Starting phenix.real_space_refine on Wed Oct 28 00:10:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ub1_63999/10_2026/9ub1_63999.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ub1_63999/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ub1_63999/10_2026/9ub1_63999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ub1_63999/10_2026/9ub1_63999.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ub1_63999/10_2026/9ub1_63999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ub1_63999/10_2026/9ub1_63999.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/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: 4.93, 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=52, 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=" SG CYS B 112 " - pdb=" SG CYS B 437 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 213 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 250 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 257 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 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 112 " - pdb=" SG CYS C 437 " distance=2.03 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 195 " - pdb=" SG CYS C 213 " distance=2.03 Simple disulfide: pdb=" SG CYS C 203 " - pdb=" SG CYS C 250 " distance=2.03 Simple disulfide: pdb=" SG CYS C 252 " - pdb=" SG CYS C 257 " distance=2.03 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 309 " distance=2.03 Simple disulfide: pdb=" SG CYS C 338 " - pdb=" SG CYS C 357 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 467 " distance=2.03 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 437 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 195 " - pdb=" SG CYS D 213 " distance=2.03 Simple disulfide: pdb=" SG CYS D 203 " - pdb=" SG CYS D 250 " distance=2.03 Simple disulfide: pdb=" SG CYS D 252 " - pdb=" SG CYS D 257 " distance=2.03 Simple disulfide: pdb=" SG CYS D 298 " - pdb=" SG CYS D 311 " distance=2.03 Simple disulfide: pdb=" SG CYS D 300 " - pdb=" SG CYS D 309 " distance=2.03 Simple disulfide: pdb=" SG CYS D 338 " - pdb=" SG CYS D 357 " distance=2.03 Simple disulfide: pdb=" SG CYS D 441 " - pdb=" SG CYS D 467 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 153 " - pdb=" SG CYS E 209 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.05 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 153 " - pdb=" SG CYS G 209 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.05 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 153 " - pdb=" SG CYS I 209 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.05 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS J 194 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 153 " - pdb=" SG CYS K 209 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 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: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.58 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: 5.38 Time building geometry restraints manager: 2.90 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: 15413 22.21 - 44.41: 747 44.41 - 66.62: 216 66.62 - 88.82: 52 88.82 - 111.03: 16 Dihedral angle restraints: 16444 sinusoidal: 6968 harmonic: 9476 Sorted by residual: 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 dihedral pdb=" CA CYS C 357 " pdb=" C CYS C 357 " pdb=" N LEU C 358 " pdb=" CA LEU C 358 " ideal model delta harmonic sigma weight residual 180.00 153.90 26.10 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 16441 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: 2.13 - 2.68: 645 2.68 - 3.24: 22645 3.24 - 3.79: 36634 3.79 - 4.35: 51640 4.35 - 4.90: 88909 Nonbonded interactions: 200473 Sorted by model distance: nonbonded pdb=" ND2 ASN K 210 " pdb=" OD1 ASP K 221 " model vdw 2.126 3.120 nonbonded pdb=" ND2 ASN I 210 " pdb=" OD1 ASP I 221 " model vdw 2.127 3.120 nonbonded pdb=" ND2 ASN E 210 " pdb=" OD1 ASP E 221 " model vdw 2.127 3.120 nonbonded pdb=" ND2 ASN G 210 " pdb=" OD1 ASP G 221 " model vdw 2.127 3.120 nonbonded pdb=" O SER E 169 " pdb=" OG SER E 169 " model vdw 2.141 3.040 ... (remaining 200468 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: 9.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.680 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.720 ------------------------------------------------------------------------------- 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 : 0.006 0.066 26684 Z= 0.252 Angle : 1.179 33.837 36348 Z= 0.519 Chirality : 0.087 1.683 4124 Planarity : 0.004 0.043 4600 Dihedral : 15.050 111.030 10240 Min Nonbonded Distance : 2.126 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 0.00573 / 0.38 ( 52) SS BOND : angle 1.79743 / 1.33 ( 104) 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 : 0.918 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: 0.7687 time to fit residues: 366.2794 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 : 0.787 ------------------------------------------------------------------------------- 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: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 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 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** F 100 GLN ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 GLN H 3 GLN H 100 GLN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 GLN ** 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: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.070357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.041933 restraints weight = 84172.654| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 3.58 r_work: 0.2560 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2441 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9289 