Starting phenix.real_space_refine on Sat Aug 8 07:25:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ub1_63999/08_2026/9ub1_63999.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ub1_63999/08_2026/9ub1_63999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ub1_63999/08_2026/9ub1_63999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ub1_63999/08_2026/9ub1_63999.map" model { file = "/net/cci-nas-00/data/ceres_data/9ub1_63999/08_2026/9ub1_63999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ub1_63999/08_2026/9ub1_63999.cif" } resolution = 2.35 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= -0.000 sd= 0.025 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 Ca 4 9.91 5 S 132 5.16 5 C 16184 2.51 5 N 4412 2.21 5 O 5280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26012 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3008 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "E" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1727 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 12, 'TRANS': 215} Chain: "F" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1631 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain: "M" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, D, G, I, K, H, J, L, N, O, P Time building chain proxies: 4.84, per 1000 atoms: 0.19 Number of scatterers: 26012 At special positions: 0 Unit cell: (189.75, 189.75, 112.47, 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) Ca 4 19.99 S 132 16.00 O 5280 8.00 N 4412 7.00 C 16184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 437 " distance=2.03 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 213 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 250 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 257 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 467 " distance=2.03 Simple disulfide: pdb=" CA CYS B 195 " - pdb=" SG CYS B 195 " distance=2.82 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 437 " distance=2.03 Simple disulfide: pdb=" SG CYS C 112 " - pdb=" SG CYS C 437 " distance=2.03 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 437 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 213 " distance=2.03 Simple disulfide: pdb=" SG CYS C 195 " - pdb=" SG CYS C 213 " distance=2.03 Simple disulfide: pdb=" SG CYS D 195 " - pdb=" SG CYS D 213 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 250 " distance=2.03 Simple disulfide: pdb=" SG CYS C 203 " - pdb=" SG CYS C 250 " distance=2.03 Simple disulfide: pdb=" SG CYS D 203 " - pdb=" SG CYS D 250 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 257 " distance=2.03 Simple disulfide: pdb=" SG CYS C 252 " - pdb=" SG CYS C 257 " distance=2.03 Simple disulfide: pdb=" SG CYS D 252 " - pdb=" SG CYS D 257 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 311 " distance=2.03 Simple disulfide: pdb=" SG CYS D 298 " - pdb=" SG CYS D 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 309 " distance=2.03 Simple disulfide: pdb=" SG CYS D 300 " - pdb=" SG CYS D 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS C 338 " - pdb=" SG CYS C 357 " distance=2.03 Simple disulfide: pdb=" SG CYS D 338 " - pdb=" SG CYS D 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 467 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 467 " distance=2.03 Simple disulfide: pdb=" SG CYS D 441 " - pdb=" SG CYS D 467 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN N 4 " - " MAN N 5 " " MAN O 4 " - " MAN O 5 " " MAN P 4 " - " MAN P 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " MAN M 6 " - " MAN M 7 " " BMA N 3 " - " MAN N 4 " " MAN N 6 " - " MAN N 7 " " BMA O 3 " - " MAN O 4 " " MAN O 6 " - " MAN O 7 " " BMA P 3 " - " MAN P 4 " " MAN P 6 " - " MAN P 7 " ALPHA1-6 " BMA M 3 " - " MAN M 6 " " MAN M 6 " - " MAN M 8 " " BMA N 3 " - " MAN N 6 " " MAN N 6 " - " MAN N 8 " " BMA O 3 " - " MAN O 6 " " MAN O 6 " - " MAN O 8 " " BMA P 3 " - " MAN P 6 " " MAN P 6 " - " MAN P 8 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG A 501 " - " ASN A 166 " " NAG A 502 " - " ASN A 254 " " NAG A 503 " - " ASN A 349 " " NAG B 501 " - " ASN B 166 " " NAG B 502 " - " ASN B 254 " " NAG B 503 " - " ASN B 349 " " NAG C 501 " - " ASN C 166 " " NAG C 502 " - " ASN C 254 " " NAG C 503 " - " ASN C 349 " " NAG D 501 " - " ASN D 166 " " NAG D 502 " - " ASN D 254 " " NAG D 503 " - " ASN D 349 " " NAG M 1 " - " ASN A 220 " " NAG N 1 " - " ASN B 220 " " NAG O 1 " - " ASN C 220 " " NAG P 1 " - " ASN D 220 " Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 977.0 milliseconds 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6048 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 68 sheets defined 5.0% alpha, 45.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.547A pdb=" N LEU A 128 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 166 removed outlier: 3.547A pdb=" N SER A 165 " --> pdb=" O ASN A 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN A 166 " --> pdb=" O VAL A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 162 through 166' Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.546A pdb=" N LEU B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 166 removed outlier: 3.546A pdb=" N SER B 165 " --> pdb=" O ASN B 162 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN B 166 " --> pdb=" O VAL B 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 162 through 166' Processing helix chain 'C' and resid 124 through 129 removed outlier: 3.546A pdb=" N LEU C 128 " --> pdb=" O ASN C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 166 removed outlier: 3.548A pdb=" N SER C 165 " --> pdb=" O ASN C 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN C 166 " --> pdb=" O VAL C 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 162 through 166' Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.546A pdb=" N LEU D 128 " --> pdb=" O ASN D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 166 removed outlier: 3.547A pdb=" N SER D 165 " --> pdb=" O ASN D 162 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN D 166 " --> pdb=" O VAL D 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 162 through 166' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.608A pdb=" N THR E 91 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 205 Processing helix chain 'E' and resid 214 through 217 Processing helix chain 'F' and resid 121 through 128 removed outlier: 3.507A pdb=" N LEU F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 188 removed outlier: 4.076A pdb=" N GLU F 187 " --> pdb=" O LYS F 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.608A pdb=" N THR G 91 " --> pdb=" O VAL G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 205 Processing helix chain 'G' and resid 214 through 217 Processing helix chain 'H' and resid 121 through 128 removed outlier: 3.507A pdb=" N LEU H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 188 removed outlier: 4.076A pdb=" N GLU H 187 " --> pdb=" O LYS H 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.607A pdb=" N THR I 91 " --> pdb=" O VAL I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 205 Processing helix chain 'I' and resid 214 through 217 Processing helix chain 'J' and resid 121 through 128 removed outlier: 3.508A pdb=" N LEU J 125 " --> pdb=" O SER J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 188 removed outlier: 4.076A pdb=" N GLU J 187 " --> pdb=" O LYS J 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.608A pdb=" N THR K 91 " --> pdb=" O VAL K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 205 Processing helix chain 'K' and resid 214 through 217 Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.507A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 removed outlier: 4.077A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 122 removed outlier: 4.065A pdb=" N GLY A 116 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A 465 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS A 122 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE A 463 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG A 440 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 144 removed outlier: 4.877A pdb=" N TRP A 135 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR A 158 " --> pdb=" O TRP A 135 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N THR A 137 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS A 156 