Starting phenix.real_space_refine on Wed Mar 4 23:52:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dd2_27332/03_2026/8dd2_27332.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dd2_27332/03_2026/8dd2_27332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dd2_27332/03_2026/8dd2_27332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dd2_27332/03_2026/8dd2_27332.map" model { file = "/net/cci-nas-00/data/ceres_data/8dd2_27332/03_2026/8dd2_27332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dd2_27332/03_2026/8dd2_27332.cif" } resolution = 2.9 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 11282 2.51 5 N 2838 2.21 5 O 3242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17459 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2729 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {'ABU': 1, 'NAG': 1, 'R5R': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {'ABU': 1, 'NAG': 1, 'R5R': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'R5R': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.01, per 1000 atoms: 0.23 Number of scatterers: 17459 At special positions: 0 Unit cell: (130.938, 139.278, 120.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 97 16.00 O 3242 8.00 N 2838 7.00 C 11282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.04 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.04 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN G 8 " - " MAN G 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 10 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 401 " - " ASN A 80 " " NAG C 401 " - " ASN C 80 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN D 111 " " NAG N 1 " - " ASN E 208 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 813.5 milliseconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 30 sheets defined 33.7% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 9 through 21 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 217 through 236 removed outlier: 4.613A pdb=" N PHE A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 237 through 242 removed outlier: 4.146A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 242 " --> pdb=" O VAL A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 237 through 242' Processing helix chain 'A' and resid 246 through 272 removed outlier: 3.920A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 306 Processing helix chain 'A' and resid 309 through 340 removed outlier: 4.364A pdb=" N ASP A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 318 " --> pdb=" O ALA A 314 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 73 through 76 Processing helix chain 'B' and resid 88 through 94 removed outlier: 4.084A pdb=" N SER B 92 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 223 through 243 removed outlier: 5.198A pdb=" N LEU B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 244 through 247 Processing helix chain 'B' and resid 251 through 275 removed outlier: 3.506A pdb=" N ARG B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 310 Processing helix chain 'B' and resid 314 through 347 removed outlier: 3.828A pdb=" N ARG B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Proline residue: B 330 - end of helix removed outlier: 3.690A pdb=" N ASN B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'C' and resid 139 through 143 removed outlier: 4.495A pdb=" N ARG C 142 " --> pdb=" O ASP C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 242 removed outlier: 4.714A pdb=" N PHE C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N MET C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix removed outlier: 3.577A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 272 removed outlier: 3.741A pdb=" N THR C 271 " --> pdb=" O HIS C 267 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 309 through 339 removed outlier: 3.798A pdb=" N ALA C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 322 " --> pdb=" O ARG C 318 " (cutoff:3.500A) Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 12 through 24 Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 87 through 94 removed outlier: 3.555A pdb=" N ILE D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 230 through 243 Processing helix chain 'D' and resid 244 through 247 Processing helix chain 'D' and resid 251 through 277 removed outlier: 3.576A pdb=" N ASN D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 311 Processing helix chain 'D' and resid 314 through 346 removed outlier: 3.810A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) Proline residue: D 