp) cc_final: 0.8888 (tpp) REVERT: XN 254 ASP cc_start: 0.7782 (m-30) cc_final: 0.7437 (m-30) REVERT: XN 312 ASP cc_start: 0.8414 (m-30) cc_final: 0.8014 (m-30) REVERT: XO 266 ARG cc_start: 0.7090 (mtm110) cc_final: 0.6520 (mtm110) REVERT: XO 300 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7099 (mm-30) REVERT: XP 247 GLU cc_start: 0.7274 (tp30) cc_final: 0.6693 (tt0) REVERT: XP 250 ARG cc_start: 0.7865 (mpp80) cc_final: 0.7620 (mtm110) REVERT: XQ 329 GLU cc_start: 0.8674 (tp30) cc_final: 0.8451 (tt0) REVERT: XQ 331 MET cc_start: 0.7249 (tpp) cc_final: 0.6052 (tpp) REVERT: XR 276 ASP cc_start: 0.8410 (m-30) cc_final: 0.8054 (m-30) REVERT: XR 282 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7055 (tt) REVERT: XR 324 ARG cc_start: 0.7247 (ptt-90) cc_final: 0.6769 (ptt-90) REVERT: XS 326 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7520 (mm) REVERT: XT 241 GLN cc_start: 0.7501 (tm-30) cc_final: 0.7178 (tm-30) REVERT: XT 255 TYR cc_start: 0.8226 (t80) cc_final: 0.7328 (t80) REVERT: XT 265 GLU cc_start: 0.8508 (tp30) cc_final: 0.8036 (tp30) REVERT: XU 331 MET cc_start: 0.8092 (tpp) cc_final: 0.7616 (tpp) REVERT: XV 276 ASP cc_start: 0.8396 (m-30) cc_final: 0.7931 (m-30) REVERT: XW 307 ARG cc_start: 0.8201 (mtm180) cc_final: 0.7805 (mtp180) REVERT: XW 332 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7957 (tm-30) REVERT: XW 345 ASP cc_start: 0.7544 (m-30) cc_final: 0.7254 (m-30) outliers start: 62 outliers final: 47 residues processed: 685 average time/residue: 0.4145 time to fit residues: 393.5480 Evaluate side-chains 661 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 608 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain XA residue 260 ASN Chi-restraints excluded: chain XA residue 351 MET Chi-restraints excluded: chain XB residue 221 GLU Chi-restraints excluded: chain XD residue 243 GLN Chi-restraints excluded: chain XD residue 313 VAL Chi-restraints excluded: chain XD residue 317 SER Chi-restraints excluded: chain XE residue 267 GLU Chi-restraints excluded: chain XF residue 257 VAL Chi-restraints excluded: chain XF residue 261 LEU Chi-restraints excluded: chain XF residue 312 ASP Chi-restraints excluded: chain XG residue 269 GLU Chi-restraints excluded: chain XG residue 274 GLU Chi-restraints excluded: chain XG residue 300 GLU Chi-restraints excluded: chain XG residue 351 MET Chi-restraints excluded: chain XH residue 232 GLU Chi-restraints excluded: chain XI residue 300 GLU Chi-restraints excluded: chain XI residue 338 THR Chi-restraints excluded: chain XI residue 352 VAL Chi-restraints excluded: chain XI residue 353 LEU Chi-restraints excluded: chain XJ residue 274 GLU Chi-restraints excluded: chain XJ residue 290 ASP Chi-restraints excluded: chain XL residue 224 TYR Chi-restraints excluded: chain XL residue 232 GLU Chi-restraints excluded: chain XL residue 263 GLU Chi-restraints excluded: chain XL residue 271 MET Chi-restraints excluded: chain XL residue 314 MET Chi-restraints excluded: chain XM residue 267 GLU Chi-restraints excluded: chain XM residue 289 GLU Chi-restraints excluded: chain XM residue 349 ASN Chi-restraints excluded: chain XN residue 285 ASP Chi-restraints excluded: chain XO residue 282 GLN Chi-restraints excluded: chain XO residue 289 GLU Chi-restraints excluded: chain XO residue 300 GLU Chi-restraints excluded: chain XO residue 328 ILE Chi-restraints excluded: chain XO residue 334 VAL Chi-restraints excluded: chain XO residue 338 THR Chi-restraints excluded: chain XP residue 232 GLU Chi-restraints excluded: chain XP residue 263 GLU Chi-restraints excluded: chain XQ residue 255 ILE Chi-restraints excluded: chain XQ residue 289 GLU Chi-restraints excluded: chain XQ residue 300 GLU Chi-restraints excluded: chain XQ residue 302 GLN Chi-restraints excluded: chain XQ residue 322 THR Chi-restraints excluded: chain XR residue 282 LEU Chi-restraints excluded: chain XR residue 285 ASP Chi-restraints excluded: chain XS residue 312 LEU Chi-restraints excluded: chain XS residue 326 LEU Chi-restraints excluded: chain XS residue 353 LEU Chi-restraints excluded: chain XV residue 263 GLU Chi-restraints excluded: chain XV residue 312 ASP Chi-restraints excluded: chain XV residue 317 SER Chi-restraints excluded: chain XX residue 227 MET Chi-restraints excluded: chain XX residue 261 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 26 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 230 optimal weight: 0.4980 chunk 131 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 245 optimal weight: 0.6980 chunk 166 optimal weight: 0.0970 chunk 168 optimal weight: 0.9980 chunk 177 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** XA 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** XE 296 GLN XF 241 GLN XL 241 GLN XS 280 ASN ** XT 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XU 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.114081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.091126 restraints weight = 155816.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.095248 restraints weight = 50392.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.097712 restraints weight = 26311.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.099096 restraints weight = 18592.