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 26684 Z= 0.210 Angle : 0.709 7.189 36348 Z= 0.367 Chirality : 0.048 0.177 4124 Planarity : 0.004 0.042 4600 Dihedral : 9.078 84.553 4473 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.18 % Allowed : 12.14 % Favored : 85.68 % 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: -1.67 (0.14), residues: 3288 helix: -3.02 (0.36), residues: 108 sheet: 0.29 (0.14), residues: 1336 loop : -2.19 (0.12), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 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 D 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (26588) covalent geometry : angle 0.69296 / 0.36 (36112) SS BOND : bond 0.00513 / 0.34 ( 52) SS BOND : angle 1.33577 / 0.97 ( 104) hydrogen bonds : bond 0.04408 / 2.94 ( 912) hydrogen bonds : angle 6.06637 / 4.27 ( 2664) link_ALPHA1-2 : bond 0.00042 / 0.02 ( 4) link_ALPHA1-2 : angle 1.78528 / 1.09 ( 12) link_ALPHA1-3 : bond 0.01022 / 0.57 ( 8) link_ALPHA1-3 : angle 2.27884 / 1.31 ( 24) link_ALPHA1-6 : bond 0.00759 / 0.39 ( 8) link_ALPHA1-6 : angle 1.42600 / 0.82 ( 24) link_BETA1-4 : bond 0.01017 / 0.48 ( 8) link_BETA1-4 : angle 3.24272 / 1.78 ( 24) link_NAG-ASN : bond 0.00228 / 0.12 ( 16) link_NAG-ASN : angle 2.46961 / 1.53 ( 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 255 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 192 time to evaluate : 1.110 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 247 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8892 (mp0) REVERT: A 250 CYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8686 (p) REVERT: B 247 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8887 (mp0) REVERT: B 250 CYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8705 (p) REVERT: C 247 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8905 (mp0) REVERT: C 250 CYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8652 (p) REVERT: D 247 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8946 (mp0) REVERT: D 250 CYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8688 (p) REVERT: E 76 GLU cc_start: 0.8830 (mp0) cc_final: 0.8577 (mp0) REVERT: E 130 LYS cc_start: 0.9149 (ttpp) cc_final: 0.8920 (ptmm) REVERT: E 156 LYS cc_start: 0.8848 (tppp) cc_final: 0.8609 (tppp) REVERT: F 100 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.9006 (pm20) REVERT: F 192 TYR cc_start: 0.9251 (m-80) cc_final: 0.8983 (m-80) REVERT: F 194 CYS cc_start: 0.7890 (t) cc_final: 0.7473 (t) REVERT: G 140 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8198 (p) REVERT: G 156 LYS cc_start: 0.9025 (ttmm) cc_final: 0.8646 (tptp) REVERT: G 214 LYS cc_start: 0.9354 (mtpp) cc_final: 0.9111 (tmmt) REVERT: H 100 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8950 (pm20) REVERT: H 123 GLU cc_start: 0.9677 (mt-10) cc_final: 0.9458 (mp0) REVERT: H 211 ARG cc_start: 0.8753 (tpp80) cc_final: 0.8434 (tpp80) REVERT: I 89 GLU cc_start: 0.9423 (pm20) cc_final: 0.9222 (pm20) REVERT: I 130 LYS cc_start: 0.9131 (ttpp) cc_final: 0.8835 (ptmm) REVERT: J 211 ARG cc_start: 0.8819 (tpp80) cc_final: 0.8523 (tpp80) REVERT: K 140 SER cc_start: 0.8431 (OUTLIER) cc_final: 0.8162 (p) REVERT: K 214 LYS cc_start: 0.9267 (mtpp) cc_final: 0.9028 (tmmt) REVERT: L 100 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.9010 (pm20) REVERT: L 123 GLU cc_start: 0.9655 (mt-10) cc_final: 0.9365 (pm20) REVERT: L 199 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8791 (pp30) outliers start: 63 outliers final: 23 residues processed: 254 average time/residue: 0.7999 time to fit residues: 229.2972 Evaluate side-chains 220 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 172 THR Chi-restraints excluded: chain F residue 209 PHE 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 117 ILE 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: [143, 297, 312, 189, 147, 149, 277, 271, 63, 171, 301] chunk 143 optimal weight: 4.9990 chunk 297 optimal weight: 2.9990 chunk 312 optimal weight: 0.7980 chunk 189 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 277 optimal weight: 10.0000 chunk 271 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 171 optimal weight: 7.9990 chunk 301 optimal weight: 8.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 367 HIS ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 HIS ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 ASN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 ASN ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 ASN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.085804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.056391 restraints weight = 62057.718| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 4.13 r_work: 0.2562 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2444 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9238 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26684 Z= 0.177 Angle : 0.659 7.356 36348 Z= 0.343 Chirality : 0.047 0.167 4124 Planarity : 0.004 0.043 4600 Dihedral : 8.310 77.440 4460 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.53 % Allowed : 12.86 % Favored : 85.61 % 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: -1.30 (0.14), residues: 3288 helix: -2.19 (0.45), residues: 108 sheet: 0.51 (0.15), residues: 1324 loop : -1.93 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 18 TYR 0.011 0.001 TYR F 140 PHE 0.029 0.002 PHE H 209 TRP 0.017 0.001 TRP B 198 HIS 0.004 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (26588) covalent geometry : angle 0.64367 / 0.34 (36112) SS BOND : bond 0.00462 / 0.31 ( 52) SS BOND : angle 1.18693 / 0.85 ( 104) hydrogen bonds : bond 0.04176 / 2.79 ( 912) hydrogen bonds : angle 5.77485 / 4.06 ( 2664) link_ALPHA1-2 : bond 0.00127 / 0.06 ( 4) link_ALPHA1-2 : angle 1.78466 / 1.14 ( 12) link_ALPHA1-3 : bond 