330 - end of helix Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 85 through 88 Processing helix chain 'E' and resid 99 through 103 removed outlier: 3.639A pdb=" N MET E 102 " --> pdb=" O ASN E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 253 removed outlier: 4.776A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix Processing helix chain 'E' and resid 261 through 286 removed outlier: 3.522A pdb=" N SER E 286 " --> pdb=" O ILE E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 324 removed outlier: 4.162A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 357 removed outlier: 3.835A pdb=" N ALA E 328 " --> pdb=" O GLN E 324 " (cutoff:3.500A) Proline residue: E 340 - end of helix Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.715A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.789A pdb=" N LEU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.993A pdb=" N GLN K 65 " --> pdb=" O PRO K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.776A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.333A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.875A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.636A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.636A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 83 through 86 removed outlier: 4.217A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 104 through 109 removed outlier: 6.963A pdb=" N ARG B 136 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER B 107 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR B 134 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA B 109 " --> pdb=" O ARG B 132 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ARG B 132 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.283A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU B 193 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 81 through 83 removed outlier: 4.479A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.819A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.857A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 83 through 86 removed outlier: 3.878A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 108 through 109 removed outlier: 7.071A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.142A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.142A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 95 through 98 removed outlier: 4.347A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 116 through 121 removed outlier: 6.881A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA E 121 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ARG E 144 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 111 through 113 Processing sheet with id=AB9, first strand: chain 'E' and resid 162 through 166 removed outlier: 3.539A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'I' and resid 10 through 12 removed outlier: 4.009A pdb=" N GLU I 104 " --> pdb=" O MET I 11 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N TYR I 49 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 10 through 12 removed outlier: 4.009A pdb=" N GLU I 104 " --> pdb=" O MET I 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.725A pdb=" N THR J 78 " --> pdb=" O ASP J 73 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.841A pdb=" N THR J 115 " --> pdb=" O GLU J 10 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.841A pdb=" N THR J 115 " --> pdb=" O GLU J 10 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR J 107 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.350A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.546A pdb=" N THR L 96 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.532A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL K 18 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.542A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.083A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 986 hydrogen bonds defined for protein. 