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU A 139 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU A 154 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 177 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU A 178 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS A 192 " --> pdb=" O MET A 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 204 removed outlier: 6.450A pdb=" N TYR A 227 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU A 231 " --> pdb=" O TYR A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 244 removed outlier: 4.011A pdb=" N VAL A 251 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 243 through 244 removed outlier: 6.482A pdb=" N GLU A 278 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 296 through 303 removed outlier: 5.671A pdb=" N GLU A 297 " --> pdb=" O ARG A 312 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG A 312 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 373 through 376 removed outlier: 5.841A pdb=" N LEU A 392 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ARG A 420 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR A 396 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL A 416 " --> pdb=" O THR A 396 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N LYS A 398 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG A 414 " --> pdb=" O LYS A 398 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 116 through 122 removed outlier: 4.065A pdb=" N GLY B 116 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 465 " --> pdb=" O PHE B 120 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS B 122 " --> pdb=" O ILE B 463 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE B 463 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG B 440 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 135 through 144 removed outlier: 4.877A pdb=" N TRP B 135 " --> pdb=" O THR B 158 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR B 158 " --> pdb=" O TRP B 135 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N THR B 137 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS B 156 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU B 139 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 154 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR B 177 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B 178 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS B 192 " --> pdb=" O MET B 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 199 through 204 removed outlier: 6.450A pdb=" N TYR B 227 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU B 231 " --> pdb=" O TYR B 227 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 243 through 244 removed outlier: 4.009A pdb=" N VAL B 251 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 243 through 244 removed outlier: 6.482A pdb=" N GLU B 278 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 296 through 303 removed outlier: 5.670A pdb=" N GLU B 297 " --> pdb=" O ARG B 312 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG B 312 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 373 through 376 removed outlier: 5.842A pdb=" N LEU B 392 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ARG B 420 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR B 396 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL B 416 " --> pdb=" O THR B 396 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N LYS B 398 " --> pdb=" O ARG B 414 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG B 414 " --> pdb=" O LYS B 398 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 116 through 122 removed outlier: 4.064A pdb=" N GLY C 116 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL C 465 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LYS C 122 " --> pdb=" O ILE C 463 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE C 463 " --> pdb=" O LYS C 122 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG C 440 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 135 through 144 removed outlier: 4.877A pdb=" N TRP C 135 " --> pdb=" O THR C 158 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR C 158 " --> pdb=" O TRP C 135 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N THR C 137 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS C 156 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLU C 139 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU C 154 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR C 177 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU C 178 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS C 192 " --> pdb=" O MET C 180 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 199 through 204 removed outlier: 6.450A pdb=" N TYR C 227 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU C 231 " --> pdb=" O TYR C 227 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 243 through 244 removed outlier: 4.011A pdb=" N VAL C 251 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 243 through 244 removed outlier: 6.482A pdb=" N GLU C 278 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 296 through 303 removed outlier: 5.671A pdb=" N GLU C 297 " --> pdb=" O ARG C 312 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG C 312 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 373 through 376 removed outlier: 5.841A pdb=" N LEU C 392 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG C 420 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR C 396 " --> pdb=" O VAL C 416 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL C 416 " --> pdb=" O THR C 396 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N LYS C 398 " --> pdb=" O ARG C 414 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG C 414 " --> pdb=" O LYS C 398 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 116 through 122 removed outlier: 4.065A pdb=" N GLY D 116 " --> pdb=" O THR D 469 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL D 465 " --> pdb=" O PHE D 120 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS D 122 " --> pdb=" O ILE D 463 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE D 463 " --> pdb=" O LYS D 122 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG D 440 " --> pdb=" O GLY D 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 135 through 144 removed outlier: 4.876A pdb=" N TRP D 135 " --> pdb=" O THR D 158 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR D 158 " --> pdb=" O TRP D 135 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N THR D 137 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS D 156 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLU D 139 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU D 154 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR D 177 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU D 178 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS D 192 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 199 through 204 removed outlier: 6.450A pdb=" N TYR D 227 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU D 231 " --> pdb=" O TYR D 227 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 243 through 244 removed outlier: 4.009A pdb=" N VAL D 251 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 243 through 244 removed outlier: 6.482A pdb=" N GLU D 278 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 296 through 303 removed outlier: 5.671A pdb=" N GLU D 297 " --> pdb=" O ARG D 312 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG D 312 " --> pdb=" O GLU D 297 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 373 through 376 removed outlier: 5.842A pdb=" N LEU D 392 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG D 420 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR D 396 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL D 416 " --> pdb=" O THR D 396 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N LYS D 398 " --> pdb=" O ARG D 414 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG D 414 " --> pdb=" O LYS D 398 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.149A pdb=" N GLY E 10 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 133 through 137 Processing sheet with id=AD5, first strand: chain 'E' and resid 133 through 137 Processing sheet with id=AD6, first strand: chain 'E' and resid 164 through 167 removed outlier: 4.233A pdb=" N TYR E 207 " --> pdb=" O VAL E 224 