0.00922 / 0.50 ( 8) link_ALPHA1-3 : angle 1.60655 / 0.92 ( 24) link_ALPHA1-6 : bond 0.00510 / 0.28 ( 8) link_ALPHA1-6 : angle 1.53097 / 0.89 ( 24) link_BETA1-4 : bond 0.01114 / 0.55 ( 8) link_BETA1-4 : angle 2.98565 / 1.62 ( 24) link_NAG-ASN : bond 0.00232 / 0.13 ( 16) link_NAG-ASN : angle 2.47142 / 1.54 ( 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 241 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 1.032 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 247 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8870 (mp0) REVERT: A 250 CYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8627 (p) REVERT: B 247 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8872 (mp0) REVERT: B 250 CYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8636 (p) REVERT: C 250 CYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8606 (p) REVERT: D 247 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8904 (mp0) REVERT: D 250 CYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8617 (p) REVERT: E 130 LYS cc_start: 0.9010 (ttpp) cc_final: 0.8408 (tptp) REVERT: F 42 ARG cc_start: 0.9124 (ttm-80) cc_final: 0.8726 (mmm-85) REVERT: F 192 TYR cc_start: 0.9206 (m-80) cc_final: 0.9004 (m-80) REVERT: G 130 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8519 (tptp) REVERT: H 42 ARG cc_start: 0.9110 (ttm-80) cc_final: 0.8729 (mmm-85) REVERT: H 55 GLU cc_start: 0.8570 (tp30) cc_final: 0.8347 (tp30) REVERT: H 123 GLU cc_start: 0.9685 (mt-10) cc_final: 0.9367 (pm20) REVERT: I 89 GLU cc_start: 0.9426 (pm20) cc_final: 0.9203 (pm20) REVERT: I 156 LYS cc_start: 0.8836 (ttmm) cc_final: 0.8529 (tppp) REVERT: I 184 GLN cc_start: 0.8691 (mt0) cc_final: 0.8104 (mp10) REVERT: J 192 TYR cc_start: 0.9209 (m-80) cc_final: 0.8952 (m-80) REVERT: K 43 LYS cc_start: 0.9101 (mmmm) cc_final: 0.8891 (mmmm) REVERT: K 130 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8550 (tptp) REVERT: L 123 GLU cc_start: 0.9675 (mt-10) cc_final: 0.9467 (mp0) REVERT: L 192 TYR cc_start: 0.9198 (m-80) cc_final: 0.8974 (m-80) outliers start: 44 outliers final: 22 residues processed: 238 average time/residue: 0.8562 time to fit residues: 228.4342 Evaluate side-chains 214 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 164 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 209 PHE 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 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 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 117 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: [186, 263, 53, 284, 162, 289, 151, 36, 83, 122, 248] chunk 186 optimal weight: 0.4980 chunk 263 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 289 optimal weight: 8.9990 chunk 151 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN B 246 GLN D 246 GLN ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS ** I 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 189 HIS L 189 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.069924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.042119 restraints weight = 83856.680| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 3.38 r_work: 0.2575 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9267 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 26684 Z= 0.156 Angle : 0.636 6.823 36348 Z= 0.329 Chirality : 0.046 0.164 4124 Planarity : 0.004 0.046 4600 Dihedral : 7.530 69.186 4457 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.87 % Allowed : 12.52 % Favored : 85.61 % 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: -1.02 (0.14), residues: 3288 helix: -1.68 (0.47), residues: 108 sheet: 0.64 (0.15), residues: 1324 loop : -1.69 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 18 TYR 0.013 0.001 TYR I 189 PHE 0.029 0.001 PHE H 209 TRP 0.016 0.001 TRP D 198 HIS 0.003 0.001 HIS D 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (26588) covalent geometry : angle 0.62228 / 0.33 (36112) SS BOND : bond 0.00410 / 0.27 ( 52) SS BOND : angle 1.09795 / 0.78 ( 104) hydrogen bonds : bond 0.03816 / 2.55 ( 912) hydrogen bonds : angle 5.55418 / 3.90 ( 2664) link_ALPHA1-2 : bond 0.00072 / 0.04 ( 4) link_ALPHA1-2 : angle 1.67685 / 1.06 ( 12) link_ALPHA1-3 : bond 0.00908 / 0.50 ( 8) link_ALPHA1-3 : angle 1.54041 / 0.88 ( 24) link_ALPHA1-6 : bond 0.00425 / 0.23 ( 8) link_ALPHA1-6 : angle 1.45599 / 0.85 ( 24) link_BETA1-4 : bond 0.01022 / 0.51 ( 8) link_BETA1-4 : angle 2.76555 / 1.51 ( 24) link_NAG-ASN : bond 0.00220 / 0.12 ( 16) link_NAG-ASN : angle 2.35110 / 1.46 ( 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 243 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 189 time to evaluate : 0.859 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: A 247 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8869 (mp0) REVERT: A 250 CYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8662 (p) REVERT: B 247 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8867 (mp0) REVERT: B 250 CYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8672 (p) REVERT: C 250 CYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8630 (p) REVERT: D 247 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8892 (mp0) REVERT: D 250 CYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8660 (p) REVERT: E 76 GLU cc_start: 0.8913 (mp0) cc_final: 0.8661 (mp0) REVERT: E 130 LYS cc_start: 0.9195 (ttpp) cc_final: 0.8728 (tttm) REVERT: F 192 TYR cc_start: 0.9274 (m-80) cc_final: 0.9072 (m-80) REVERT: G 130 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8538 (tptp) REVERT: H 123 GLU cc_start: 0.9708 (mt-10) cc_final: 0.9473 (mp0) REVERT: H 181 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.8997 (pt) REVERT: H 185 ASP cc_start: 0.9655 (m-30) cc_final: 0.9280 (p0) REVERT: H 192 TYR cc_start: 0.9025 (m-80) cc_final: 0.8577 (m-80) REVERT: I 76 GLU cc_start: 0.8879 (mp0) cc_final: 0.8638 (mp0) REVERT: I 89 GLU cc_start: 0.9422 (pm20) cc_final: 0.9195 (pm20) REVERT: I 130 LYS cc_start: 0.9191 (ttpp) cc_final: 0.8725 (tttm) REVERT: I 156 LYS cc_start: 0.8898 (ttmm) cc_final: 0.8545 (tppp) REVERT: I 184 GLN cc_start: 0.8844 (mt0) cc_final: 0.8203 (mp10) REVERT: J 181 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.8919 (pt) REVERT: J 185 ASP cc_start: 0.9631 (m-30) cc_final: 0.9255 (p0) REVERT: K 43 LYS cc_start: 0.9142 (mmmm) cc_final: 0.8921 (mmmm) REVERT: K 130 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8567 (tptp) REVERT: K 223 ARG cc_start: 0.8768 (ptm160) cc_final: 0.8516 (ptm160) REVERT: L 123 GLU cc_start: 0.9695 (mt-10) cc_final: 0.9451 (mp0) REVERT: L 181 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.8956 (pt) REVERT: L 185 ASP cc_start: 0.9629 (m-30) cc_final: 0.9337 (p0) REVERT: L 192 TYR cc_start: 0.9260 (m-80) cc_final: 0.9016 (m-10) outliers start: 54 outliers final: 25 residues processed: 237 average time/residue: 0.7720 time to fit residues: 207.0508 Evaluate side-chains 217 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 164 THR Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 209 PHE 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 161 GLU 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 117 ILE 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: [67, 99, 226, 312, 2, 279, 122, 62, 301, 27, 51] chunk 67 optimal weight: 4.9990 chunk 99 optimal weight: 0.0470 chunk 226 optimal weight: 3.9990 chunk 312 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 279 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 301 optimal weight: 30.0000 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 GLN C 246 GLN D 246 GLN ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.071944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.042752 restraints weight = 80550.564| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 4.15 r_work: 0.2542 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2433 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9277 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 26684 Z= 0.191 Angle : 0.659 6.393 36348 Z= 0.342 Chirality : 0.047 0.167 4124 Planarity : 0.004 0.047 4600 Dihedral : 7.408 67.534 4456 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.70 % Allowed : 13.56 % Favored : 84.74 % 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: -0.88 (0.14), residues: 3288 helix: -1.11 (0.49), residues: 108 sheet: 0.65 (0.15), residues: 1332 loop : -1.57 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 18 TYR 0.021 0.001 TYR I 189 PHE 0.033 0.002 PHE H 209 TRP 0.016 0.001 TRP D 198 HIS 0.004 0.001 HIS D 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (26588) covalent geometry : angle 0.64153 / 0.34 (36112) SS BOND : bond 0.00447 / 0.30 ( 52) SS BOND : angle 1.62797 / 1.05 ( 104) hydrogen bonds : bond 0.04136 / 2.76 ( 912) hydrogen bonds : angle 5.50703 / 3.86 ( 2664) link_ALPHA1-2 : bond 0.00049 / 0.02 ( 4) link_ALPHA1-2 : angle 1.67131 / 1.06 ( 12) link_ALPHA1-3 : bond 0.00778 / 0.43 ( 8) link_ALPHA1-3 : angle 1.53912 / 0.87 ( 24) link_ALPHA1-6 : bond 0.00305 / 0.17 ( 8) link_ALPHA1-6 : angle 1.49869 / 0.88 ( 24) link_BETA1-4 : bond 0.00959 / 0.47 ( 8) link_BETA1-4 : angle 2.86129 / 1.56 ( 24) link_NAG-ASN : bond 0.00245 / 0.13 ( 16) link_NAG-ASN : angle 2.49635 / 1.54 ( 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 233 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 1.022 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 247 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8890 (mp0) REVERT: A 250 CYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8679 (p) REVERT: B 247 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8891 (mp0) REVERT: B 250 CYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8690 (p) REVERT: C 250 CYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8659 (p) REVERT: D 250 CYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8680 (p) REVERT: E 130 LYS cc_start: 0.9129 (ttpp) cc_final: 0.8641 (tttm) REVERT: F 42 ARG cc_start: 0.9082 (ttm-80) cc_final: 0.8742 (mmm-85) REVERT: F 185 ASP cc_start: 0.9596 (m-30) cc_final: 0.9235 (p0) REVERT: G 130 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8523 (tptp) REVERT: H 42 ARG cc_start: 0.9082 (ttm-80) cc_final: 0.8735 (mmm-85) REVERT: H 123 GLU cc_start: 0.9693 (mt-10) cc_final: 0.9473 (mp0) REVERT: H 181 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.8922 (pt) REVERT: H 185 ASP cc_start: 0.9639 (m-30) cc_final: 0.9268 (p0) REVERT: H 192 TYR cc_start: 0.8959 (m-80) cc_final: 0.8577 (m-80) REVERT: I 89 GLU cc_start: 0.9420 (pm20) cc_final: 0.9183 (pm20) REVERT: I 130 LYS cc_start: 0.9122 (ttpp) cc_final: 0.8650 (tttm) REVERT: J 192 TYR cc_start: 0.9114 (m-10) cc_final: 0.8834 (m-80) REVERT: K 130 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8589 (tptp) REVERT: L 123 GLU cc_start: 0.9675 (mt-10) cc_final: 0.9439 (mp0) REVERT: L 192 TYR cc_start: 0.9184 (m-80) cc_final: 0.8913 (m-80) outliers start: 49 outliers final: 29 residues processed: 225 average time/residue: 0.8051 time to fit residues: 204.4451 Evaluate side-chains 214 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 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 E residue 219 LYS Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 209 PHE 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 H residue 161 GLU Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 24 VAL 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 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 Chi-restraints excluded: chain L residue 117 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: [233, 238, 148, 183, 