2760 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: 3.52 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5338 1.34 - 1.46: 4362 1.46 - 1.58: 8032 1.58 - 1.70: 0 1.70 - 1.82: 167 Bond restraints: 17899 Sorted by residual: bond pdb=" C15 R5R D 601 " pdb=" N10 R5R D 601 " ideal model delta sigma weight residual 1.396 1.335 0.061 2.00e-02 2.50e+03 9.34e+00 bond pdb=" C15 R5R C 402 " pdb=" N10 R5R C 402 " ideal model delta sigma weight residual 1.396 1.337 0.059 2.00e-02 2.50e+03 8.66e+00 bond pdb=" C12 R5R D 601 " pdb=" C13 R5R D 601 " ideal model delta sigma weight residual 1.425 1.372 0.053 2.00e-02 2.50e+03 7.01e+00 bond pdb=" C15 R5R A 402 " pdb=" N10 R5R A 402 " ideal model delta sigma weight residual 1.396 1.343 0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" C12 R5R C 402 " pdb=" C13 R5R C 402 " ideal model delta sigma weight residual 1.425 1.375 0.050 2.00e-02 2.50e+03 6.13e+00 ... (remaining 17894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 23729 1.57 - 3.14: 455 3.14 - 4.71: 127 4.71 - 6.28: 29 6.28 - 7.85: 6 Bond angle restraints: 24346 Sorted by residual: angle pdb=" C MET D 114 " pdb=" N PRO D 115 " pdb=" CA PRO D 115 " ideal model delta sigma weight residual 119.93 115.94 3.99 1.07e+00 8.73e-01 1.39e+01 angle pdb=" N MET C 286 " pdb=" CA MET C 286 " pdb=" CB MET C 286 " ideal model delta sigma weight residual 110.12 113.73 -3.61 1.47e+00 4.63e-01 6.04e+00 angle pdb=" CB MET C 286 " pdb=" CG MET C 286 " pdb=" SD MET C 286 " ideal model delta sigma weight residual 112.70 119.98 -7.28 3.00e+00 1.11e-01 5.89e+00 angle pdb=" N GLY I 50 " pdb=" CA GLY I 50 " pdb=" C GLY I 50 " ideal model delta sigma weight residual 113.18 107.63 5.55 2.37e+00 1.78e-01 5.49e+00 angle pdb=" C MET B 112 " pdb=" N THR B 113 " pdb=" CA THR B 113 " ideal model delta sigma weight residual 121.70 125.89 -4.19 1.80e+00 3.09e-01 5.41e+00 ... (remaining 24341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 10138 21.48 - 42.96: 557 42.96 - 64.45: 76 64.45 - 85.93: 44 85.93 - 107.41: 17 Dihedral angle restraints: 10832 sinusoidal: 4576 harmonic: 6256 Sorted by residual: dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual -86.00 -34.99 -51.01 1 1.00e+01 1.00e-02 3.56e+01 dihedral pdb=" CA CYS E 165 " pdb=" C CYS E 165 " pdb=" N PRO E 166 " pdb=" CA PRO E 166 " ideal model delta harmonic sigma weight residual 180.00 -156.16 -23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CB CYS C 136 " pdb=" SG CYS C 136 " pdb=" SG CYS C 150 " pdb=" CB CYS C 150 " ideal model delta sinusoidal sigma weight residual 93.00 54.81 38.19 1 1.00e+01 1.00e-02 2.06e+01 ... (remaining 10829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 2795 0.163 - 0.326: 7 0.326 - 0.489: 2 0.489 - 0.652: 2 0.652 - 0.815: 1 Chirality restraints: 2807 Sorted by residual: chirality pdb=" C1 MAN G 9 " pdb=" O2 MAN G 8 " pdb=" C2 MAN G 9 " pdb=" O5 MAN G 9 " both_signs ideal model delta sigma weight residual False 2.40 2.16 0.24 2.00e-02 2.50e+03 1.49e+02 chirality pdb=" C1 MAN G 7 " pdb=" O6 BMA G 3 " pdb=" C2 MAN G 7 " pdb=" O5 MAN G 7 " both_signs ideal model delta sigma weight residual False 2.40 2.21 0.19 2.00e-02 2.50e+03 9.00e+01 chirality pdb=" C1 MAN G 10 " pdb=" O3 MAN G 7 " pdb=" C2 MAN G 10 " pdb=" O5 MAN G 10 " both_signs ideal model delta sigma weight residual False 2.40 2.28 0.12 2.00e-02 2.50e+03 3.60e+01 ... (remaining 2804 not shown) Planarity restraints: 2998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.336 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG M 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " -0.166 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.509 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.211 2.00e-02 2.50e+03 1.74e-01 3.80e+02 pdb=" C7 NAG M 2 " 0.057 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.152 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.284 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 80 " 0.031 2.00e-02 2.50e+03 3.46e-02 1.50e+01 pdb=" CG ASN A 80 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN A 80 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 80 " -0.057 2.00e-02 2.50e+03 pdb=" C1 NAG A 401 " 0.040 2.00e-02 2.50e+03 ... (remaining 2995 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 237 2.61 - 3.18: 15634 3.18 - 3.76: 26887 3.76 - 4.33: 40071 4.33 - 4.90: 66129 Nonbonded interactions: 148958 Sorted by model distance: nonbonded pdb=" O LEU A 259 " pdb=" OG1 THR A 262 " model vdw 2.041 3.040 nonbonded pdb=" OG1 THR A 202 " pdb=" OE2 ABU A 403 " model vdw 2.119 3.040 nonbonded pdb=" O PHE B 296 " pdb=" OG SER B 299 " model vdw 2.123 3.040 nonbonded pdb=" OH TYR A 97 " pdb=" OE2 GLU A 155 " model vdw 2.131 3.040 nonbonded pdb=" OG SER C 211 " pdb=" O7 NAG H 1 " model vdw 2.133 3.040 ... (remaining 148953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 10 through 347) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.620 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 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 : 0.005 0.163 17932 Z= 0.229 Angle : 0.667 16.024 24433 Z= 0.319 Chirality : 0.050 0.815 2807 Planarity : 0.007 