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.099869 restraints weight = 15512.446| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 1.0089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20772 Z= 0.165 Angle : 0.592 6.273 27904 Z= 0.319 Chirality : 0.035 0.184 2955 Planarity : 0.004 0.047 3774 Dihedral : 3.278 24.401 2910 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.20 % Allowed : 21.54 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.16 (0.16), residues: 2508 helix: 3.03 (0.10), residues: 1970 sheet: None (None), residues: 0 loop : -1.81 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGXV 266 TYR 0.021 0.001 TYRXB 325 PHE 0.024 0.001 PHEXD 296 HIS 0.007 0.001 HISXB 238 Details of bonding type rmsd covalent geometry : bond 0.00329 (20772) covalent geometry : angle 0.59207 (27904) hydrogen bonds : bond 0.05876 ( 1760) hydrogen bonds : angle 4.17157 ( 5226) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 310 is missing expected H atoms. Skipping. Evaluate side-chains 714 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 648 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: XA 294 LYS cc_start: 0.6910 (pttt) cc_final: 0.6670 (ptmm) REVERT: XA 324 GLU cc_start: 0.8088 (tp30) cc_final: 0.7733 (mm-30) REVERT: XB 310 ASN cc_start: 0.6648 (p0) cc_final: 0.5424 (t0) REVERT: XC 324 GLU cc_start: 0.7950 (tp30) cc_final: 0.7069 (tp30) REVERT: XC 345 ASP cc_start: 0.7417 (t70) cc_final: 0.7217 (t0) REVERT: XD 244 GLU cc_start: 0.4091 (tt0) cc_final: 0.2736 (tp30) REVERT: XE 258 ARG cc_start: 0.3756 (mtt-85) cc_final: 0.3132 (mtt180) REVERT: XE 324 GLU cc_start: 0.8674 (tp30) cc_final: 0.8169 (mt-10) REVERT: XE 344 ASN cc_start: 0.7244 (t0) cc_final: 0.6884 (t0) REVERT: XE 346 LYS cc_start: 0.6836 (mmmt) cc_final: 0.6401 (mmmt) REVERT: XF 265 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7645 (mm-30) REVERT: XF 292 ASP cc_start: 0.8322 (m-30) cc_final: 0.8047 (p0) REVERT: XF 310 ASN cc_start: 0.6624 (p0) cc_final: 0.6314 (m-40) REVERT: XF 315 VAL cc_start: 0.8157 (t) cc_final: 0.7799 (t) REVERT: XF 321 ASP cc_start: 0.6543 (p0) cc_final: 0.6343 (p0) REVERT: XF 326 MET cc_start: 0.7775 (tpp) cc_final: 0.7406 (tpp) REVERT: XG 267 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8510 (mm-30) REVERT: XG 329 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8503 (tm-30) REVERT: XG 342 LEU cc_start: 0.6838 (mm) cc_final: 0.5696 (tp) REVERT: XI 266 ARG cc_start: 0.8516 (mmt-90) cc_final: 0.8250 (mmt-90) REVERT: XI 271 TYR cc_start: 0.8244 (t80) cc_final: 0.7877 (t80) REVERT: XI 278 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7825 (mtp85) REVERT: XI 324 GLU cc_start: 0.7235 (tp30) cc_final: 0.6616 (mm-30) REVERT: XI 328 ILE cc_start: 0.8282 (mt) cc_final: 0.8051 (mt) REVERT: XI 344 ASN cc_start: 0.7949 (p0) cc_final: 0.7746 (p0) REVERT: XI 353 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.6382 (tp) REVERT: XJ 250 ARG cc_start: 0.6804 (mpt-90) cc_final: 0.6568 (mmt90) REVERT: XJ 269 ARG cc_start: 0.8060 (mtt-85) cc_final: 0.7645 (mpt-90) REVERT: XL 265 GLU cc_start: 0.7946 (tp30) cc_final: 0.7368 (tp30) REVERT: XL 292 ASP cc_start: 0.8519 (p0) cc_final: 0.7973 (p0) REVERT: XL 328 THR cc_start: 0.7375 (m) cc_final: 0.6992 (p) REVERT: XM 264 TYR cc_start: 0.7579 (m-10) cc_final: 0.7044 (m-10) REVERT: XM 293 TYR cc_start: 0.7726 (t80) cc_final: 0.7259 (t80) REVERT: XM 331 MET cc_start: 0.9191 (tpp) cc_final: 0.8902 (tpp) REVERT: XN 254 ASP cc_start: 0.7987 (m-30) cc_final: 0.7691 (m-30) REVERT: XN 312 ASP cc_start: 0.8509 (m-30) cc_final: 0.8107 (m-30) REVERT: XN 314 MET cc_start: 0.6834 (ptm) cc_final: 0.6629 (ptm) REVERT: XO 300 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.6873 (mm-30) REVERT: XO 308 PHE cc_start: 0.7959 (t80) cc_final: 0.7079 (t80) REVERT: XP 247 GLU cc_start: 0.7432 (tp30) cc_final: 0.6972 (tt0) REVERT: XP 250 ARG cc_start: 0.8023 (mpp80) cc_final: 0.7811 (mtm110) REVERT: XQ 329 GLU cc_start: 0.8718 (tp30) cc_final: 0.8513 (tt0) REVERT: XQ 331 MET cc_start: 0.7855 (tpp) cc_final: 0.6840 (tpp) REVERT: XR 227 MET cc_start: 0.6376 (mpp) cc_final: 0.6092 (mpp) REVERT: XR 276 ASP cc_start: 0.8433 (m-30) cc_final: 0.7986 (m-30) REVERT: XR 314 MET cc_start: 0.7496 (ptm) cc_final: 0.7209 (ptm) REVERT: XR 324 ARG cc_start: 0.6933 (ptt-90) cc_final: 0.6434 (ptt-90) REVERT: XS 326 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7654 (mm) REVERT: XT 241 GLN cc_start: 0.7525 (tm-30) cc_final: 0.7194 (tm-30) REVERT: XT 250 ARG cc_start: 0.8509 (ttm110) cc_final: 0.8262 (mmm160) REVERT: XT 255 TYR cc_start: 0.8248 (t80) cc_final: 0.7309 (t80) REVERT: XT 265 GLU cc_start: 0.8581 (tp30) cc_final: 0.7922 (tp30) REVERT: XU 299 LEU cc_start: 0.8387 (mt) cc_final: 0.7992 (mt) REVERT: XU 300 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7518 (mm-30) REVERT: XU 331 MET cc_start: 0.8134 (tpp) cc_final: 0.7855 (tpp) REVERT: XV 265 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8755 (mm-30) REVERT: XV 276 ASP cc_start: 0.8422 (m-30) cc_final: 0.7907 (m-30) REVERT: XV 319 ASP cc_start: 0.8701 (m-30) cc_final: 0.8373 (m-30) REVERT: XW 307 ARG cc_start: 0.8378 (mtm180) cc_final: 0.8007 (mtp180) REVERT: XW 312 LEU cc_start: 0.8546 (mt) cc_final: 0.8103 (mm) REVERT: XW 332 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8238 (tm-30) REVERT: XW 345 ASP cc_start: 0.7784 (m-30) cc_final: 0.7488 (m-30) outliers start: 66 outliers final: 53 residues processed: 678 average time/residue: 0.4259 time to fit residues: 400.5149 Evaluate side-chains 666 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 608 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain XA residue 260 ASN Chi-restraints excluded: chain XA residue 351 MET Chi-restraints excluded: chain XB residue 221 GLU Chi-restraints excluded: chain XB residue 247 GLU Chi-restraints excluded: chain XC residue 259 GLU Chi-restraints excluded: chain XC residue 291 ARG Chi-restraints excluded: chain XD residue 221 GLU Chi-restraints excluded: chain XD residue 243 GLN Chi-restraints excluded: chain XD residue 313 VAL Chi-restraints excluded: chain XD residue 317 SER Chi-restraints excluded: chain XE residue 267 GLU Chi-restraints excluded: chain XF residue 257 VAL Chi-restraints excluded: chain XG residue 267 GLU Chi-restraints excluded: chain XG residue 269 GLU Chi-restraints excluded: chain XG residue 351 MET Chi-restraints excluded: chain XH residue 232 GLU Chi-restraints excluded: chain XI residue 300 GLU Chi-restraints excluded: chain XI residue 338 THR Chi-restraints excluded: chain XI residue 342 LEU Chi-restraints excluded: chain XI residue 353 LEU Chi-restraints excluded: chain XJ residue 