272, 201, 292, 275, 219, 181, 221] chunk 233 optimal weight: 6.9990 chunk 238 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 272 optimal weight: 0.3980 chunk 201 optimal weight: 5.9990 chunk 292 optimal weight: 7.9990 chunk 275 optimal weight: 0.2980 chunk 219 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 chunk 221 optimal weight: 0.0980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 GLN D 246 GLN ** E 168 ASN ** 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** K 217 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.077083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.048262 restraints weight = 71644.858| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 4.11 r_work: 0.2559 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2443 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9237 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26684 Z= 0.140 Angle : 0.633 6.326 36348 Z= 0.326 Chirality : 0.046 0.169 4124 Planarity : 0.004 0.047 4600 Dihedral : 6.931 61.055 4456 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.77 % Allowed : 14.11 % Favored : 84.12 % 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: -0.71 (0.15), residues: 3288 helix: -0.65 (0.51), residues: 108 sheet: 0.75 (0.15), residues: 1332 loop : -1.47 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 18 TYR 0.013 0.001 TYR E 189 PHE 0.034 0.001 PHE H 209 TRP 0.016 0.001 TRP A 198 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (26588) covalent geometry : angle 0.61845 / 0.32 (36112) SS BOND : bond 0.00377 / 0.25 ( 52) SS BOND : angle 1.31406 / 0.86 ( 104) hydrogen bonds : bond 0.03648 / 2.44 ( 912) hydrogen bonds : angle 5.37196 / 3.77 ( 2664) link_ALPHA1-2 : bond 0.00071 / 0.04 ( 4) link_ALPHA1-2 : angle 1.72314 / 1.09 ( 12) link_ALPHA1-3 : bond 0.00949 / 0.53 ( 8) link_ALPHA1-3 : angle 1.54338 / 0.88 ( 24) link_ALPHA1-6 : bond 0.00414 / 0.23 ( 8) link_ALPHA1-6 : angle 1.45915 / 0.85 ( 24) link_BETA1-4 : bond 0.00976 / 0.48 ( 8) link_BETA1-4 : angle 2.58102 / 1.41 ( 24) link_NAG-ASN : bond 0.00231 / 0.13 ( 16) link_NAG-ASN : angle 2.34548 / 1.45 ( 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 234 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 0.843 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: A 247 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8879 (mp0) REVERT: A 250 CYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8643 (p) REVERT: B 247 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8877 (mp0) REVERT: B 250 CYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8652 (p) REVERT: C 250 CYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8627 (p) REVERT: D 250 CYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8641 (p) REVERT: E 76 GLU cc_start: 0.8962 (mp0) cc_final: 0.8753 (mp0) REVERT: E 130 LYS cc_start: 0.9087 (ttpp) cc_final: 0.8591 (tttm) REVERT: F 42 ARG cc_start: 0.9053 (ttm-80) cc_final: 0.8761 (mmm-85) REVERT: F 185 ASP cc_start: 0.9596 (m-30) cc_final: 0.9211 (p0) REVERT: F 192 TYR cc_start: 0.9003 (m-80) cc_final: 0.8680 (m-80) REVERT: G 130 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8529 (tptp) REVERT: H 42 ARG cc_start: 0.9059 (ttm-80) cc_final: 0.8772 (mmm-85) REVERT: H 123 GLU cc_start: 0.9694 (mt-10) cc_final: 0.9475 (mp0) REVERT: I 76 GLU cc_start: 0.8936 (mp0) cc_final: 0.8725 (mp0) REVERT: I 89 GLU cc_start: 0.9429 (pm20) cc_final: 0.9187 (pm20) REVERT: I 130 LYS cc_start: 0.9091 (ttpp) cc_final: 0.8624 (tttp) REVERT: I 183 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.9015 (tm) REVERT: J 192 TYR cc_start: 0.9089 (m-10) cc_final: 0.8852 (m-80) REVERT: K 130 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8572 (tptp) REVERT: K 156 LYS cc_start: 0.8801 (ttmm) cc_final: 0.8449 (tppp) REVERT: K 184 GLN cc_start: 0.8582 (mt0) cc_final: 0.8129 (mp10) REVERT: L 123 GLU cc_start: 0.9667 (mt-10) cc_final: 0.9415 (mp0) REVERT: L 185 ASP cc_start: 0.9575 (m-30) cc_final: 0.9248 (p0) REVERT: L 192 TYR cc_start: 0.9185 (m-80) cc_final: 0.8970 (m-10) outliers start: 51 outliers final: 27 residues processed: 229 average time/residue: 0.7993 time to fit residues: 206.8445 Evaluate side-chains 208 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 E residue 219 LYS Chi-restraints excluded: chain G residue 3 GLN 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 161 GLU Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 24 VAL 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 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 Chi-restraints excluded: chain L residue 117 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: [72, 32, 22, 287, 101, 246, 271, 95, 316, 307, 139] chunk 72 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 287 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 246 optimal weight: 9.9990 chunk 271 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 316 optimal weight: 5.9990 chunk 307 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 GLN A 461 ASN B 193 GLN B 461 ASN C 461 ASN D 193 GLN D 461 ASN ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 ASN ** 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** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.068942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.040174 restraints weight = 84287.674| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 3.68 r_work: 0.2487 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2371 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9308 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 26684 Z= 0.389 Angle : 0.799 7.238 36348 Z= 0.416 Chirality : 0.052 0.186 4124 Planarity : 0.005 0.050 4600 Dihedral : 8.301 77.880 4456 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.08 % Allowed : 14.53 % Favored : 83.39 % 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: -0.26 (0.53), residues: 108 sheet: 0.56 (0.14), residues: 1428 loop : -1.65 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 18 TYR 0.018 0.002 TYR E 50 PHE 0.035 0.002 PHE F 209 TRP 0.018 0.001 TRP A 198 HIS 0.005 0.001 HIS C 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00935 / 0.39 (26588) covalent geometry : angle 0.77855 / 0.41 (36112) SS BOND : bond 0.00674 / 0.44 ( 52) SS BOND : angle 2.07737 / 1.38 ( 104) hydrogen bonds : bond 0.05381 / 3.58 ( 912) hydrogen bonds : angle 5.78431 / 4.05 ( 2664) link_ALPHA1-2 : bond 0.00365 / 0.18 ( 4) link_ALPHA1-2 : angle 1.65533 / 1.04 ( 12) link_ALPHA1-3 : bond 0.00665 / 0.38 ( 8) link_ALPHA1-3 : angle 1.77657 / 1.01 ( 24) link_ALPHA1-6 : bond 0.00049 / 0.03 ( 8) link_ALPHA1-6 : angle 1.60854 / 0.94 ( 24) link_BETA1-4 : bond 0.00945 / 0.46 ( 8) link_BETA1-4 : angle 3.55552 / 1.95 ( 24) link_NAG-ASN : bond 0.00416 / 0.21 ( 16) link_NAG-ASN : angle 2.91151 / 1.80 ( 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 236 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 176 time to evaluate : 0.855 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: 0.8929 (OUTLIER) cc_final: 0.8677 (p) REVERT: B 250 CYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8691 (p) REVERT: C 250 CYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8696 (p) REVERT: D 250 CYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8698 (p) REVERT: E 130 LYS cc_start: 0.9052 (ttpp) cc_final: 0.8763 (ttpp) REVERT: F 142 ARG cc_start: 0.8936 (tpp80) cc_final: 0.8693 (tpp80) REVERT: F 192 TYR cc_start: 0.9004 (m-80) cc_final: 0.8510 (m-80) REVERT: H 123 GLU cc_start: 0.9683 (mt-10) cc_final: 0.9453 (mp0) REVERT: H 192 TYR cc_start: 0.8988 (m-80) cc_final: 0.8701 (m-80) REVERT: I 89 GLU cc_start: 0.9463 (pm20) cc_final: 0.9238 (pm20) REVERT: I 130 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8447 (tptp) REVERT: I 183 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8980 (tm) REVERT: J 192 TYR cc_start: 0.8948 (m-10) cc_final: 0.8685 (m-80) REVERT: K 156 LYS cc_start: 0.8866 (ttmm) cc_final: 0.8366 (tppp) REVERT: K 183 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9052 (tm) REVERT: L 123 GLU cc_start: 0.9666 (mt-10) cc_final: 0.9409 (mp0) REVERT: L 192 TYR cc_start: 0.9212 (m-80) cc_final: 0.8995 (m-10) outliers start: 60 outliers final: 31 residues processed: 222 average time/residue: 0.7748 time to fit residues: 194.3855 Evaluate side-chains 212 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 37 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 37 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 H residue 161 GLU Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 37 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 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 37 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 Chi-restraints excluded: chain L residue 117 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: [231, 247, 290, 55, 152, 171, 197, 91, 282, 212, 291] chunk 231 optimal weight: 8.9990 chunk 247 optimal weight: 5.9990 chunk 290 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 282 optimal weight: 20.0000 chunk 212 optimal weight: 4.9990 chunk 291 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.078664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.047924 restraints weight = 67801.818| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 4.65 r_work: 0.2532 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2415 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9275 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 26684 Z= 0.217 Angle : 0.703 7.463 36348 Z= 0.364 Chirality : 0.047 0.171 4124 Planarity : 0.004 0.058 4600 Dihedral : 7.777 71.399 4456 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.66 % Allowed : 15.22 % Favored : 83.11 % 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: -0.71 (0.15), residues: 3288 helix: -0.11 (0.54), residues: 108 sheet: 0.65 (0.14), residues: 1420 loop : -1.52 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 18 TYR 0.012 0.001 TYR F 192 PHE 0.039 0.002 PHE F 209 TRP 0.018 0.001 TRP B 198 HIS 0.004 0.001 HIS C 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 (26588) covalent geometry : angle 0.68723 / 0.36 (36112) SS BOND : bond 0.00466 / 0.31 ( 52) SS BOND : angle 1.51413 / 1.00 ( 104) hydrogen bonds : bond 0.04249 / 2.84 ( 912) hydrogen bonds : angle 5.57716 / 3.90 ( 2664) link_ALPHA1-2 : bond 0.00091 / 0.05 ( 4) link_ALPHA1-2 : angle 1.72976 / 1.10 ( 12) link_ALPHA1-3 : bond 0.00879 / 0.49 ( 8) link_ALPHA1-3 : angle 1.63909 / 0.93 ( 24) link_ALPHA1-6 : bond 0.00233 / 0.12 ( 8) link_ALPHA1-6 : angle 1.49681 / 0.88 ( 24) link_BETA1-4 : bond 0.00979 / 0.48 ( 8) link_BETA1-4 : angle 2.97718 / 1.62 ( 24) link_NAG-ASN : bond 0.00292 / 0.16 ( 16) link_NAG-ASN : angle 2.56059 / 1.59 ( 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 224 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 0.809 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: A 250 CYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8679 (p) REVERT: B 250 CYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8716 (p) REVERT: C 250 CYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8671 (p) REVERT: D 250 CYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8650 (p) REVERT: E 76 GLU cc_start: 0.9028 (mp0) cc_final: 0.8789 (mp0) REVERT: E 130 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8441 (tttm) REVERT: F 192 TYR cc_start: 0.8688 (m-80) cc_final: 0.8397 (m-80) REVERT: G 130 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8366 (tptp) REVERT: H 192 TYR cc_start: 0.8883 (m-80) cc_final: 0.8611 (m-80) REVERT: I 76 GLU cc_start: 