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AD8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.995A pdb=" N LEU F 33 " --> pdb=" O HIS F 49 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N HIS F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 10 through 13 removed outlier: 4.054A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 114 through 118 removed outlier: 5.952A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 145 through 150 Processing sheet with id=AE3, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.149A pdb=" N GLY G 10 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 133 through 137 Processing sheet with id=AE6, first strand: chain 'G' and resid 133 through 137 Processing sheet with id=AE7, first strand: chain 'G' and resid 164 through 167 removed outlier: 4.233A pdb=" N TYR G 207 " --> pdb=" O VAL G 224 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AE9, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.995A pdb=" N LEU H 33 " --> pdb=" O HIS H 49 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N HIS H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 10 through 13 removed outlier: 4.055A pdb=" N THR H 97 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.952A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 145 through 150 Processing sheet with id=AF4, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.148A pdb=" N GLY I 10 " --> pdb=" O THR I 123 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 133 through 137 Processing sheet with id=AF7, first strand: chain 'I' and resid 133 through 137 Processing sheet with id=AF8, first strand: chain 'I' and resid 164 through 167 removed outlier: 4.234A pdb=" N TYR I 207 " --> pdb=" O VAL I 224 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AG1, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.996A pdb=" N LEU J 33 " --> pdb=" O HIS J 49 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N HIS J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 10 through 13 removed outlier: 4.055A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 114 through 118 removed outlier: 5.952A pdb=" N TYR J 173 " --> pdb=" O ASN J 138 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 145 through 150 Processing sheet with id=AG5, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AG6, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.149A pdb=" N GLY K 10 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 133 through 137 Processing sheet with id=AG8, first strand: chain 'K' and resid 133 through 137 Processing sheet with id=AG9, first strand: chain 'K' and resid 164 through 167 removed outlier: 4.233A pdb=" N TYR K 207 " --> pdb=" O VAL K 224 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AH2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.994A pdb=" N LEU L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N HIS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.054A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.952A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 145 through 150 996 hydrogen bonds defined for protein. 2664 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: 4.58 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8436 1.35 - 1.47: 6960 1.47 - 1.60: 11032 1.60 - 1.72: 0 1.72 - 1.85: 160 Bond restraints: 26588 Sorted by residual: bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.31e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.22e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.11e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.63e+00 ... (remaining 26583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 35124 2.07 - 4.15: 833 4.15 - 6.22: 127 6.22 - 8.30: 24 8.30 - 10.37: 4 Bond angle restraints: 36112 Sorted by residual: angle pdb=" CB GLU L 165 " pdb=" CG GLU L 165 " pdb=" CD GLU L 165 " ideal model delta sigma weight residual 112.60 118.51 -5.91 1.70e+00 3.46e-01 1.21e+01 angle pdb=" CB GLU F 165 " pdb=" CG GLU F 165 " pdb=" CD GLU F 165 " ideal model delta sigma weight residual 112.60 118.50 -5.90 1.70e+00 3.46e-01 1.20e+01 angle pdb=" CB GLU J 165 " pdb=" CG GLU J 165 " pdb=" CD GLU J 165 " ideal model delta sigma weight residual 112.60 118.49 -5.89 1.70e+00 3.46e-01 1.20e+01 angle pdb=" CB GLU H 165 " pdb=" CG GLU H 165 " pdb=" CD GLU H 165 " ideal model delta sigma weight residual 112.60 118.46 -5.86 1.70e+00 3.46e-01 1.19e+01 angle pdb=" C HIS A 356 " pdb=" N CYS A 357 " pdb=" CA CYS A 357 " ideal model delta sigma weight residual 122.08 126.94 -4.86 1.47e+00 4.63e-01 1.09e+01 ... (remaining 36107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.21: 15385 22.21 - 44.41: 731 44.41 - 66.62: 212 66.62 - 88.82: 55 88.82 - 111.03: 16 Dihedral angle restraints: 16399 sinusoidal: 6923 harmonic: 9476 Sorted by residual: dihedral pdb=" CB CYS B 195 " pdb=" CA CYS B 195 " pdb=" SG CYS B 195 " pdb=" CB CYS B 195 " ideal model delta sinusoidal sigma weight residual -86.00 0.00 -86.00 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CA CYS A 357 " pdb=" C CYS A 357 " pdb=" N LEU A 358 " pdb=" CA LEU A 358 " ideal model delta harmonic sigma weight residual 180.00 153.86 26.14 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA CYS D 357 " pdb=" C CYS D 357 " pdb=" N LEU D 358 " pdb=" CA LEU D 358 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 16396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.337: 4096 0.337 - 0.673: 20 0.673 - 1.010: 4 1.010 - 1.347: 0 1.347 - 1.683: 4 Chirality restraints: 4124 Sorted by residual: chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-02 2.50e+03 7.08e+03 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-02 2.50e+03 7.08e+03 chirality pdb=" C1 BMA P 3 " pdb=" O4 NAG P 2 " pdb=" C2 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-02 2.50e+03 7.08e+03 ... (remaining 4121 not shown) Planarity restraints: 4616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 145 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO B 146 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 145 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO C 146 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 146 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 146 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 145 " 0.029 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO A 146 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.024 5.00e-02 4.00e+02 ... (remaining 4613 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 281 2.61 - 3.18: 20430 3.18 - 3.75: 35782 3.75 - 4.33: 53268 4.33 - 4.90: 90757 Nonbonded interactions: 200518 Sorted by model distance: nonbonded pdb=" SG CYS H 134 " pdb=" SG CYS H 194 " model vdw 2.036 3.760 nonbonded pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " model vdw 2.036 3.760 nonbonded pdb=" SG CYS F 134 " pdb=" SG CYS F 194 " model vdw 2.036 3.760 nonbonded pdb=" SG CYS J 134 " pdb=" SG CYS J 194 " model vdw 2.036 3.760 nonbonded pdb=" SG CYS K 153 " pdb=" SG CYS K 209 " model vdw 2.038 3.760 ... (remaining 200513 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 20.290 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 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 : 0.007 0.791 26669 Z= 0.349 Angle : 1.293 74.766 36318 Z= 0.577 Chirality : 0.087 1.683 4124 Planarity : 0.004 0.043 4600 Dihedral : 15.050 111.030 10240 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.69 % Allowed : 5.69 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.13), residues: 3288 helix: -3.17 (0.37), residues: 76 sheet: -0.24 (0.13), residues: 1448 loop : -2.59 (0.12), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 211 TYR 0.016 0.002 TYR G 109 PHE 0.017 0.002 PHE C 374 TRP 0.019 0.001 TRP B 198 HIS 0.004 0.001 HIS J 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.23 (26588) covalent geometry : angle 0.79446 / 0.43 (36112) SS BOND : bond 0.12999 / 4.33 ( 37) SS BOND : angle 11.92139 / 6.59 ( 74) hydrogen bonds : bond 0.13317 / 8.89 ( 912) hydrogen bonds : angle 7.16600 / 5.02 ( 2664) link_ALPHA1-2 : bond 0.06505 / 3.26 ( 4) link_ALPHA1-2 : angle 18.41670 / 11.61 ( 12) link_ALPHA1-3 : bond 0.06537 / 3.42 ( 8) link_ALPHA1-3 : angle 15.32606 / 8.92 ( 24) link_ALPHA1-6 : bond 0.06565 / 3.43 ( 8) link_ALPHA1-6 : angle 16.33467 / 9.05 ( 24) link_BETA1-4 : bond 0.06473 / 3.38 ( 8) link_BETA1-4 : angle 21.23483 / 12.03 ( 