290 ASP Chi-restraints excluded: chain XK residue 343 VAL Chi-restraints excluded: chain XK residue 350 LEU Chi-restraints excluded: chain XK residue 352 VAL Chi-restraints excluded: chain XL residue 224 TYR Chi-restraints excluded: chain XL residue 232 GLU Chi-restraints excluded: chain XL residue 241 GLN Chi-restraints excluded: chain XM residue 278 ARG Chi-restraints excluded: chain XM residue 289 GLU Chi-restraints excluded: chain XM residue 296 GLN Chi-restraints excluded: chain XM residue 349 ASN Chi-restraints excluded: chain XN residue 285 ASP Chi-restraints excluded: chain XO residue 282 GLN Chi-restraints excluded: chain XO residue 289 GLU Chi-restraints excluded: chain XO residue 300 GLU Chi-restraints excluded: chain XO residue 312 LEU Chi-restraints excluded: chain XO residue 328 ILE Chi-restraints excluded: chain XP residue 232 GLU Chi-restraints excluded: chain XP residue 263 GLU Chi-restraints excluded: chain XQ residue 255 ILE Chi-restraints excluded: chain XQ residue 267 GLU Chi-restraints excluded: chain XQ residue 289 GLU Chi-restraints excluded: chain XQ residue 300 GLU Chi-restraints excluded: chain XQ residue 322 THR Chi-restraints excluded: chain XR residue 282 LEU Chi-restraints excluded: chain XS residue 255 ILE Chi-restraints excluded: chain XS residue 269 GLU Chi-restraints excluded: chain XS residue 312 LEU Chi-restraints excluded: chain XS residue 326 LEU Chi-restraints excluded: chain XS residue 338 THR Chi-restraints excluded: chain XS residue 353 LEU Chi-restraints excluded: chain XT residue 256 GLU Chi-restraints excluded: chain XU residue 300 GLU Chi-restraints excluded: chain XU residue 353 LEU Chi-restraints excluded: chain XV residue 263 GLU Chi-restraints excluded: chain XV residue 317 SER Chi-restraints excluded: chain XX residue 227 MET Chi-restraints excluded: chain XX residue 261 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 116 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 43 optimal weight: 0.0270 chunk 246 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 chunk 106 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** XA 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** XK 296 GLN ** XK 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** XQ 262 GLN XS 282 GLN ** XT 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XU 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.109374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.087108 restraints weight = 152314.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.091412 restraints weight = 46597.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.093994 restraints weight = 23494.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.095449 restraints weight = 16229.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.096236 restraints weight = 13352.663| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 1.0451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20772 Z= 0.151 Angle : 0.584 7.402 27904 Z= 0.313 Chirality : 0.035 0.189 2955 Planarity : 0.004 0.053 3774 Dihedral : 3.236 24.964 2910 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.52 % Allowed : 22.90 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.29 (0.16), residues: 2508 helix: 3.11 (0.10), residues: 1975 sheet: None (None), residues: 0 loop : -1.75 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGXK 278 TYR 0.014 0.001 TYRXV 294 PHE 0.019 0.001 PHEXD 296 HIS 0.007 0.001 HISXT 238 Details of bonding type rmsd covalent geometry : bond 0.00293 (20772) covalent geometry : angle 0.58373 (27904) hydrogen bonds : bond 0.05773 ( 1760) hydrogen bonds : angle 4.08007 ( 5226) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 310 is missing expected H atoms. Skipping. Evaluate side-chains 677 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 625 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: XA 294 LYS cc_start: 0.6961 (pttt) cc_final: 0.6726 (ptmm) REVERT: XA 324 GLU cc_start: 0.8262 (tp30) cc_final: 0.7843 (mm-30) REVERT: XB 308 SER cc_start: 0.8889 (t) cc_final: 0.8531 (m) REVERT: XB 310 ASN cc_start: 0.6725 (p0) cc_final: 0.5310 (t0) REVERT: XC 258 ARG cc_start: 0.6671 (ttm-80) cc_final: 0.6441 (ttm-80) REVERT: XC 324 GLU cc_start: 0.7915 (tp30) cc_final: 0.7033 (tp30) REVERT: XC 345 ASP cc_start: 0.7673 (t70) cc_final: 0.7434 (t0) REVERT: XE 324 GLU cc_start: 0.8635 (tp30) cc_final: 0.8195 (mm-30) REVERT: XE 344 ASN cc_start: 0.7302 (t0) cc_final: 0.6956 (t0) REVERT: XE 346 LYS cc_start: 0.6950 (mmmt) cc_final: 0.6542 (mmmt) REVERT: XF 265 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7837 (mm-30) REVERT: XF 292 ASP cc_start: 0.8324 (m-30) cc_final: 0.7974 (p0) REVERT: XF 310 ASN cc_start: 0.6812 (p0) cc_final: 0.6282 (m-40) REVERT: XF 315 VAL cc_start: 0.8175 (t) cc_final: 0.7837 (t) REVERT: XF 321 ASP cc_start: 0.6775 (p0) cc_final: 0.6481 (p0) REVERT: XF 326 MET cc_start: 0.7758 (tpp) cc_final: 0.7353 (tpp) REVERT: XG 304 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7712 (mm-30) REVERT: XG 329 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8424 (tm-30) REVERT: XG 342 LEU cc_start: 0.6830 (mm) cc_final: 0.5654 (tp) REVERT: XI 266 ARG cc_start: 0.8721 (mmt-90) cc_final: 0.8404 (mmt-90) REVERT: XI 344 ASN cc_start: 0.8071 (p0) cc_final: 0.7863 (p0) REVERT: XI 353 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.6582 (tp) REVERT: XL 265 GLU cc_start: 0.8128 (tp30) cc_final: 0.7468 (tp30) REVERT: XL 292 ASP cc_start: 0.8511 (p0) cc_final: 0.8099 (p0) REVERT: XL 328 THR cc_start: 0.7495 (m) cc_final: 0.7162 (p) REVERT: XM 271 TYR cc_start: 0.8983 (t80) cc_final: 0.8725 (t80) REVERT: XM 276 GLN cc_start: 0.6915 (tm-30) cc_final: 0.6300 (tm-30) REVERT: XM 293 TYR cc_start: 0.7812 (t80) cc_final: 0.7350 (t80) REVERT: XN 254 ASP cc_start: 0.7948 (m-30) cc_final: 0.7666 (m-30) REVERT: XN 312 ASP cc_start: 0.8553 (m-30) cc_final: 0.8086 (m-30) REVERT: XO 339 ARG cc_start: 0.6274 (mpt180) cc_final: 0.5973 (mpp80) REVERT: XP 244 GLU cc_start: 0.5526 (tt0) cc_final: 0.4655 (tt0) REVERT: XQ 331 MET cc_start: 0.7893 (tpp) cc_final: 0.7049 (mmt) REVERT: XR 276 ASP cc_start: 0.8483 (m-30) cc_final: 0.8061 (m-30) REVERT: XR 314 MET cc_start: 0.7645 (ptm) cc_final: 0.7409 (ptm) REVERT: XS 326 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7780 (mm) REVERT: XT 241 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7528 (tm-30) REVERT: XT 250 ARG cc_start: 0.8599 (ttm110) cc_final: 0.8344 (mmm160) REVERT: XT 255 TYR cc_start: 0.8290 (t80) cc_final: 0.7322 (t80) REVERT: XT 265 GLU cc_start: 0.8690 (tp30) cc_final: 0.7981 (tp30) REVERT: XU 299 LEU cc_start: 0.8399 (mt) cc_final: 0.8032 (mt) REVERT: XU 300 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7770 (mm-30) REVERT: XU 331 MET cc_start: 0.8266 (tpp) cc_final: 0.7382 (tpp) REVERT: XV 265 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8645 (mm-30) REVERT: XV 276 ASP cc_start: 0.8382 (m-30) cc_final: 0.7894 (m-30) REVERT: XV 319 ASP cc_start: 0.8778 (m-30) cc_final: 0.8523 (m-30) REVERT: XW 288 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7774 (mm-30) REVERT: XW 307 ARG cc_start: 0.8477 (mtm180) cc_final: 0.8152 (mtp180) REVERT: XW 332 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8280 (tm-30) REVERT: XW 345 ASP cc_start: 0.7912 (m-30) cc_final: 0.7594 (m-30) outliers start: 52 outliers final: 42 residues processed: 655 average time/residue: 0.4589 time to fit residues: 417.1302 Evaluate side-chains 639 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 594 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain XA residue 260 ASN Chi-restraints excluded: chain XA residue 351 MET Chi-restraints excluded: chain XB residue 221 GLU Chi-restraints excluded: chain XB residue 247 GLU Chi-restraints excluded: chain XD residue 243 GLN Chi-restraints excluded: chain XD residue 313 VAL Chi-restraints excluded: chain XD residue 317 SER Chi-restraints excluded: chain XE residue 267 GLU Chi-restraints excluded: chain XE residue 350 LEU Chi-restraints excluded: chain XF residue 257 VAL Chi-restraints excluded: chain XG residue 300 GLU Chi-restraints excluded: chain XG residue 350 LEU Chi-restraints excluded: chain XH residue 232 GLU Chi-restraints excluded: chain XI residue 300 GLU Chi-restraints excluded: chain XI residue 353 LEU Chi-restraints excluded: chain XJ residue 290 ASP Chi-restraints excluded: chain XK residue 343 VAL Chi-restraints excluded: chain XK residue 352 VAL Chi-restraints excluded: chain XL residue 232 GLU Chi-restraints excluded: chain XL residue 241 GLN Chi-restraints excluded: chain XM residue 262 GLN Chi-restraints excluded: chain XM residue 289 GLU Chi-restraints excluded: chain XM residue 296 GLN Chi-restraints excluded: chain XM residue 349 ASN Chi-restraints excluded: chain XN residue 285 ASP Chi-restraints excluded: chain XO residue 282 GLN Chi-restraints excluded: chain XO residue 289 GLU Chi-restraints excluded: chain XO residue 304 GLU Chi-restraints excluded: chain XO residue 312 LEU Chi-restraints excluded: chain XO residue 328 ILE Chi-restraints excluded: chain XP residue 232 GLU Chi-restraints excluded: chain XQ residue 255 ILE Chi-restraints excluded: chain XQ residue 289 GLU Chi-restraints excluded: chain XQ residue 300 GLU Chi-restraints excluded: chain XQ residue 322 THR Chi-restraints excluded: chain XR residue 258 THR Chi-restraints excluded: chain XS residue 255 ILE Chi-restraints excluded: chain XS residue 269 GLU Chi-restraints excluded: chain XS residue 326 LEU Chi-restraints excluded: chain XT residue 256 GLU Chi-restraints excluded: chain XU residue 300 GLU Chi-restraints excluded: chain XV residue 263 GLU Chi-restraints excluded: chain XV residue 312 ASP Chi-restraints excluded: chain XV residue 317 SER Chi-restraints excluded: chain XX residue 227 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 129 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 224 optimal weight: 0.6980 chunk 220 optimal weight: 0.9990 chunk 47 optimal weight: 0.1980 chunk 219 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** XA 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XK 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** XT 241 GLN ** XU 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.110514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.088439 restraints weight = 152760.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.092771 restraints weight = 46080.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.095349 restraints weight = 23120.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.096794 restraints weight = 15924.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.097576 restraints weight = 13097.838| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 1.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20772 Z= 0.164 Angle : 0.603 10.903 27904 Z= 0.324 Chirality : 0.035 0.200 2955 Planarity : 0.004 0.074 3774 Dihedral : 3.255 24.680 2910 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.77 % Allowed : 23.58 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.33 (0.16), residues: 2508 helix: 3.13 (0.10), residues: 1976 sheet: None (None), residues: 0 loop : -1.74 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGXO 266 TYR 0.015 0.001 TYRXB 325 PHE 0.017 0.001 PHEXD 296 HIS 0.006 0.001 HISXT 238 Details of bonding type rmsd covalent geometry : bond 0.00332 (20772) covalent geometry : angle 0.60339 (27904) hydrogen bonds : bond 0.05595 ( 1760) hydrogen bonds : angle 4.08788 ( 5226) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 310 is missing expected H atoms. Skipping. Evaluate side-chains 687 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 630 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: XA 294 LYS cc_start: 0.7280 (pttt) cc_final: 0.6873 (ptmm) REVERT: XA 324 GLU cc_start: 0.8372 (tp30) cc_final: 0.7908 (mm-30) REVERT: XB 