0.288 2991 Dihedral : 14.592 107.412 6785 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.66 (0.18), residues: 2103 helix: 2.10 (0.21), residues: 566 sheet: 0.17 (0.20), residues: 634 loop : -0.37 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 321 TYR 0.017 0.001 TYR C 157 PHE 0.019 0.001 PHE D 226 TRP 0.009 0.001 TRP C 237 HIS 0.006 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00446 (17899) covalent geometry : angle 0.61144 (24346) SS BOND : bond 0.00399 ( 9) SS BOND : angle 0.74672 ( 18) hydrogen bonds : bond 0.16155 ( 862) hydrogen bonds : angle 7.16835 ( 2760) Misc. bond : bond 0.00064 ( 1) link_ALPHA1-2 : bond 0.00581 ( 3) link_ALPHA1-2 : angle 1.22144 ( 9) link_ALPHA1-3 : bond 0.00377 ( 2) link_ALPHA1-3 : angle 3.15167 ( 6) link_ALPHA1-6 : bond 0.00623 ( 2) link_ALPHA1-6 : angle 1.78448 ( 6) link_BETA1-4 : bond 0.00261 ( 9) link_BETA1-4 : angle 2.36819 ( 27) link_NAG-ASN : bond 0.09623 ( 7) link_NAG-ASN : angle 8.49500 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 232 LEU cc_start: 0.8723 (mm) cc_final: 0.8520 (mm) REVERT: B 266 MET cc_start: 0.8681 (mmm) cc_final: 0.8472 (mmm) REVERT: C 321 ARG cc_start: 0.6550 (ttm-80) cc_final: 0.6012 (ttm110) REVERT: K 90 ASP cc_start: 0.8586 (m-30) cc_final: 0.8348 (m-30) REVERT: K 98 ARG cc_start: 0.8151 (ttp80) cc_final: 0.7936 (ttt-90) outliers start: 0 outliers final: 1 residues processed: 386 average time/residue: 0.6308 time to fit residues: 270.6598 Evaluate side-chains 315 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 275 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN C 224 GLN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 ASN K 43 GLN K 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.127417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.088129 restraints weight = 24314.797| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.99 r_work: 0.2894 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 17932 Z= 0.222 Angle : 0.665 8.926 24433 Z= 0.339 Chirality : 0.046 0.280 2807 Planarity : 0.005 0.050 2991 Dihedral : 9.794 87.197 2847 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.12 % Allowed : 11.47 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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 (0.18), residues: 2103 helix: 2.00 (0.22), residues: 578 sheet: 0.33 (0.20), residues: 632 loop : -0.38 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 194 TYR 0.018 0.002 TYR C 157 PHE 0.018 0.002 PHE E 299 TRP 0.010 0.001 TRP K 47 HIS 0.008 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00516 (17899) covalent geometry : angle 0.65143 (24346) SS BOND : bond 0.00943 ( 9) SS BOND : angle 2.08655 ( 18) hydrogen bonds : bond 0.04740 ( 862) hydrogen bonds : angle 5.32923 ( 2760) Misc. bond : bond 0.00039 ( 1) link_ALPHA1-2 : bond 0.00531 ( 3) link_ALPHA1-2 : angle 1.73018 ( 9) link_ALPHA1-3 : bond 0.00817 ( 2) link_ALPHA1-3 : angle 1.82100 ( 6) link_ALPHA1-6 : bond 0.00220 ( 2) link_ALPHA1-6 : angle 1.84124 ( 6) link_BETA1-4 : bond 0.00429 ( 9) link_BETA1-4 : angle 2.52914 ( 27) link_NAG-ASN : bond 0.00563 ( 7) link_NAG-ASN : angle 2.70149 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 336 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8485 (ttt90) REVERT: A 103 LYS cc_start: 0.8887 (ptmm) cc_final: 0.8482 (tttp) REVERT: A 294 MET cc_start: 0.7885 (mmm) cc_final: 0.7618 (mmt) REVERT: B 93 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8617 (mptp) REVERT: B 232 LEU cc_start: 0.8734 (mm) cc_final: 0.8434 (mm) REVERT: C 286 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7848 (mtp) REVERT: C 321 ARG cc_start: 0.6696 (ttm-80) cc_final: 0.5921 (ttm110) REVERT: D 304 PHE cc_start: 0.8865 (t80) cc_final: 0.8631 (t80) REVERT: E 244 CYS cc_start: 0.8986 (m) cc_final: 0.8744 (m) REVERT: E 348 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6582 (tm) REVERT: K 90 ASP cc_start: 0.8121 (m-30) cc_final: 0.7915 (m-30) outliers start: 40 outliers final: 22 residues processed: 352 average time/residue: 0.5932 time to fit residues: 233.3637 Evaluate side-chains 337 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 311 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 170 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 200 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 HIS D 308 ASN E 152 GLN I 53 ASN K 28 ASN K 43 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.127718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.088510 restraints weight = 24428.454| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.99 