24) link_NAG-ASN : bond 0.00197 / 0.12 ( 16) link_NAG-ASN : angle 3.12863 / 1.93 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 288 time to evaluate : 0.869 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 outliers start: 164 outliers final: 17 residues processed: 422 average time/residue: 0.7102 time to fit residues: 338.3471 Evaluate side-chains 191 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 143 SER Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain K residue 143 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 55.1482 > 50:) chunk 298 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN A 188 HIS A 204 HIS A 246 GLN A 293 GLN A 367 HIS A 413 ASN A 415 GLN A 439 ASN A 461 ASN B 124 ASN B 188 HIS B 204 HIS B 246 GLN B 293 GLN B 367 HIS B 413 ASN B 415 GLN B 439 ASN B 461 ASN C 124 ASN C 188 HIS C 204 HIS C 246 GLN C 293 GLN C 413 ASN C 415 GLN C 439 ASN C 461 ASN D 124 ASN D 188 HIS D 204 HIS D 246 GLN D 293 GLN D 367 HIS D 413 ASN D 415 GLN D 439 ASN D 461 ASN ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN F 100 GLN ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 GLN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 100 GLN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 GLN ** I 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 199 GLN ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 100 GLN L 138 ASN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.068027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.040528 restraints weight = 86497.957| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 3.25 r_work: 0.2568 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9285 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 26669 Z= 0.213 Angle : 0.836 55.231 36318 Z= 0.421 Chirality : 0.048 0.173 4124 Planarity : 0.004 0.042 4600 Dihedral : 9.257 86.846 4473 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.05 % Allowed : 12.45 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.14), residues: 3288 helix: -3.11 (0.35), residues: 108 sheet: 0.29 (0.14), residues: 1340 loop : -2.26 (0.12), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 18 TYR 0.013 0.002 TYR J 192 PHE 0.027 0.002 PHE L 209 TRP 0.018 0.001 TRP A 198 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (26588) covalent geometry : angle 0.73054 / 0.38 (36112) SS BOND : bond 0.00664 / 0.39 ( 37) SS BOND : angle 8.43320 / 4.71 ( 74) hydrogen bonds : bond 0.04558 / 3.05 ( 912) hydrogen bonds : angle 6.11311 / 4.30 ( 2664) link_ALPHA1-2 : bond 0.00327 / 0.16 ( 4) link_ALPHA1-2 : angle 1.96202 / 1.22 ( 12) link_ALPHA1-3 : bond 0.00733 / 0.40 ( 8) link_ALPHA1-3 : angle 2.07595 / 1.20 ( 24) link_ALPHA1-6 : bond 0.00874 / 0.49 ( 8) link_ALPHA1-6 : angle 1.65231 / 0.95 ( 24) link_BETA1-4 : bond 0.01813 / 0.86 ( 8) link_BETA1-4 : angle 3.48415 / 1.89 ( 24) link_NAG-ASN : bond 0.00310 / 0.17 ( 16) link_NAG-ASN : angle 2.55197 / 1.58 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 187 time to evaluate : 0.938 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: A 247 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8883 (mp0) REVERT: A 250 CYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8685 (p) REVERT: B 247 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8878 (mp0) REVERT: B 250 CYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8695 (p) REVERT: C 247 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8886 (mp0) REVERT: C 250 CYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8651 (p) REVERT: D 247 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8921 (mp0) REVERT: D 250 CYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8685 (p) REVERT: E 76 GLU cc_start: 0.8785 (mp0) cc_final: 0.8568 (mp0) REVERT: E 130 LYS cc_start: 0.9071 (ttpp) cc_final: 0.8685 (tmmm) REVERT: E 156 LYS cc_start: 0.8857 (tppp) cc_final: 0.8625 (tppp) REVERT: F 42 ARG cc_start: 0.9170 (ttm-80) cc_final: 0.8857 (mtp85) REVERT: F 100 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8957 (pm20) REVERT: F 199 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8928 (pp30) REVERT: G 140 SER cc_start: 0.8439 (OUTLIER) cc_final: 0.8157 (p) REVERT: G 156 LYS cc_start: 0.9061 (ttmm) cc_final: 0.8669 (tptp) REVERT: G 214 LYS cc_start: 0.9366 (mtpp) cc_final: 0.9090 (tmmt) REVERT: H 100 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8932 (pm20) REVERT: H 123 GLU cc_start: 0.9681 (mt-10) cc_final: 0.9444 (mp0) REVERT: I 130 LYS cc_start: 0.9064 (ttpp) cc_final: 0.8793 (tmmm) REVERT: J 165 GLU cc_start: 0.9252 (mm-30) cc_final: 0.9049 (mm-30) REVERT: K 130 LYS cc_start: 0.9085 (tptm) cc_final: 0.8789 (tptp) REVERT: K 140 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.8137 (p) REVERT: K 214 LYS cc_start: 0.9284 (mtpp) cc_final: 0.9059 (tmmt) REVERT: L 100 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8975 (pm20) REVERT: L 123 GLU cc_start: 0.9672 (mt-10) cc_final: 0.9438 (mp0) REVERT: L 199 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8775 (pp30) outliers start: 59 outliers final: 20 residues processed: 246 average time/residue: 0.7373 time to fit residues: 204.8798 Evaluate side-chains 216 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 199 GLN Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 210 ASN Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 210 ASN Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain K residue 140 SER Chi-restraints excluded: chain K residue 164 THR Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain K residue 210 ASN Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 199 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 143 optimal weight: 4.9990 chunk 297 optimal weight: 0.8980 chunk 312 optimal weight: 3.9990 chunk 189 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 277 optimal weight: 9.9990 chunk 271 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 301 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 367 HIS ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 HIS ** 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 = 0.3538 r_free = 0.3538 target = 0.069472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.041576 restraints weight = 85398.360| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 3.53 r_work: 0.2554 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2436 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9285 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 26669 Z= 0.190 Angle : 0.791 55.738 36318 Z= 0.399 Chirality : 0.047 0.167 4124 Planarity : 0.004 0.044 4600 Dihedral : 8.509 79.662 4460 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.60 % Allowed : 13.04 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.14), residues: 3288 helix: -2.35 (0.43), residues: 108 sheet: 0.39 (0.15), residues: 1336 loop : -1.94 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 223 TYR 0.012 0.001 TYR F 140 PHE 0.031 0.002 PHE F 209 TRP 0.017 0.001 TRP A 198 HIS 0.004 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (26588) covalent geometry : angle 0.68073 / 0.35 (36112) SS BOND : bond 0.00546 / 0.30 ( 37) SS BOND : angle 8.46102 / 4.72 ( 74) hydrogen bonds : bond 0.04265 / 2.85 ( 912) hydrogen bonds : angle 5.85770 / 4.11 ( 2664) link_ALPHA1-2 : bond 0.00022 / 0.01 ( 4) link_ALPHA1-2 : angle 1.69412 / 1.08 ( 12) link_ALPHA1-3 : bond 0.00893 / 0.50 ( 8) link_ALPHA1-3 : angle 1.60483 / 0.91 ( 24) link_ALPHA1-6 : bond 0.00429 / 0.24 ( 8) link_ALPHA1-6 : angle 1.49590 / 0.87 ( 24) link_BETA1-4 : bond 0.01111 / 0.55 ( 8) link_BETA1-4 : angle 3.09572 / 1.69 ( 24) link_NAG-ASN : bond 0.00248 / 0.13 ( 16) link_NAG-ASN : angle 2.51887 / 1.57 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 1.068 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: A 247 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8892 (mp0) REVERT: A 250 CYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8691 (p) REVERT: B 247 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8887 (mp0) REVERT: B 250 CYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8699 (p) REVERT: C 250 CYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8675 (p) REVERT: D 247 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8923 (mp0) REVERT: D 250 CYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8676 (p) REVERT: F 192 TYR cc_start: 0.9250 (m-80) cc_final: 0.9020 (m-80) REVERT: G 130 