308 SER cc_start: 0.8769 (t) cc_final: 0.8468 (m) REVERT: XB 310 ASN cc_start: 0.6955 (p0) cc_final: 0.5545 (t0) REVERT: XC 252 ASP cc_start: 0.8859 (m-30) cc_final: 0.8113 (t70) REVERT: XC 285 ARG cc_start: 0.7190 (mtp180) cc_final: 0.6640 (mmt180) REVERT: XC 345 ASP cc_start: 0.7766 (t70) cc_final: 0.7523 (t0) REVERT: XE 324 GLU cc_start: 0.8825 (tp30) cc_final: 0.8307 (mm-30) REVERT: XE 344 ASN cc_start: 0.7456 (t0) cc_final: 0.7057 (t0) REVERT: XE 345 ASP cc_start: 0.7475 (t0) cc_final: 0.7066 (t70) REVERT: XE 346 LYS cc_start: 0.7135 (mmmt) cc_final: 0.6549 (mmmt) REVERT: XF 292 ASP cc_start: 0.8472 (m-30) cc_final: 0.8095 (p0) REVERT: XF 310 ASN cc_start: 0.7055 (p0) cc_final: 0.6548 (m-40) REVERT: XF 315 VAL cc_start: 0.8286 (t) cc_final: 0.7944 (t) REVERT: XF 321 ASP cc_start: 0.6871 (p0) cc_final: 0.6660 (p0) REVERT: XF 326 MET cc_start: 0.7834 (tpp) cc_final: 0.7444 (tpp) REVERT: XG 271 TYR cc_start: 0.8093 (t80) cc_final: 0.7744 (t80) REVERT: XG 304 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7535 (mm-30) REVERT: XG 329 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8425 (tm-30) REVERT: XG 342 LEU cc_start: 0.6992 (mm) cc_final: 0.5865 (tp) REVERT: XH 271 MET cc_start: 0.7715 (mtm) cc_final: 0.7139 (ptp) REVERT: XI 266 ARG cc_start: 0.8768 (mmt-90) cc_final: 0.8414 (mmt-90) REVERT: XI 344 ASN cc_start: 0.8149 (p0) cc_final: 0.7937 (p0) REVERT: XI 353 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.6986 (tp) REVERT: XJ 315 VAL cc_start: 0.8918 (t) cc_final: 0.8688 (m) REVERT: XK 324 GLU cc_start: 0.8047 (tp30) cc_final: 0.7599 (tp30) REVERT: XL 265 GLU cc_start: 0.8264 (tp30) cc_final: 0.7738 (tp30) REVERT: XL 292 ASP cc_start: 0.8732 (p0) cc_final: 0.8291 (p0) REVERT: XM 264 TYR cc_start: 0.7967 (m-10) cc_final: 0.7351 (m-10) REVERT: XM 276 GLN cc_start: 0.7174 (tm-30) cc_final: 0.6504 (tm-30) REVERT: XM 293 TYR cc_start: 0.7920 (t80) cc_final: 0.7535 (t80) REVERT: XN 254 ASP cc_start: 0.8052 (m-30) cc_final: 0.7780 (m-30) REVERT: XN 312 ASP cc_start: 0.8277 (m-30) cc_final: 0.7815 (m-30) REVERT: XN 314 MET cc_start: 0.6755 (ptm) cc_final: 0.6522 (ptm) REVERT: XO 300 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7708 (mm-30) REVERT: XO 308 PHE cc_start: 0.7701 (t80) cc_final: 0.7268 (t80) REVERT: XR 244 GLU cc_start: 0.8166 (tt0) cc_final: 0.7724 (tt0) REVERT: XR 276 ASP cc_start: 0.8540 (m-30) cc_final: 0.8174 (m-30) REVERT: XS 326 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7873 (mm) REVERT: XT 250 ARG cc_start: 0.8642 (ttm110) cc_final: 0.8404 (mmm160) REVERT: XT 265 GLU cc_start: 0.8734 (tp30) cc_final: 0.8026 (tp30) REVERT: XT 319 ASP cc_start: 0.9031 (m-30) cc_final: 0.8814 (m-30) REVERT: XU 299 LEU cc_start: 0.8396 (mt) cc_final: 0.8006 (mt) REVERT: XU 300 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7858 (mm-30) REVERT: XU 331 MET cc_start: 0.8313 (tpp) cc_final: 0.7706 (tpp) REVERT: XV 265 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8622 (mm-30) REVERT: XV 276 ASP cc_start: 0.8467 (m-30) cc_final: 0.7864 (m-30) REVERT: XV 319 ASP cc_start: 0.8981 (m-30) cc_final: 0.8642 (m-30) REVERT: XW 288 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7624 (mm-30) REVERT: XW 307 ARG cc_start: 0.8493 (mtm180) cc_final: 0.7664 (mtp180) REVERT: XW 332 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8232 (tt0) REVERT: XW 345 ASP cc_start: 0.7786 (m-30) cc_final: 0.7501 (m-30) outliers start: 57 outliers final: 45 residues processed: 660 average time/residue: 0.4660 time to fit residues: 429.4717 Evaluate side-chains 657 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 608 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain XA residue 260 ASN Chi-restraints excluded: chain XA residue 278 ARG Chi-restraints excluded: chain XA residue 351 MET Chi-restraints excluded: chain XB residue 221 GLU Chi-restraints excluded: chain XB residue 247 GLU Chi-restraints excluded: chain XC residue 259 GLU Chi-restraints excluded: chain XD residue 243 GLN Chi-restraints excluded: chain XD residue 313 VAL Chi-restraints excluded: chain XD residue 317 SER Chi-restraints excluded: chain XE residue 267 GLU Chi-restraints excluded: chain XE residue 350 LEU Chi-restraints excluded: chain XF residue 257 VAL Chi-restraints excluded: chain XG residue 267 GLU Chi-restraints excluded: chain XG residue 269 GLU Chi-restraints excluded: chain XH residue 232 GLU Chi-restraints excluded: chain XI residue 300 GLU Chi-restraints excluded: chain XI residue 342 LEU Chi-restraints excluded: chain XI residue 353 LEU Chi-restraints excluded: chain XJ residue 290 ASP Chi-restraints excluded: chain XK residue 343 VAL Chi-restraints excluded: chain XK residue 352 VAL Chi-restraints excluded: chain XL residue 232 GLU Chi-restraints excluded: chain XM residue 258 ARG Chi-restraints excluded: chain XM residue 262 GLN Chi-restraints excluded: chain XM residue 289 GLU Chi-restraints excluded: chain XM residue 296 GLN Chi-restraints excluded: chain XM residue 349 ASN Chi-restraints excluded: chain XN residue 248 LYS Chi-restraints excluded: chain XN residue 285 ASP Chi-restraints excluded: chain XO residue 289 GLU Chi-restraints excluded: chain XO residue 300 GLU Chi-restraints excluded: chain XO residue 304 GLU Chi-restraints excluded: chain XO residue 312 LEU Chi-restraints excluded: chain XO residue 328 ILE Chi-restraints excluded: chain XP residue 232 GLU Chi-restraints excluded: chain XQ residue 255 ILE Chi-restraints excluded: chain XQ residue 289 GLU Chi-restraints excluded: chain XQ residue 300 GLU Chi-restraints excluded: chain XR residue 258 THR Chi-restraints excluded: chain XS residue 255 ILE Chi-restraints excluded: chain XS residue 300 GLU Chi-restraints excluded: chain XS residue 326 LEU Chi-restraints excluded: chain XS residue 330 THR Chi-restraints excluded: chain XT residue 256 GLU Chi-restraints excluded: chain XU residue 300 GLU Chi-restraints excluded: chain XV residue 263 GLU Chi-restraints excluded: chain XV residue 317 SER Chi-restraints excluded: chain XX residue 227 MET Chi-restraints excluded: chain XX residue 261 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 204 optimal weight: 0.8980 chunk 163 optimal weight: 0.2980 chunk 231 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 130 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** XA 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** XQ 337 ASN XR 238 HIS XS 276 GLN XS 280 ASN ** XU 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.109982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.087469 restraints weight = 154960.