0.9012 (mp0) cc_final: 0.8757 (mp0) REVERT: I 89 GLU cc_start: 0.9456 (pm20) cc_final: 0.9223 (pm20) REVERT: I 130 LYS cc_start: 0.8932 (ttpp) cc_final: 0.8689 (ttpp) REVERT: I 183 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8961 (tm) REVERT: J 192 TYR cc_start: 0.8836 (m-10) cc_final: 0.8613 (m-80) REVERT: K 76 GLU cc_start: 0.8956 (mp0) cc_final: 0.8705 (mp0) REVERT: K 130 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8455 (tptp) REVERT: K 156 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8345 (tppp) REVERT: L 192 TYR cc_start: 0.9001 (m-80) cc_final: 0.8328 (m-80) outliers start: 48 outliers final: 28 residues processed: 215 average time/residue: 0.8011 time to fit residues: 194.9483 Evaluate side-chains 208 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 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 H residue 161 GLU Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 24 VAL 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 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 210 ASN Chi-restraints excluded: chain L residue 117 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: [297, 136, 256, 195, 213, 179, 279, 37, 36, 0, 152] chunk 297 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 chunk 195 optimal weight: 3.9990 chunk 213 optimal weight: 0.9990 chunk 179 optimal weight: 10.0000 chunk 279 optimal weight: 30.0000 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 77 ASN ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.074384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.044995 restraints weight = 75375.390| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 4.31 r_work: 0.2532 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2417 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9267 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26684 Z= 0.184 Angle : 0.698 7.602 36348 Z= 0.360 Chirality : 0.047 0.169 4124 Planarity : 0.004 0.061 4600 Dihedral : 7.424 66.924 4456 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.63 % Allowed : 15.43 % Favored : 82.94 % 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: -0.57 (0.15), residues: 3288 helix: -0.06 (0.53), residues: 108 sheet: 0.74 (0.14), residues: 1420 loop : -1.42 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 18 TYR 0.022 0.001 TYR L 192 PHE 0.037 0.002 PHE F 209 TRP 0.017 0.001 TRP B 198 HIS 0.003 0.001 HIS L 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (26588) covalent geometry : angle 0.68317 / 0.36 (36112) SS BOND : bond 0.00427 / 0.29 ( 52) SS BOND : angle 1.38486 / 0.92 ( 104) hydrogen bonds : bond 0.03995 / 2.67 ( 912) hydrogen bonds : angle 5.48432 / 3.84 ( 2664) link_ALPHA1-2 : bond 0.00040 / 0.02 ( 4) link_ALPHA1-2 : angle 1.69880 / 1.07 ( 12) link_ALPHA1-3 : bond 0.00874 / 0.49 ( 8) link_ALPHA1-3 : angle 1.58934 / 0.90 ( 24) link_ALPHA1-6 : bond 0.00303 / 0.16 ( 8) link_ALPHA1-6 : angle 1.48689 / 0.87 ( 24) link_BETA1-4 : bond 0.00961 / 0.47 ( 8) link_BETA1-4 : angle 2.85044 / 1.56 ( 24) link_NAG-ASN : bond 0.00241 / 0.13 ( 16) link_NAG-ASN : angle 2.50502 / 1.55 ( 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 225 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 178 time to evaluate : 1.129 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: 0.8906 (OUTLIER) cc_final: 0.8677 (p) REVERT: B 250 CYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8678 (p) REVERT: C 250 CYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8649 (p) REVERT: D 250 CYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8650 (p) REVERT: E 76 GLU cc_start: 0.9053 (mp0) cc_final: 0.8809 (mp0) REVERT: E 130 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8571 (tttm) REVERT: F 42 ARG cc_start: 0.9032 (ttm-80) cc_final: 0.8757 (mmm-85) REVERT: F 192 TYR cc_start: 0.8791 (m-80) cc_final: 0.8459 (m-80) REVERT: G 76 GLU cc_start: 0.8984 (mp0) cc_final: 0.8742 (mp0) REVERT: G 130 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8474 (tptp) REVERT: H 42 ARG cc_start: 0.9049 (ttm-80) cc_final: 0.8768 (mmm-85) REVERT: H 192 TYR cc_start: 0.8959 (m-80) cc_final: 0.8622 (m-80) REVERT: I 76 GLU cc_start: 0.9042 (mp0) cc_final: 0.8782 (mp0) REVERT: I 89 GLU cc_start: 0.9466 (pm20) cc_final: 0.9239 (pm20) REVERT: I 130 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8837 (ttpp) REVERT: I 183 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9071 (tm) REVERT: J 192 TYR cc_start: 0.8870 (m-10) cc_final: 0.8631 (m-80) REVERT: K 76 GLU cc_start: 0.8996 (mp0) cc_final: 0.8742 (mp0) REVERT: K 130 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8511 (tptp) REVERT: K 156 LYS cc_start: 0.8801 (ttmm) cc_final: 0.8596 (tppp) REVERT: K 184 GLN cc_start: 0.8518 (mt0) cc_final: 0.8174 (mp10) outliers start: 47 outliers final: 33 residues processed: 215 average time/residue: 0.8019 time to fit residues: 195.1748 Evaluate side-chains 213 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 E residue 219 LYS Chi-restraints excluded: chain F residue 74 THR 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 H residue 74 THR Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 50 TYR 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 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 210 ASN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 209 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: [36, 20, 273, 197, 233, 323, 35, 56, 265, 296, 207] chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 273 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 chunk 233 optimal weight: 8.9990 chunk 323 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 chunk 296 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 ASN ** 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 