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8525 (tptp) REVERT: G 223 ARG cc_start: 0.8698 (ptm160) cc_final: 0.8481 (ptm160) REVERT: H 55 GLU cc_start: 0.8579 (tp30) cc_final: 0.8340 (tp30) REVERT: H 123 GLU cc_start: 0.9700 (mt-10) cc_final: 0.9468 (mp0) REVERT: H 192 TYR cc_start: 0.9212 (m-80) cc_final: 0.8955 (m-80) REVERT: I 33 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8747 (mt-10) REVERT: I 130 LYS cc_start: 0.9109 (ttpp) cc_final: 0.8584 (tttm) REVERT: I 156 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8548 (tppp) REVERT: I 184 GLN cc_start: 0.8768 (mt0) cc_final: 0.8146 (mp10) REVERT: L 123 GLU cc_start: 0.9687 (mt-10) cc_final: 0.9456 (mp0) REVERT: L 192 TYR cc_start: 0.9249 (m-80) cc_final: 0.9022 (m-80) outliers start: 46 outliers final: 22 residues processed: 242 average time/residue: 0.7363 time to fit residues: 200.3501 Evaluate side-chains 207 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 210 ASN Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain K residue 164 THR Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain K residue 210 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 186 optimal weight: 0.0980 chunk 263 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 284 optimal weight: 5.9990 chunk 162 optimal weight: 0.2980 chunk 289 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 GLN E 168 ASN F 189 HIS H 138 ASN H 189 HIS J 138 ASN ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 ASN L 189 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.069874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.042362 restraints weight = 85123.753| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.38 r_work: 0.2597 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2482 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9255 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26669 Z= 0.122 Angle : 0.751 55.716 36318 Z= 0.375 Chirality : 0.046 0.160 4124 Planarity : 0.004 0.046 4600 Dihedral : 7.321 66.093 4458 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.49 % Allowed : 13.45 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.14), residues: 3288 helix: -1.75 (0.46), residues: 108 sheet: 0.58 (0.14), residues: 1324 loop : -1.72 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 223 TYR 0.011 0.001 TYR E 189 PHE 0.034 0.001 PHE J 209 TRP 0.015 0.001 TRP D 198 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (26588) covalent geometry : angle 0.63834 / 0.33 (36112) SS BOND : bond 0.00557 / 0.25 ( 37) SS BOND : angle 8.40144 / 4.68 ( 74) hydrogen bonds : bond 0.03419 / 2.30 ( 912) hydrogen bonds : angle 5.48911 / 3.84 ( 2664) link_ALPHA1-2 : bond 0.00188 / 0.09 ( 4) link_ALPHA1-2 : angle 1.71563 / 1.08 ( 12) link_ALPHA1-3 : bond 0.00984 / 0.55 ( 8) link_ALPHA1-3 : angle 1.53262 / 0.87 ( 24) link_ALPHA1-6 : bond 0.00524 / 0.29 ( 8) link_ALPHA1-6 : angle 1.39737 / 0.82 ( 24) link_BETA1-4 : bond 0.01023 / 0.51 ( 8) link_BETA1-4 : angle 2.59113 / 1.41 ( 24) link_NAG-ASN : bond 0.00273 / 0.15 ( 16) link_NAG-ASN : angle 2.20719 / 1.37 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 195 time to evaluate : 0.961 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: A 250 CYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8641 (p) REVERT: B 250 CYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8679 (p) REVERT: C 250 CYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8617 (p) REVERT: D 250 CYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8645 (p) REVERT: E 76 GLU cc_start: 0.8897 (mp0) cc_final: 0.8647 (mp0) REVERT: F 18 ARG cc_start: 0.9286 (ttm110) cc_final: 0.8679 (ttm-80) REVERT: F 42 ARG cc_start: 0.9123 (ttm-80) cc_final: 0.8770 (mmm-85) REVERT: F 192 TYR cc_start: 0.9272 (m-80) cc_final: 0.9051 (m-80) REVERT: G 33 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8583 (mt-10) REVERT: G 76 GLU cc_start: 0.8861 (mp0) cc_final: 0.8509 (mp0) REVERT: G 130 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8582 (tptp) REVERT: H 42 ARG cc_start: 0.9097 (ttm-80) cc_final: 0.8763 (mmm-85) REVERT: H 55 GLU cc_start: 0.8582 (tp30) cc_final: 0.8361 (tp30) REVERT: H 123 GLU cc_start: 0.9720 (mt-10) cc_final: 0.9478 (mp0) REVERT: H 181 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.8952 (pt) REVERT: H 185 ASP cc_start: 0.9666 (m-30) cc_final: 0.9290 (p0) REVERT: H 192 TYR cc_start: 0.9238 (m-80) cc_final: 0.9037 (m-80) REVERT: I 76 GLU cc_start: 0.8872 (mp0) cc_final: 0.8632 (mp0) REVERT: I 156 LYS cc_start: 0.8947 (ttmm) cc_final: 0.8703 (tppp) REVERT: J 181 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.8898 (pt) REVERT: J 185 ASP cc_start: 0.9626 (m-30) cc_final: 0.9250 (p0) REVERT: K 33 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8779 (mt-10) REVERT: K 76 GLU cc_start: 0.8872 (mp0) cc_final: 0.8510 (mp0) REVERT: K 130 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.8698 (tptp) REVERT: L 123 GLU cc_start: 0.9702 (mt-10) cc_final: 0.9467 (mp0) REVERT: L 181 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.8952 (pt) REVERT: L 185 ASP cc_start: 0.9616 (m-30) cc_final: 0.9339 (p0) REVERT: L 192 TYR cc_start: 0.9243 (m-80) cc_final: 0.8931 (m-80) REVERT: L 211 ARG cc_start: 0.8786 (tpp80) cc_final: 0.8574 (tpp80) outliers start: 43 outliers final: 22 residues processed: 235 average time/residue: 0.7123 time to fit residues: 189.3593 Evaluate side-chains 212 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 210 ASN Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 210 ASN Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 130 LYS Chi-restraints excluded: chain K residue 164 THR Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain K residue 210 ASN Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 67 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 226 optimal weight: 0.9980 chunk 312 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 279 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 301 optimal weight: 30.0000 chunk 27 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN B 246 GLN D 246 GLN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 189 HIS ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.070793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.042577 restraints weight = 81577.645| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.71 r_work: 0.2574 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2459 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9263 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26669 Z= 0.142 Angle : 0.752 55.727 36318 Z= 0.376 Chirality : 0.046 0.170 4124 Planarity : 0.004 0.060 4600 Dihedral : 6.934 61.704 4456 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.73 % Allowed : 13.18 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.14), residues: 3288 helix: -1.17 (0.48), residues: 108 sheet: 0.66 (0.15), residues: 1324 loop : -1.54 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 18 TYR 0.018 0.001 TYR I 189 PHE 0.034 0.001 PHE F 209 TRP 0.015 0.001 TRP B 198 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (26588) covalent geometry : angle 0.63924 / 0.33 (36112) SS BOND : bond 0.00558 / 0.26 ( 37) SS BOND : angle 8.41067 / 4.69 ( 74) hydrogen bonds : bond 0.03633 / 2.44 ( 912) hydrogen bonds : angle 5.41787 / 3.79 ( 2664) link_ALPHA1-2 : bond 0.00119 / 0.06 ( 4) link_ALPHA1-2 : angle 1.64708 / 1.04 ( 12) link_ALPHA1-3 : bond 0.00943 / 0.53 ( 8) link_ALPHA1-3 : angle 1.50297 / 0.85 ( 24) link_ALPHA1-6 : bond 0.00445 / 0.24 ( 8) link_ALPHA1-6 : angle 1.46354 / 0.85 ( 24) link_BETA1-4 : bond 0.00970 / 0.48 ( 8) link_BETA1-4 : angle 2.57483 / 1.41 ( 24) link_NAG-ASN : bond 0.00216 / 0.12 ( 16) link_NAG-ASN : angle 2.27646 / 1.42 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 0.772 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: A 250 CYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8680 (p) REVERT: B 250 CYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8695 (p) REVERT: C 250 CYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8649 (p) REVERT: D 250 CYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8660 (p) REVERT: E 76 GLU cc_start: 0.8928 (mp0) cc_final: 0.8636 (mp0) REVERT: E 130 LYS cc_start: 0.9156 (ttpp) cc_final: 0.8710 (tttm) REVERT: F 42 ARG cc_start: 0.9072 (ttm-80) cc_final: 0.8750 (mmm-85) REVERT: F 185 ASP cc_start: 0.9630 (m-30) cc_final: 0.9306 (p0) REVERT: F 