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.091825 restraints weight = 46705.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.094434 restraints weight = 23685.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.095868 restraints weight = 16504.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.096656 restraints weight = 13641.545| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 1.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20772 Z= 0.171 Angle : 0.632 11.346 27904 Z= 0.340 Chirality : 0.036 0.215 2955 Planarity : 0.005 0.107 3774 Dihedral : 3.345 25.531 2910 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.72 % Allowed : 24.16 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.19 (0.16), residues: 2508 helix: 2.98 (0.10), residues: 1988 sheet: None (None), residues: 0 loop : -1.66 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARGXK 266 TYR 0.019 0.002 TYRXB 325 PHE 0.040 0.002 PHEXQ 251 HIS 0.007 0.001 HISXT 238 Details of bonding type rmsd covalent geometry : bond 0.00345 (20772) covalent geometry : angle 0.63170 (27904) hydrogen bonds : bond 0.05506 ( 1760) hydrogen bonds : angle 4.12000 ( 5226) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 310 is missing expected H atoms. Skipping. Evaluate side-chains 700 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 644 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: XA 248 LYS cc_start: 0.8003 (mttt) cc_final: 0.7791 (mptt) REVERT: XA 324 GLU cc_start: 0.8389 (tp30) cc_final: 0.7949 (mm-30) REVERT: XB 308 SER cc_start: 0.8433 (t) cc_final: 0.8085 (m) REVERT: XB 310 ASN cc_start: 0.7299 (p0) cc_final: 0.5973 (t0) REVERT: XC 252 ASP cc_start: 0.8761 (m-30) cc_final: 0.8013 (t70) REVERT: XC 285 ARG cc_start: 0.7381 (mtp180) cc_final: 0.6870 (mmt180) REVERT: XC 345 ASP cc_start: 0.7872 (t70) cc_final: 0.7665 (t0) REVERT: XE 324 GLU cc_start: 0.8747 (tp30) cc_final: 0.8329 (mm-30) REVERT: XE 346 LYS cc_start: 0.7315 (mmmt) cc_final: 0.6880 (mmmt) REVERT: XF 244 GLU cc_start: 0.5695 (tt0) cc_final: 0.4792 (tp30) REVERT: XF 292 ASP cc_start: 0.8484 (m-30) cc_final: 0.8226 (p0) REVERT: XF 310 ASN cc_start: 0.7586 (p0) cc_final: 0.7182 (m-40) REVERT: XF 315 VAL cc_start: 0.8424 (t) cc_final: 0.8107 (t) REVERT: XF 321 ASP cc_start: 0.6747 (p0) cc_final: 0.6457 (p0) REVERT: XF 326 MET cc_start: 0.7949 (tpp) cc_final: 0.7622 (tpp) REVERT: XG 271 TYR cc_start: 0.8141 (t80) cc_final: 0.7806 (t80) REVERT: XG 304 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7521 (mm-30) REVERT: XG 329 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8646 (tm-30) REVERT: XH 247 GLU cc_start: 0.7832 (tp30) cc_final: 0.7619 (tp30) REVERT: XH 278 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7904 (tp30) REVERT: XI 266 ARG cc_start: 0.8797 (mmt-90) cc_final: 0.8407 (mmt-90) REVERT: XI 353 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7006 (tp) REVERT: XJ 265 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8512 (mm-30) REVERT: XK 263 GLN cc_start: 0.7778 (tm-30) cc_final: 0.6508 (tm-30) REVERT: XK 267 GLU cc_start: 0.8551 (mm-30) cc_final: 0.7979 (mm-30) REVERT: XK 278 ARG cc_start: 0.8185 (mmm-85) cc_final: 0.7794 (mmp80) REVERT: XK 293 TYR cc_start: 0.8389 (t80) cc_final: 0.7966 (t80) REVERT: XK 297 THR cc_start: 0.8611 (m) cc_final: 0.8268 (p) REVERT: XK 324 GLU cc_start: 0.8196 (tp30) cc_final: 0.7796 (tp30) REVERT: XL 292 ASP cc_start: 0.8841 (p0) cc_final: 0.8438 (p0) REVERT: XM 264 TYR cc_start: 0.7876 (m-10) cc_final: 0.7274 (m-10) REVERT: XM 276 GLN cc_start: 0.7375 (tm-30) cc_final: 0.6706 (tm-30) REVERT: XM 293 TYR cc_start: 0.8031 (t80) cc_final: 0.7687 (t80) REVERT: XM 331 MET cc_start: 0.9381 (tpp) cc_final: 0.9166 (tpp) REVERT: XN 254 ASP cc_start: 0.8222 (m-30) cc_final: 0.7988 (m-30) REVERT: XN 312 ASP cc_start: 0.8375 (m-30) cc_final: 0.7917 (m-30) REVERT: XO 278 ARG cc_start: 0.8827 (mmm-85) cc_final: 0.8500 (mmm-85) REVERT: XO 300 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7798 (mm-30) REVERT: XO 308 PHE cc_start: 0.7960 (t80) cc_final: 0.7465 (t80) REVERT: XP 321 ASP cc_start: 0.8513 (p0) cc_final: 0.8205 (p0) REVERT: XQ 331 MET cc_start: 0.8667 (tpp) cc_final: 0.7635 (tpp) REVERT: XR 276 ASP cc_start: 0.8583 (m-30) cc_final: 0.8262 (m-30) REVERT: XS 296 GLN cc_start: 0.8660 (tt0) cc_final: 0.8445 (tm-30) REVERT: XT 265 GLU cc_start: 0.8712 (tp30) cc_final: 0.7887 (tp30) REVERT: XU 285 ARG cc_start: 0.8826 (mtp85) cc_final: 0.8241 (ttm-80) REVERT: XU 299 LEU cc_start: 0.8385 (mt) cc_final: 0.7923 (mt) REVERT: XU 300 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7881 (mm-30) REVERT: XU 331 MET cc_start: 0.8332 (tpp) cc_final: 0.7995 (tpp) REVERT: XV 265 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8664 (mm-30) REVERT: XV 276 ASP cc_start: 0.8423 (m-30) cc_final: 0.8181 (m-30) REVERT: XV 319 ASP cc_start: 0.8962 (m-30) cc_final: 0.8626 (m-30) REVERT: XW 332 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8435 (tt0) REVERT: XW 345 ASP cc_start: 0.7998 (m-30) cc_final: 0.7525 (m-30) outliers start: 56 outliers final: 47 residues processed: 669 average time/residue: 0.4343 time to fit residues: 405.2542 Evaluate side-chains 650 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 600 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain XA residue 260 ASN