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 = 0.3548 r_free = 0.3548 target = 0.073302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.044168 restraints weight = 78100.080| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 4.09 r_work: 0.2542 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2429 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9266 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26684 Z= 0.175 Angle : 0.708 9.141 36348 Z= 0.364 Chirality : 0.047 0.170 4124 Planarity : 0.004 0.066 4600 Dihedral : 7.187 63.377 4456 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.46 % Allowed : 15.92 % 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: -0.50 (0.15), residues: 3288 helix: -0.12 (0.53), residues: 108 sheet: 0.81 (0.15), residues: 1376 loop : -1.32 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 18 TYR 0.012 0.001 TYR L 192 PHE 0.040 0.002 PHE F 209 TRP 0.017 0.001 TRP A 198 HIS 0.005 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 (26588) covalent geometry : angle 0.69505 / 0.36 (36112) SS BOND : bond 0.00407 / 0.27 ( 52) SS BOND : angle 1.31534 / 0.87 ( 104) hydrogen bonds : bond 0.03879 / 2.61 ( 912) hydrogen bonds : angle 5.43124 / 3.80 ( 2664) link_ALPHA1-2 : bond 0.00050 / 0.03 ( 4) link_ALPHA1-2 : angle 1.71127 / 1.08 ( 12) link_ALPHA1-3 : bond 0.00895 / 0.50 ( 8) link_ALPHA1-3 : angle 1.56233 / 0.89 ( 24) link_ALPHA1-6 : bond 0.00329 / 0.18 ( 8) link_ALPHA1-6 : angle 1.47870 / 0.87 ( 24) link_BETA1-4 : bond 0.00932 / 0.46 ( 8) link_BETA1-4 : angle 2.73835 / 1.49 ( 24) link_NAG-ASN : bond 0.00236 / 0.13 ( 16) link_NAG-ASN : angle 2.47396 / 1.53 ( 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 218 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 1.085 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: 0.8902 (OUTLIER) cc_final: 0.8675 (p) REVERT: B 250 CYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8677 (p) REVERT: C 250 CYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8651 (p) REVERT: D 250 CYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8653 (p) REVERT: E 76 GLU cc_start: 0.9061 (mp0) cc_final: 0.8808 (mp0) REVERT: E 130 LYS cc_start: 0.9110 (ttpp) cc_final: 0.8882 (ttpp) REVERT: F 42 ARG cc_start: 0.9036 (ttm-80) cc_final: 0.8763 (mmm-85) REVERT: F 192 TYR cc_start: 0.8788 (m-80) cc_final: 0.8462 (m-80) REVERT: G 76 GLU cc_start: 0.9016 (mp0) cc_final: 0.8769 (mp0) REVERT: G 130 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8489 (tptp) REVERT: H 42 ARG cc_start: 0.9048 (ttm-80) cc_final: 0.8765 (mmm-85) REVERT: H 192 TYR cc_start: 0.8979 (m-80) cc_final: 0.8642 (m-80) REVERT: I 76 GLU cc_start: 0.9060 (mp0) cc_final: 0.8798 (mp0) REVERT: I 89 GLU cc_start: 0.9458 (pm20) cc_final: 0.9223 (pm20) REVERT: I 130 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8862 (ttpp) REVERT: I 183 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8961 (tm) REVERT: I 184 GLN cc_start: 0.8609 (mt0) cc_final: 0.8332 (mp10) REVERT: J 192 TYR cc_start: 0.8884 (m-10) cc_final: 0.8611 (m-80) REVERT: K 76 GLU cc_start: 0.9031 (mp0) cc_final: 0.8764 (mp0) REVERT: K 130 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8555 (tptp) REVERT: K 184 GLN cc_start: 0.8477 (mt0) cc_final: 0.8108 (mp10) REVERT: L 192 TYR cc_start: 0.8914 (m-80) cc_final: 0.8696 (m-80) outliers start: 42 outliers final: 31 residues processed: 211 average time/residue: 0.8273 time to fit residues: 197.3534 Evaluate side-chains 211 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 164 THR Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain F residue 74 THR 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 H residue 74 THR Chi-restraints excluded: chain H residue 161 GLU 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 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 210 ASN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 117 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: [297, 153, 211, 174, 40, 61, 93, 182, 132, 56, 294] chunk 297 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 294 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 168 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.082643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.055305 restraints weight = 85636.735| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.18 r_work: 0.2588 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9247 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26684 Z= 0.129 Angle : 0.686 10.550 36348 Z= 0.351 Chirality : 0.046 0.178 4124 Planarity : 0.004 0.064 4600 Dihedral : 6.560 54.400 4456 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.35 % Allowed : 15.98 % 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: -0.40 (0.15), residues: 3288 helix: -0.18 (0.53), residues: 108 sheet: 0.88 (0.15), residues: 1376 loop : -1.25 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 18 TYR 0.010 0.001 TYR E 60 PHE 0.041 0.001 PHE F 209 TRP 0.017 0.001 TRP B 198 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (26588) covalent geometry : angle 0.67491 / 0.35 (36112) SS BOND : bond 0.00324 / 0.22 ( 52) SS BOND : angle 1.07428 / 0.71 ( 104) hydrogen bonds : bond 0.03312 / 2.23 ( 912) hydrogen bonds : angle 5.28756 / 3.70 ( 2664) link_ALPHA1-2 : bond 0.00333 / 0.17 ( 4) link_ALPHA1-2 : angle 1.81909 / 1.14 ( 12) link_ALPHA1-3 : bond 0.01022 / 0.57 ( 8) link_ALPHA1-3 : angle 1.47938 / 0.84 ( 24) link_ALPHA1-6 : bond 0.00477 / 0.26 ( 8) link_ALPHA1-6 : angle 1.43131 / 0.84 ( 24) link_BETA1-4 : bond 0.00931 / 0.47 ( 8) link_BETA1-4 : angle 2.35131 / 1.28 ( 24) link_NAG-ASN : bond 0.00241 / 0.13 ( 16) link_NAG-ASN : angle 2.22312 / 1.38 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15877.49 seconds wall clock time: 269 minutes 12.50 seconds (16152.50 seconds total)