192 TYR cc_start: 0.9294 (m-80) cc_final: 0.9000 (m-80) REVERT: G 130 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8585 (tptp) REVERT: H 42 ARG cc_start: 0.9067 (ttm-80) cc_final: 0.8787 (mmm-85) REVERT: H 123 GLU cc_start: 0.9708 (mt-10) cc_final: 0.9461 (mp0) REVERT: H 181 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.8915 (pt) REVERT: H 185 ASP cc_start: 0.9669 (m-30) cc_final: 0.9277 (p0) REVERT: H 192 TYR cc_start: 0.9235 (m-80) cc_final: 0.9025 (m-80) REVERT: I 130 LYS cc_start: 0.9162 (ttpp) cc_final: 0.8656 (tttm) REVERT: I 156 LYS cc_start: 0.8847 (ttmm) cc_final: 0.8514 (tppp) REVERT: I 184 GLN cc_start: 0.8845 (mt0) cc_final: 0.8134 (mp10) REVERT: J 192 TYR cc_start: 0.9105 (m-10) cc_final: 0.8732 (m-80) REVERT: K 130 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8590 (tptp) REVERT: L 123 GLU cc_start: 0.9694 (mt-10) cc_final: 0.9444 (mp0) REVERT: L 192 TYR cc_start: 0.9249 (m-80) cc_final: 0.8983 (m-80) REVERT: L 211 ARG cc_start: 0.8757 (tpp80) cc_final: 0.8527 (tpp80) outliers start: 50 outliers final: 23 residues processed: 232 average time/residue: 0.7033 time to fit residues: 184.2369 Evaluate side-chains 207 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 210 ASN Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 210 ASN Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 130 LYS Chi-restraints excluded: chain K residue 164 THR Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain K residue 210 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 233 optimal weight: 7.9990 chunk 238 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 272 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 292 optimal weight: 5.9990 chunk 275 optimal weight: 0.3980 chunk 219 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 GLN C 246 GLN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 ASN F 138 ASN F 199 GLN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 217 ASN L 199 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.068391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.040066 restraints weight = 85918.883| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 3.54 r_work: 0.2513 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2397 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9307 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 26669 Z= 0.278 Angle : 0.838 55.733 36318 Z= 0.423 Chirality : 0.049 0.174 4124 Planarity : 0.005 0.050 4600 Dihedral : 7.636 70.211 4456 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.01 % Allowed : 13.77 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3288 helix: -0.50 (0.52), residues: 108 sheet: 0.54 (0.14), residues: 1424 loop : -1.60 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 18 TYR 0.018 0.002 TYR I 189 PHE 0.034 0.002 PHE F 209 TRP 0.016 0.001 TRP A 198 HIS 0.005 0.001 HIS C 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.28 (26588) covalent geometry : angle 0.73000 / 0.38 (36112) SS BOND : bond 0.00620 / 0.33 ( 37) SS BOND : angle 8.63437 / 4.84 ( 74) hydrogen bonds : bond 0.04745 / 3.17 ( 912) hydrogen bonds : angle 5.62282 / 3.93 ( 2664) link_ALPHA1-2 : bond 0.00253 / 0.13 ( 4) link_ALPHA1-2 : angle 1.65134 / 1.04 ( 12) link_ALPHA1-3 : bond 0.00795 / 0.46 ( 8) link_ALPHA1-3 : angle 1.64763 / 0.93 ( 24) link_ALPHA1-6 : bond 0.00142 / 0.07 ( 8) link_ALPHA1-6 : angle 1.56949 / 0.91 ( 24) link_BETA1-4 : bond 0.00948 / 0.46 ( 8) link_BETA1-4 : angle 3.18970 / 1.75 ( 24) link_NAG-ASN : bond 0.00314 / 0.16 ( 16) link_NAG-ASN : angle 2.69906 / 1.67 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 183 time to evaluate : 0.910 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: A 247 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8807 (mp0) REVERT: A 250 CYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8692 (p) REVERT: B 247 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8824 (mp0) REVERT: B 250 CYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8708 (p) REVERT: C 250 CYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8692 (p) REVERT: D 247 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.8816 (mp0) REVERT: D 250 CYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8699 (p) REVERT: E 130 LYS cc_start: 0.9128 (ttpp) cc_final: 0.8882 (tmmm) REVERT: F 185 ASP cc_start: 0.9621 (m-30) cc_final: 0.9252 (p0) REVERT: F 192 TYR cc_start: 0.9284 (m-80) cc_final: 0.9022 (m-80) REVERT: F 211 ARG cc_start: 0.8684 (tpp80) cc_final: 0.8453 (tpp80) REVERT: G 130 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8536 (tptp) REVERT: H 123 GLU cc_start: 0.9704 (mt-10) cc_final: 0.9460 (mp0) REVERT: I 76 GLU cc_start: 0.8932 (mp0) cc_final: 0.8699 (mp0) REVERT: I 130 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8628 (tttm) REVERT: J 192 TYR cc_start: 0.9139 (m-10) cc_final: 0.8870 (m-80) REVERT: K 130 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8521 (ttpp) REVERT: K 156 LYS cc_start: 0.8909 (ttmm) cc_final: 0.8543 (tppp) REVERT: K 184 GLN cc_start: 0.8667 (mt0) cc_final: 0.8289 (mp10) REVERT: L 123 GLU cc_start: 0.9675 (mt-10) cc_final: 0.9421 (mp0) REVERT: L 185 ASP cc_start: 0.9604 (m-30) cc_final: 0.9314 (p0) REVERT: L 192 TYR cc_start: 0.9265 (m-80) cc_final: 0.9005 (m-80) outliers start: 58 outliers final: 26 residues processed: 228 average time/residue: 0.7647 time to fit residues: 196.5561 Evaluate side-chains 209 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 210 ASN Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 210 ASN Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 130 LYS Chi-restraints excluded: chain K residue 164 THR Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain K residue 210 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 72 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 287 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 271 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 316 optimal weight: 10.0000 chunk 307 optimal weight: 7.9990 chunk 139 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 GLN D 246 GLN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 HIS ** 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 = 0.3537 r_free = 0.3537 target = 0.068350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.040630 restraints weight = 85708.900| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.35 r_work: 0.2561 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9270 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26669 Z= 0.152 Angle : 0.785 55.716 36318 Z= 0.392 Chirality : 0.046 0.168 4124 Planarity : 0.004 0.049 4600 Dihedral : 7.008 61.543 4456 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.63 % Allowed : 14.60 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.15), residues: 3288 helix: -0.26 (0.52), residues: 108 sheet: 0.71 (0.15), residues: 1380 loop : -1.46 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 18 TYR 0.010 0.001 TYR K 189 PHE 0.036 0.001 PHE F 209 TRP 0.017 0.001 TRP D 198 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (26588) covalent geometry : angle 0.67511 / 0.35 (36112) SS BOND : bond 0.00547 / 0.26 ( 37) SS BOND : angle 8.48263 / 4.74 ( 74) hydrogen bonds : bond 0.03710 / 2.49 ( 912) hydrogen bonds : angle 5.42037 / 3.78 ( 2664) link_ALPHA1-2 : bond 0.00024 / 0.01 ( 4) link_ALPHA1-2 : angle 1.77164 / 1.12 ( 12) link_ALPHA1-3 : bond 0.00973 / 0.55 ( 8) link_ALPHA1-3 : angle 1.60466 / 0.91 ( 24) link_ALPHA1-6 : bond 0.00378 / 0.20 ( 8) link_ALPHA1-6 : angle 1.46546 / 0.86 ( 24) link_BETA1-4 : bond 0.00983 / 0.49 ( 8) link_BETA1-4 : angle 2.61433 / 1.42 ( 24) link_NAG-ASN : bond 0.00270 / 0.15 ( 16) link_NAG-ASN : angle 2.39167 / 1.48 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 184 time to evaluate : 1.066 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: A 250 CYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8665 (p) REVERT: B 250 CYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8662 (p) REVERT: C 250 CYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8660 (p) REVERT: D 250 CYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8657 (p) REVERT: E 76 GLU cc_start: 0.8977 (mp0) cc_final: 0.8764 (mp0) REVERT: E 130 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8589 (tttm) REVERT: F 42 ARG cc_start: 0.9056 (ttm-80) cc_final: 0.8749 (mmm-85) REVERT: F 185 ASP cc_start: 0.9659 (m-30) cc_final: 0.9244 (p0) REVERT: F 192 TYR cc_start: 0.9263 (m-80) cc_final: 0.9002 (m-80) REVERT: F 211 ARG cc_start: 0.8665 (tpp80) cc_final: 0.8412 (tpp80) REVERT: G 130 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8550 (tptp) REVERT: H 42 ARG cc_start: 0.9073 (ttm-80) cc_final: 0.8767 (mmm-85) REVERT: H 123 GLU cc_start: 0.9703 (mt-10) cc_final: 0.9469 (mp0) REVERT: H 192 TYR cc_start: 0.9212 (m-80) cc_final: 0.8505 (m-80) REVERT: I 76 GLU cc_start: 0.8948 (mp0) cc_final: 0.8701 (mp0) REVERT: I 130 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8555 (tptp) REVERT: I 183 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8877 (tm) REVERT: I 184 GLN cc_start: 0.8699 (mt0) cc_final: 0.8366 (mp10) REVERT: J 192 TYR cc_start: 0.8938 (m-10) cc_final: 0.8604 (m-80) REVERT: K 130 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8573 (ttpp) REVERT: K 156 LYS cc_start: 0.8837 (ttmm) cc_final: 0.8538 (tppp) REVERT: K 183 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8999 (tm) REVERT: K 184 GLN cc_start: 0.8594 (mt0) cc_final: 0.8134 (mp10) REVERT: K 219 LYS cc_start: 0.8538 (mppt) cc_final: 0.8271 (mmpt) REVERT: L 123 GLU cc_start: 0.9690 (mt-10) cc_final: 0.9420 (mp0) REVERT: L 192 TYR cc_start: 0.9252 (m-80) cc_final: 0.9020 (m-80) outliers start: 47 outliers final: 25 residues processed: 219 average time/residue: 0.7433 time to fit residues: 183.5186 Evaluate side-chains 212 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 210 ASN Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 210 ASN Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 130 LYS Chi-restraints excluded: chain K residue 164 THR Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 210 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 231 optimal weight: 9.9990 chunk 247 optimal weight: 0.9990 chunk 290 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 chunk 197 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 282 optimal weight: 20.0000 chunk 212 optimal weight: 0.9990 chunk 291 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 GLN D 246 GLN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** 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 = 0.3524 r_free = 0.3524 target = 0.068132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.040077 restraints weight = 86190.738| |-----------------------------------------------------------------------------| r_work (start): 0.2658 rms_B_bonded: 3.45 r_work: 0.2530 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2414 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9292 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 26669 Z= 0.217 Angle : 0.819 55.728 36318 Z= 0.411 Chirality : 0.047 0.177 4124 Planarity : 0.004 0.057 4600 Dihedral : 7.225 64.398 4456 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.70 % Allowed : 15.12 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 3288 helix: 0.02 (0.54), residues: 108 sheet: 0.69 (0.14), residues: 1424 loop : -1.47 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 18 TYR 0.022 0.002 TYR H 192 PHE 0.037 0.002 PHE J 209 TRP 0.016 0.001 TRP D 198 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 (26588) covalent geometry : angle 0.71216 / 0.37 (36112) SS BOND : bond 0.00563 / 0.29 ( 37) SS BOND : angle 8.52895 / 4.77 ( 74) hydrogen bonds : bond 0.04254 / 2.85 ( 912) hydrogen bonds : angle 5.48036 / 3.82 ( 2664) link_ALPHA1-2 : bond 0.00244 / 0.12 ( 4) link_ALPHA1-2 : angle 1.63154 / 1.02 ( 12) link_ALPHA1-3 : bond 0.00854 / 0.48 ( 8) link_ALPHA1-3 : angle 1.60531 / 0.91 ( 24) link_ALPHA1-6 : bond 0.00223 / 0.12 ( 8) link_ALPHA1-6 : angle 1.53718 / 0.90 ( 24) link_BETA1-4 : bond 0.00959 / 0.47 ( 8) link_BETA1-4 : angle 2.92759 / 1.60 ( 24) link_NAG-ASN : bond 0.00260 / 0.14 ( 16) link_NAG-ASN : angle 2.53575 / 1.57 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 181 time to evaluate : 0.675 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: A 247 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8857 (mp0) REVERT: A 250 CYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8680 (p) REVERT: B 247 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8864 (mp0) REVERT: B 250 CYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8678 (p) REVERT: C 250 CYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8689 (p) REVERT: D 247 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8859 (mp0) REVERT: D 250 CYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8679 (p) REVERT: E 43 LYS cc_start: 0.9046 (mmmm) cc_final: 0.8808 (mmmm) REVERT: E 76 GLU cc_start: 0.8993 (mp0) cc_final: 0.8759 (mp0) REVERT: E 130 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8637 (tttm) REVERT: F 42 ARG cc_start: 0.9068 (ttm-80) cc_final: 0.8779 (mmm-85) REVERT: F 192 TYR cc_start: 0.9261 (m-80) cc_final: 0.9009 (m-80) REVERT: F 211 ARG cc_start: 0.8635 (tpp80) cc_final: 0.8368 (tpp80) REVERT: G 43 LYS cc_start: 0.9069 (mmmm) cc_final: 0.8846 (mmmm) REVERT: G 76 GLU cc_start: 0.8904 (mp0) cc_final: 0.8654 (mp0) REVERT: G 130 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8562 (tptp) REVERT: H 42 ARG cc_start: 0.9083 (ttm-80) cc_final: 0.8791 (mmm-85) REVERT: H 123 GLU cc_start: 0.9690 (mt-10) cc_final: 0.9445 (mp0) REVERT: I 43 LYS cc_start: 0.9082 (mmmm) cc_final: 0.8846 (mmmm) REVERT: I 130 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8608 (tptp) REVERT: I 156 LYS cc_start: 0.8761 (tppp) cc_final: 0.8543 (tppp) REVERT: I 183 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9105 (tm) REVERT: J 142 ARG cc_start: 0.9093 (tpp80) cc_final: 0.8801 (tpp80) REVERT: J 192 TYR cc_start: 0.9036 (m-10) cc_final: 0.8781 (m-80) REVERT: K 43 LYS cc_start: 0.9071 (mmmm) cc_final: 0.8838 (mmmm) REVERT: K 76 GLU cc_start: 0.8927 (mp0) cc_final: 0.8679 (mp0) REVERT: K 156 LYS cc_start: 0.8895 (ttmm) cc_final: 0.8379 (tppp) REVERT: K 183 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9150 (tm) REVERT: L 123 GLU cc_start: 0.9679 (mt-10) cc_final: 0.9423 (mp0) REVERT: L 142 ARG cc_start: 0.9041 (tpp80) cc_final: 0.8737 (tpp80) outliers start: 49 outliers final: 25 residues processed: 218 average time/residue: 0.7465 time to fit residues: 183.1397 Evaluate side-chains 211 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 210 ASN Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 210 ASN Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 164 THR Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 210 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 297 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 256 optimal weight: 10.0000 chunk 195 optimal weight: 5.9990 chunk 213 optimal weight: 0.8980 chunk 179 optimal weight: 10.0000 chunk 279 optimal weight: 30.0000 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** 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 = 0.3523 r_free = 0.3523 target = 0.068074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.040102 restraints weight = 86360.028| |-----------------------------------------------------------------------------| r_work (start): 0.2658 rms_B_bonded: 3.40 r_work: 0.2530 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2416 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9286 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26669 Z= 0.225 Angle : 0.825 55.714 36318 Z= 0.415 Chirality : 0.048 0.174 4124 Planarity : 0.004 0.063 4600 Dihedral : 7.300 65.065 4456 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.60 % Allowed : 15.78 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.15), residues: 3288 helix: 0.02 (0.54), residues: 108 sheet: 0.68 (0.14), residues: 1424 loop : -1.44 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 18 TYR 0.014 0.002 TYR K 189 PHE 0.034 0.002 PHE F 209 TRP 0.016 0.001 TRP D 198 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.23 (26588) covalent geometry : angle 0.71924 / 0.37 (36112) SS BOND : bond 0.00567 / 0.29 ( 37) SS BOND : angle 8.52825 / 4.77 ( 74) hydrogen bonds : bond 0.04269 / 2.85 ( 912) hydrogen bonds : angle 5.49665 / 3.83 ( 2664) link_ALPHA1-2 : bond 0.00109 / 0.05 ( 4) link_ALPHA1-2 : angle 1.69658 / 1.08 ( 12) link_ALPHA1-3 : bond 0.00849 / 0.47 ( 8) link_ALPHA1-3 : angle 1.63304 / 0.93 ( 24) link_ALPHA1-6 : bond 0.00213 / 0.11 ( 8) link_ALPHA1-6 : angle 1.52037 / 0.89 ( 24) link_BETA1-4 : bond 0.00948 / 0.47 ( 8) link_BETA1-4 : angle 2.92039 / 1.60 ( 24) link_NAG-ASN : bond 