r_work: 0.2901 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17932 Z= 0.190 Angle : 0.626 10.249 24433 Z= 0.318 Chirality : 0.045 0.269 2807 Planarity : 0.004 0.048 2991 Dihedral : 7.990 85.619 2847 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.66 % Allowed : 14.34 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.68 (0.18), residues: 2103 helix: 1.95 (0.22), residues: 579 sheet: 0.30 (0.20), residues: 632 loop : -0.37 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 194 TYR 0.022 0.002 TYR L 49 PHE 0.015 0.002 PHE C 289 TRP 0.009 0.001 TRP K 103 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00436 (17899) covalent geometry : angle 0.61314 (24346) SS BOND : bond 0.00563 ( 9) SS BOND : angle 2.40593 ( 18) hydrogen bonds : bond 0.04116 ( 862) hydrogen bonds : angle 4.94988 ( 2760) Misc. bond : bond 0.00048 ( 1) link_ALPHA1-2 : bond 0.00466 ( 3) link_ALPHA1-2 : angle 1.58119 ( 9) link_ALPHA1-3 : bond 0.00776 ( 2) link_ALPHA1-3 : angle 1.44757 ( 6) link_ALPHA1-6 : bond 0.00132 ( 2) link_ALPHA1-6 : angle 1.83082 ( 6) link_BETA1-4 : bond 0.00225 ( 9) link_BETA1-4 : angle 2.50850 ( 27) link_NAG-ASN : bond 0.00358 ( 7) link_NAG-ASN : angle 2.18795 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 316 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8502 (ttt90) REVERT: A 103 LYS cc_start: 0.8864 (ptmm) cc_final: 0.8508 (tttp) REVERT: A 222 ILE cc_start: 0.8183 (mm) cc_final: 0.7972 (mm) REVERT: A 286 MET cc_start: 0.8079 (mpp) cc_final: 0.7873 (mmp) REVERT: A 294 MET cc_start: 0.7882 (mmm) cc_final: 0.7619 (mmt) REVERT: A 304 TYR cc_start: 0.6815 (t80) cc_final: 0.6522 (t80) REVERT: B 232 LEU cc_start: 0.8690 (mm) cc_final: 0.8334 (mm) REVERT: C 286 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7858 (mtp) REVERT: C 321 ARG cc_start: 0.6690 (ttm-80) cc_final: 0.5923 (ttm110) REVERT: E 244 CYS cc_start: 0.8962 (m) cc_final: 0.8752 (m) REVERT: E 347 ASN cc_start: 0.5580 (OUTLIER) cc_final: 0.5196 (t0) REVERT: E 348 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6600 (tm) REVERT: J 90 ASP cc_start: 0.7970 (m-30) cc_final: 0.7544 (m-30) REVERT: L 70 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8035 (m-30) outliers start: 50 outliers final: 24 residues processed: 338 average time/residue: 0.5726 time to fit residues: 216.8649 Evaluate side-chains 327 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 298 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 100 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 163 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 265 ASN C 267 HIS E 152 GLN J 28 ASN K 28 ASN K 43 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.087694 restraints weight = 24380.600| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.99 r_work: 0.2889 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 17932 Z= 0.212 Angle : 0.639 13.233 24433 Z= 0.323 Chirality : 0.045 0.253 2807 Planarity : 0.004 0.047 2991 Dihedral : 7.373 82.450 2847 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.93 % Allowed : 15.51 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.58 (0.18), residues: 2103 helix: 1.84 (0.22), residues: 579 sheet: 0.30 (0.20), residues: 620 loop : -0.45 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 18 TYR 0.019 0.002 TYR C 157 PHE 0.015 0.002 PHE E 113 TRP 0.010 0.001 TRP C 237 HIS 0.004 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00495 (17899) covalent geometry : angle 0.62647 (24346) SS BOND : bond 0.00500 ( 9) SS BOND : angle 2.48261 ( 18) hydrogen bonds : bond 0.03988 ( 862) hydrogen bonds : angle 4.89171 ( 2760) Misc. bond : bond 0.00068 ( 1) link_ALPHA1-2 : bond 0.00435 ( 3) link_ALPHA1-2 : angle 1.71827 ( 9) link_ALPHA1-3 : bond 0.00840 ( 2) link_ALPHA1-3 : angle 1.31414 ( 6) link_ALPHA1-6 : bond 0.00150 ( 2) link_ALPHA1-6 : angle 1.93815 ( 6) link_BETA1-4 : bond 0.00243 ( 9) link_BETA1-4 : angle 2.50030 ( 27) link_NAG-ASN : bond 0.00378 ( 7) link_NAG-ASN : angle 2.11137 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 312 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8298 (mp0) cc_final: 0.8005 (mp0) REVERT: A 68 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8513 (ttt90) REVERT: A 103 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8568 (tttp) REVERT: A 180 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8240 (mppt) REVERT: A 222 ILE cc_start: 0.8175 (mm) cc_final: 0.7927 (mm) REVERT: A 286 MET cc_start: 0.8056 (mpp) cc_final: 0.7846 (mmp) REVERT: A 294 MET cc_start: 0.7927 (mmm) cc_final: 0.7659 (mmt) REVERT: B 93 