Chi-restraints excluded: chain XA residue 351 MET Chi-restraints excluded: chain XB residue 221 GLU Chi-restraints excluded: chain XB residue 247 GLU Chi-restraints excluded: chain XC residue 259 GLU Chi-restraints excluded: chain XD residue 243 GLN Chi-restraints excluded: chain XD residue 313 VAL Chi-restraints excluded: chain XD residue 317 SER Chi-restraints excluded: chain XE residue 267 GLU Chi-restraints excluded: chain XE residue 328 ILE Chi-restraints excluded: chain XE residue 350 LEU Chi-restraints excluded: chain XF residue 257 VAL Chi-restraints excluded: chain XG residue 267 GLU Chi-restraints excluded: chain XH residue 232 GLU Chi-restraints excluded: chain XI residue 259 GLU Chi-restraints excluded: chain XI residue 300 GLU Chi-restraints excluded: chain XI residue 338 THR Chi-restraints excluded: chain XI residue 342 LEU Chi-restraints excluded: chain XI residue 353 LEU Chi-restraints excluded: chain XJ residue 290 ASP Chi-restraints excluded: chain XK residue 343 VAL Chi-restraints excluded: chain XK residue 352 VAL Chi-restraints excluded: chain XL residue 232 GLU Chi-restraints excluded: chain XM residue 258 ARG Chi-restraints excluded: chain XM residue 262 GLN Chi-restraints excluded: chain XM residue 289 GLU Chi-restraints excluded: chain XM residue 296 GLN Chi-restraints excluded: chain XM residue 349 ASN Chi-restraints excluded: chain XN residue 285 ASP Chi-restraints excluded: chain XO residue 282 GLN Chi-restraints excluded: chain XO residue 289 GLU Chi-restraints excluded: chain XO residue 300 GLU Chi-restraints excluded: chain XO residue 304 GLU Chi-restraints excluded: chain XO residue 312 LEU Chi-restraints excluded: chain XO residue 328 ILE Chi-restraints excluded: chain XP residue 232 GLU Chi-restraints excluded: chain XQ residue 255 ILE Chi-restraints excluded: chain XQ residue 289 GLU Chi-restraints excluded: chain XQ residue 300 GLU Chi-restraints excluded: chain XR residue 258 THR Chi-restraints excluded: chain XS residue 300 GLU Chi-restraints excluded: chain XS residue 326 LEU Chi-restraints excluded: chain XT residue 256 GLU Chi-restraints excluded: chain XU residue 300 GLU Chi-restraints excluded: chain XU residue 312 LEU Chi-restraints excluded: chain XU residue 330 THR Chi-restraints excluded: chain XV residue 263 GLU Chi-restraints excluded: chain XV residue 317 SER Chi-restraints excluded: chain XX residue 227 MET Chi-restraints excluded: chain XX residue 261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 212 optimal weight: 2.9990 chunk 194 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 44 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 201 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 146 optimal weight: 0.0040 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** XA 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** XJ 243 GLN XQ 337 ASN ** XU 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.110612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.088070 restraints weight = 154034.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.092462 restraints weight = 46679.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.095074 restraints weight = 23725.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.096528 restraints weight = 16519.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.097315 restraints weight = 13639.536| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 1.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20772 Z= 0.155 Angle : 0.632 10.091 27904 Z= 0.337 Chirality : 0.037 0.210 2955 Planarity : 0.005 0.084 3774 Dihedral : 3.358 25.152 2910 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.18 % Allowed : 24.94 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.30 (0.16), residues: 2508 helix: 3.03 (0.10), residues: 1999 sheet: None (None), residues: 0 loop : -1.60 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARGXD 324 TYR 0.028 0.002 TYRXM 271 PHE 0.023 0.001 PHEXK 251 HIS 0.005 0.001 HISXT 238 Details of bonding type rmsd covalent geometry : bond 0.00311 (20772) covalent geometry : angle 0.63165 (27904) hydrogen bonds : bond 0.05392 ( 1760) hydrogen bonds : angle 4.06871 ( 5226) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 310 is missing expected H atoms. Skipping. Evaluate side-chains 671 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 626 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: XA 248 LYS cc_start: 0.7999 (mttt) cc_final: 0.7781 (mptt) REVERT: XA 324 GLU cc_start: 0.8449 (tp30) cc_final: 0.8036 (mm-30) REVERT: XA 342 LEU cc_start: 0.7310 (mm) cc_final: 0.6395 (tp) REVERT: XB 310 ASN cc_start: 0.7137 (p0) cc_final: 0.5854 (t0) REVERT: XC 252 ASP cc_start: 0.8720 (m-30) cc_final: 0.7937 (t70) REVERT: XC 285 ARG cc_start: 0.7228 (mtp180) cc_final: 0.6669 (mmt180) REVERT: XE 324 GLU cc_start: 0.8928 (tp30) cc_final: 0.8546 (mm-30) REVERT: XF 244 GLU cc_start: 0.5767 (tt0) cc_final: 0.4795 (tp30) REVERT: XF 292 ASP cc_start: 0.8507 (m-30) cc_final: 0.8259 (p0) REVERT: XF 310 ASN cc_start: 0.7637 (p0) cc_final: 0.7290 (m-40) REVERT: XF 315 VAL cc_start: 0.8477 (t) cc_final: 0.8172 (t) REVERT: XF 321 ASP cc_start: 0.7074 (p0) cc_final: 0.6831 (p0) REVERT: XF 326 MET cc_start: 0.8252 (tpp) cc_final: 0.7844 (tpp) REVERT: XG 271 TYR cc_start: 0.8133 (t80) cc_final: 0.7838 (t80) REVERT: XG 304 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7565 (mm-30) REVERT: XG 329 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8666 (tm-30) REVERT: XH 271 MET cc_start: 0.7939 (mtm) cc_final: 0.7283 (ptp) REVERT: XI 266 ARG cc_start: 0.8802 (mmt-90) cc_final: 0.8415 (mmt-90) REVERT: XI 353 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.6804 (tp) REVERT: XJ 224 TYR cc_start: 0.8065 (m-10) cc_final: 0.7754 (m-10) REVERT: XJ 265 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8562 (mm-30) REVERT: XK 263 GLN cc_start: 0.7848 (tm-30) cc_final: 0.6503 (tm-30) REVERT: XK 267 GLU