0.00266 / 0.14 ( 16) link_NAG-ASN : angle 2.56840 / 1.59 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 1.072 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: A 250 CYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8675 (p) REVERT: B 250 CYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8689 (p) REVERT: C 250 CYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8665 (p) REVERT: D 250 CYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8675 (p) REVERT: E 130 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8620 (tttm) REVERT: F 192 TYR cc_start: 0.9251 (m-80) cc_final: 0.8673 (m-80) REVERT: G 76 GLU cc_start: 0.8953 (mp0) cc_final: 0.8699 (mp0) REVERT: G 130 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8529 (tptp) REVERT: H 123 GLU cc_start: 0.9688 (mt-10) cc_final: 0.9445 (mp0) REVERT: H 192 TYR cc_start: 0.8907 (m-80) cc_final: 0.8603 (m-80) REVERT: I 76 GLU cc_start: 0.9022 (mp0) cc_final: 0.8773 (mp0) REVERT: I 130 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8855 (ttpp) REVERT: I 183 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8938 (tm) REVERT: I 184 GLN cc_start: 0.8711 (mt0) cc_final: 0.8390 (mp10) REVERT: J 142 ARG cc_start: 0.9096 (tpp80) cc_final: 0.8782 (tpp80) REVERT: J 192 TYR cc_start: 0.9016 (m-10) cc_final: 0.8734 (m-80) REVERT: K 76 GLU cc_start: 0.8972 (mp0) cc_final: 0.8712 (mp0) REVERT: K 130 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8423 (tptp) REVERT: K 156 LYS cc_start: 0.8858 (ttmm) cc_final: 0.8412 (tppp) REVERT: K 183 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9095 (tm) REVERT: L 123 GLU cc_start: 0.9677 (mt-10) cc_final: 0.9419 (mp0) REVERT: L 142 ARG cc_start: 0.9049 (tpp80) cc_final: 0.8730 (tpp80) REVERT: L 192 TYR cc_start: 0.9259 (m-80) cc_final: 0.8595 (m-80) outliers start: 46 outliers final: 27 residues processed: 217 average time/residue: 0.7940 time to fit residues: 193.7025 Evaluate side-chains 211 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 210 ASN Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 210 ASN Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 130 LYS Chi-restraints excluded: chain K residue 164 THR Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 210 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 273 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 233 optimal weight: 8.9990 chunk 323 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 265 optimal weight: 10.0000 chunk 296 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN ** J 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 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 = 0.3511 r_free = 0.3511 target = 0.067462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.039447 restraints weight = 86342.415| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 3.38 r_work: 0.2509 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2395 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9305 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 26669 Z= 0.286 Angle : 0.873 55.716 36318 Z= 0.441 Chirality : 0.049 0.177 4124 Planarity : 0.005 0.064 4600 Dihedral : 7.718 70.228 4456 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.46 % Allowed : 15.88 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 3288 helix: 0.07 (0.54), residues: 108 sheet: 0.65 (0.14), residues: 1424 loop : -1.43 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 18 TYR 0.024 0.002 TYR L 192 PHE 0.035 0.002 PHE F 209 TRP 0.017 0.001 TRP D 198 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.29 (26588) covalent geometry : angle 0.77134 / 0.40 (36112) SS BOND : bond 0.00591 / 0.32 ( 37) SS BOND : angle 8.57793 / 4.80 ( 74) hydrogen bonds : bond 0.04676 / 3.12 ( 912) hydrogen bonds : angle 5.61177 / 3.91 ( 2664) link_ALPHA1-2 : bond 0.00220 / 0.11 ( 4) link_ALPHA1-2 : angle 1.63598 / 1.03 ( 12) link_ALPHA1-3 : bond 0.00818 / 0.46 ( 8) link_ALPHA1-3 : angle 1.69029 / 0.96 ( 24) link_ALPHA1-6 : bond 0.00113 / 0.06 ( 8) link_ALPHA1-6 : angle 1.55230 / 0.91 ( 24) link_BETA1-4 : bond 0.00945 / 0.46 ( 8) link_BETA1-4 : angle 3.20898 / 1.75 ( 24) link_NAG-ASN : bond 0.00324 / 0.17 ( 16) link_NAG-ASN : angle 2.69839 / 1.67 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 1.058 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: A 250 CYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8691 (p) REVERT: B 250 CYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8686 (p) REVERT: C 250 CYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8684 (p) REVERT: D 250 CYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8672 (p) REVERT: E 76 GLU cc_start: 0.9102 (mp0) cc_final: 0.8834 (mp0) REVERT: E 130 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8883 (ttpp) REVERT: F 192 TYR cc_start: 0.9168 (m-80) cc_final: 0.8948 (m-80) REVERT: G 76 GLU cc_start: 0.8983 (mp0) cc_final: 0.8717 (mp0) REVERT: H 123 GLU cc_start: 0.9676 (mt-10) cc_final: 0.9438 (mp0) REVERT: H 192 TYR cc_start: 0.8877 (m-80) cc_final: 0.8586 (m-80) REVERT: I 76 GLU cc_start: 0.9038 (mp0) cc_final: 0.8778 (mp0) REVERT: I 130 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8857 (ttpp) REVERT: I 183 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8943 (tm) REVERT: I 184 GLN cc_start: 0.8747 (mt0) cc_final: 0.8395 (mp10) REVERT: J 142 ARG cc_start: 0.9104 (tpp80) cc_final: 0.8787 (tpp80) REVERT: J 192 TYR cc_start: 0.9056 (m-10) cc_final: 0.8772 (m-80) REVERT: K 76 GLU cc_start: 0.8984 (mp0) cc_final: 0.8712 (mp0) REVERT: K 130 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8517 (tptp) REVERT: K 156 LYS cc_start: 0.8911 (ttmm) cc_final: 0.8670 (tppp) REVERT: K 183 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8981 (tm) REVERT: K 184 GLN cc_start: 0.8691 (mt0) cc_final: 0.8291 (mp10) REVERT: L 123 GLU cc_start: 0.9668 (mt-10) cc_final: 0.9431 (mp0) REVERT: L 142 ARG cc_start: 0.9071 (tpp80) cc_final: 0.8753 (tpp80) outliers start: 42 outliers final: 28 residues processed: 218 average time/residue: 0.7146 time to fit residues: 176.2021 Evaluate side-chains 209 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 210 ASN Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 210 ASN Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 130 LYS Chi-restraints excluded: chain K residue 164 THR Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 210 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 297 optimal weight: 1.9990 chunk 153 optimal weight: 0.0000 chunk 211 optimal weight: 0.0060 chunk 174 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 294 optimal weight: 7.9990 overall best weight: 1.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 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 = 0.3553 r_free = 0.3553 target = 0.069749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.041951 restraints weight = 85222.786| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 3.48 r_work: 0.2582 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9245 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26669 Z= 0.125 Angle : 0.802 55.677 36318 Z= 0.400 Chirality : 0.046 0.171 4124 Planarity : 0.004 0.059 4600 Dihedral : 6.650 55.560 4456 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.39 % Allowed : 15.95 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.15), residues: 3288 helix: 0.02 (0.54), residues: 108 sheet: 0.84 (0.15), residues: 1372 loop : -1.25 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 18 TYR 0.011 0.001 TYR F 192 PHE 0.036 0.001 PHE F 209 TRP 0.018 0.001 TRP D 198 HIS 0.003 0.001 HIS G 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (26588) covalent geometry : angle 0.69889 / 0.36 (36112) SS BOND : bond 0.00566 / 0.24 ( 37) SS BOND : angle 8.41751 / 4.69 ( 74) hydrogen bonds : bond 0.03239 / 2.18 ( 912) hydrogen bonds : angle 5.35211 / 3.72 ( 2664) link_ALPHA1-2 : bond 0.00173 / 0.09 ( 4) link_ALPHA1-2 : angle 1.86521 / 1.18 ( 12) link_ALPHA1-3 : bond 0.00989 / 0.54 ( 8) link_ALPHA1-3 : angle 1.52107 / 0.87 ( 24) link_ALPHA1-6 : bond 0.00492 / 0.26 ( 8) link_ALPHA1-6 : angle 1.40039 / 0.82 ( 24) link_BETA1-4 : bond 0.00991 / 0.49 ( 8) link_BETA1-4 : angle 2.31827 / 1.26 ( 24) link_NAG-ASN : bond 0.00314 / 0.17 ( 16) link_NAG-ASN : angle 2.17701 / 1.35 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13142.99 seconds wall clock time: 223 minutes 21.98 seconds (13401.98 seconds total)