cc_start: 0.8533 (mm-30) cc_final: 0.7797 (mt-10) REVERT: XK 278 ARG cc_start: 0.7632 (mmm-85) cc_final: 0.7405 (tpp80) REVERT: XK 293 TYR cc_start: 0.8362 (t80) cc_final: 0.7930 (t80) REVERT: XK 297 THR cc_start: 0.8689 (m) cc_final: 0.8355 (p) REVERT: XK 324 GLU cc_start: 0.8226 (tp30) cc_final: 0.7771 (tp30) REVERT: XL 292 ASP cc_start: 0.8861 (p0) cc_final: 0.8501 (p0) REVERT: XM 264 TYR cc_start: 0.7943 (m-10) cc_final: 0.7410 (m-10) REVERT: XM 276 GLN cc_start: 0.7453 (tm-30) cc_final: 0.6852 (tm-30) REVERT: XM 293 TYR cc_start: 0.8131 (t80) cc_final: 0.7801 (t80) REVERT: XN 254 ASP cc_start: 0.8262 (m-30) cc_final: 0.8020 (m-30) REVERT: XN 312 ASP cc_start: 0.8426 (m-30) cc_final: 0.7939 (m-30) REVERT: XO 278 ARG cc_start: 0.8825 (mmm-85) cc_final: 0.8470 (mmm-85) REVERT: XO 300 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7525 (mm-30) REVERT: XO 308 PHE cc_start: 0.7974 (t80) cc_final: 0.7474 (t80) REVERT: XP 292 ASP cc_start: 0.8760 (p0) cc_final: 0.8518 (p0) REVERT: XP 321 ASP cc_start: 0.8549 (p0) cc_final: 0.8252 (p0) REVERT: XQ 331 MET cc_start: 0.8721 (tpp) cc_final: 0.7624 (tpp) REVERT: XQ 339 ARG cc_start: 0.7542 (mpt-90) cc_final: 0.6856 (mtt90) REVERT: XQ 343 VAL cc_start: 0.8596 (t) cc_final: 0.8293 (m) REVERT: XR 276 ASP cc_start: 0.8354 (m-30) cc_final: 0.8107 (m-30) REVERT: XR 290 ASP cc_start: 0.7148 (p0) cc_final: 0.6747 (p0) REVERT: XT 265 GLU cc_start: 0.8732 (tp30) cc_final: 0.7772 (tp30) REVERT: XU 300 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7971 (mm-30) REVERT: XV 265 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8639 (mm-30) REVERT: XV 276 ASP cc_start: 0.8476 (m-30) cc_final: 0.8222 (m-30) REVERT: XV 319 ASP cc_start: 0.8977 (m-30) cc_final: 0.8666 (m-30) REVERT: XW 345 ASP cc_start: 0.7776 (m-30) cc_final: 0.7473 (m-30) outliers start: 45 outliers final: 41 residues processed: 648 average time/residue: 0.4093 time to fit residues: 370.5139 Evaluate side-chains 647 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 603 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain XA residue 351 MET Chi-restraints excluded: chain XB residue 221 GLU Chi-restraints excluded: chain XB residue 247 GLU Chi-restraints excluded: chain XC residue 259 GLU Chi-restraints excluded: chain XC residue 312 LEU Chi-restraints excluded: chain XD residue 243 GLN Chi-restraints excluded: chain XD residue 244 GLU Chi-restraints excluded: chain XD residue 313 VAL Chi-restraints excluded: chain XD residue 317 SER Chi-restraints excluded: chain XE residue 267 GLU Chi-restraints excluded: chain XE residue 350 LEU Chi-restraints excluded: chain XF residue 257 VAL Chi-restraints excluded: chain XH residue 232 GLU Chi-restraints excluded: chain XI residue 300 GLU Chi-restraints excluded: chain XI residue 342 LEU Chi-restraints excluded: chain XI residue 353 LEU Chi-restraints excluded: chain XJ residue 290 ASP Chi-restraints excluded: chain XK residue 343 VAL Chi-restraints excluded: chain XK residue 352 VAL Chi-restraints excluded: chain XL residue 232 GLU Chi-restraints excluded: chain XM residue 258 ARG Chi-restraints excluded: chain XM residue 262 GLN Chi-restraints excluded: chain XM residue 289 GLU Chi-restraints excluded: chain XM residue 349 ASN Chi-restraints excluded: chain XN residue 285 ASP Chi-restraints excluded: chain XO residue 289 GLU Chi-restraints excluded: chain XO residue 300 GLU Chi-restraints excluded: chain XO residue 304 GLU Chi-restraints excluded: chain XO residue 312 LEU Chi-restraints excluded: chain XO residue 328 ILE Chi-restraints excluded: chain XP residue 232 GLU Chi-restraints excluded: chain XQ residue 255 ILE Chi-restraints excluded: chain XQ residue 289 GLU Chi-restraints excluded: chain XQ residue 300 GLU Chi-restraints excluded: chain XR residue 258 THR Chi-restraints excluded: chain XS residue 300 GLU Chi-restraints excluded: chain XS residue 326 LEU Chi-restraints excluded: chain XT residue 256 GLU Chi-restraints excluded: chain XU residue 300 GLU Chi-restraints excluded: chain XU residue 312 LEU Chi-restraints excluded: chain XV residue 263 GLU Chi-restraints excluded: chain XV residue 317 SER Chi-restraints excluded: chain XX residue 227 MET Chi-restraints excluded: chain XX residue 261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 128 optimal weight: 0.4980 chunk 164 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** XA 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XL 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XU 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.109524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.086932 restraints weight = 154702.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.091224 restraints weight = 47085.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.093792 restraints weight = 23895.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.095217 restraints weight = 16651.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.095985 restraints weight = 13780.725| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 1.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20772 Z= 0.182 Angle : 0.663 13.422 27904 Z= 0.358 Chirality : 0.037 0.238 2955 Planarity : 0.005 0.070 3774 Dihedral : 3.423 26.820 2910 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.33 % Allowed : 25.13 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.07 (0.16), residues: 2508 helix: 2.89 (0.10), residues: 1999 sheet: None (None), residues: 0 loop : -1.74 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGXO 258 TYR 0.018 0.002 TYRXC 293 PHE 0.047 0.002 PHEXD 293 HIS 0.005 0.001 HISXT 238 Details of bonding type rmsd covalent geometry : bond 0.00374 (20772) covalent geometry : angle 0.66289 (27904) hydrogen bonds : bond 0.05344 ( 1760) hydrogen bonds : angle 4.17113 ( 5226) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9580.33 seconds wall clock time: 163 minutes 1.43 seconds (9781.43 seconds total)