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8652 (mptp) REVERT: B 112 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8715 (tpp) REVERT: C 207 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8196 (ttp80) REVERT: C 265 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8525 (t160) REVERT: C 286 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7878 (mtp) REVERT: C 321 ARG cc_start: 0.6713 (ttm-80) cc_final: 0.5904 (ttm110) REVERT: C 333 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8429 (mm) REVERT: D 310 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.6822 (m-10) REVERT: E 239 GLN cc_start: 0.7730 (mt0) cc_final: 0.7486 (mt0) REVERT: E 244 CYS cc_start: 0.8918 (m) cc_final: 0.8718 (m) REVERT: E 247 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8704 (mp) REVERT: E 347 ASN cc_start: 0.5644 (OUTLIER) cc_final: 0.5239 (t0) REVERT: E 348 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6620 (tm) REVERT: J 90 ASP cc_start: 0.7967 (m-30) cc_final: 0.7562 (m-30) REVERT: L 79 GLN cc_start: 0.6613 (OUTLIER) cc_final: 0.6311 (mm110) REVERT: K 67 LYS cc_start: 0.7510 (tptm) cc_final: 0.7253 (tptm) outliers start: 74 outliers final: 37 residues processed: 351 average time/residue: 0.5562 time to fit residues: 219.3410 Evaluate side-chains 353 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 302 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 310 PHE Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain K residue 21 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 1 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 267 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN J 28 ASN K 28 ASN K 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.127400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.088239 restraints weight = 24247.642| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.98 r_work: 0.2897 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17932 Z= 0.187 Angle : 0.621 16.081 24433 Z= 0.313 Chirality : 0.044 0.247 2807 Planarity : 0.004 0.048 2991 Dihedral : 7.181 82.844 2847 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.88 % Allowed : 16.52 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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 (0.18), residues: 2103 helix: 1.80 (0.22), residues: 579 sheet: 0.30 (0.20), residues: 620 loop : -0.43 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 18 TYR 0.024 0.002 TYR L 49 PHE 0.015 0.002 PHE B 258 TRP 0.011 0.001 TRP C 237 HIS 0.003 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00433 (17899) covalent geometry : angle 0.60912 (24346) SS BOND : bond 0.00370 ( 9) SS BOND : angle 2.44935 ( 18) hydrogen bonds : bond 0.03806 ( 862) hydrogen bonds : angle 4.79406 ( 2760) Misc. bond : bond 0.00052 ( 1) link_ALPHA1-2 : bond 0.00535 ( 3) link_ALPHA1-2 : angle 1.68570 ( 9) link_ALPHA1-3 : bond 0.01027 ( 2) link_ALPHA1-3 : angle 1.31977 ( 6) link_ALPHA1-6 : bond 0.00159 ( 2) link_ALPHA1-6 : angle 1.87108 ( 6) link_BETA1-4 : bond 0.00260 ( 9) link_BETA1-4 : angle 2.31351 ( 27) link_NAG-ASN : bond 0.00330 ( 7) link_NAG-ASN : angle 2.01897 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 309 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8296 (mp0) cc_final: 0.8016 (mp0) REVERT: A 68 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8472 (ttt90) REVERT: A 103 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8553 (tttp) REVERT: A 180 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8311 (mppt) REVERT: A 222 ILE cc_start: 0.8189 (mm) cc_final: 0.7932 (mm) REVERT: A 286 MET cc_start: 0.8010 (mpp) cc_final: 0.7790 (mmp) REVERT: A 294 MET cc_start: 0.7938 (mmm) cc_final: 0.7688 (mmt) REVERT: B 93 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8635 (mptp) REVERT: B 112 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8699 (tpp) REVERT: C 207 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8190 (ttp80) REVERT: C 231 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8078 (mp) REVERT: C 286 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7893 (mtp) REVERT: C 321 ARG cc_start: 0.6704 (ttm-80) cc_final: 0.5900 (ttm110) REVERT: C 333 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8428 (mm) REVERT: E 239 GLN cc_start: 0.7698 (mt0) cc_final: 0.7491 (mt0) REVERT: E 244 CYS cc_start: 0.8894 (m) cc_final: 0.8679 (m) REVERT: E 247 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8699 (mp) REVERT: E 347 ASN cc_start: 0.5618 (OUTLIER) cc_final: 0.5274 (t0) REVERT: E 348 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6630 (tm) REVERT: I 104 GLU cc_start: 0.4724 (OUTLIER) cc_final: 0.3942 (tt0) REVERT: J 90 ASP cc_start: 0.7951 (m-30) cc_final: 0.7531 (m-30) REVERT: L 70 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8062 (m-30) outliers start: 73 outliers final: 40 residues processed: 351 average time/residue: 0.5611 time to fit residues: 221.4512 Evaluate side-chains 352 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 298 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 21 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 142 optimal weight: 2.9990 chunk 198 optimal weight: 20.0000 chunk 93 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 185 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 206 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 265 ASN C 267 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN K 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.129585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.090767 restraints weight = 24238.211| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.98 r_work: 0.2939 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17932 Z= 0.122 Angle : 0.578 16.868 24433 Z= 0.290 Chirality : 0.042 0.192 2807 Planarity : 0.004 0.049 2991 Dihedral : 6.815 86.378 2847 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.08 % Allowed : 17.74 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.72 (0.18), residues: 2103 helix: 1.95 (0.21), residues: 577 sheet: 0.31 (0.20), residues: 621 loop : -0.30 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 18 TYR 0.023 0.001 TYR C 299 PHE 0.016 0.001 PHE B 258 TRP 0.015 0.001 TRP C 237 HIS 0.004 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00269 (17899) covalent geometry : angle 0.56738 (24346) SS BOND : bond 0.00299 ( 9) SS BOND : angle 2.36261 ( 18) hydrogen bonds : bond 0.03400 ( 862) hydrogen bonds : angle 4.56039 ( 2760) Misc. bond : bond 0.00013 ( 1) link_ALPHA1-2 : bond 0.00537 ( 3) link_ALPHA1-2 : angle 1.55138 ( 9) link_ALPHA1-3 : bond 0.01095 ( 2) link_ALPHA1-3 : angle 1.23160 ( 6) link_ALPHA1-6 : bond 0.00263 ( 2) link_ALPHA1-6 : angle 1.76407 ( 6) link_BETA1-4 : bond 0.00333 ( 9) link_BETA1-4 : angle 1.87413 ( 27) link_NAG-ASN : bond 0.00242 ( 7) link_NAG-ASN : angle 1.84490 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 321 time to evaluate : 0.727 Fit side-chains REVERT: A 52 GLU cc_start: 0.8195 (mp0) cc_final: 0.7939 (mp0) REVERT: A 68 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8481 (ttt90) REVERT: A 103 LYS cc_start: 0.8831 (ptmm) cc_final: 0.8476 (tttp) REVERT: A 286 MET cc_start: 0.8024 (mpp) cc_final: 0.7805 (mmp) REVERT: A 294 MET cc_start: 0.7941 (mmm) cc_final: 0.7706 (mmt) REVERT: A 304 TYR cc_start: 0.6806 (t80) cc_final: 0.6504 (t80) REVERT: B 93 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8611 (mptp) REVERT: C 207 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8288 (ttp80) REVERT: C 231 LEU cc_start: 0.8364 (mp) cc_final: 0.8029 (mp) REVERT: C 286 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7884 (mtp) REVERT: C 299 TYR cc_start: 0.7971 (t80) cc_final: 0.7750 (t80) REVERT: C 321 ARG cc_start: 0.6653 (ttm-80) cc_final: 0.5887 (ttm110) REVERT: C 333 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8436 (mm) REVERT: D 230 THR cc_start: 0.8754 (m) cc_final: 0.8549 (m) REVERT: E 155 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8120 (mm) REVERT: E 223 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.7765 (mtm) REVERT: E 239 GLN cc_start: 0.7718 (mt0) cc_final: 0.7499 (mt0) REVERT: E 244 CYS cc_start: 0.8930 (m) cc_final: 0.8601 (m) REVERT: E 247 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8682 (mp) REVERT: E 299 PHE cc_start: 0.8402 (t80) cc_final: 0.8161 (t80) REVERT: E 347 ASN cc_start: 0.5732 (OUTLIER) cc_final: 0.5478 (t0) REVERT: E 348 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6627 (tm) REVERT: I 54 ARG cc_start: 0.8657 (mtm-85) cc_final: 0.8286 (ttm-80) REVERT: J 90 ASP cc_start: 0.8009 (m-30) cc_final: 0.7596 (m-30) REVERT: L 70 ASP cc_start: 0.8377 (m-30) cc_final: 0.7995 (m-30) outliers start: 58 outliers final: 27 residues processed: 353 average time/residue: 0.5985 time to fit residues: 237.2166 Evaluate side-chains 336 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 299 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 223 MET Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 141 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 203 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 8 optimal weight: 0.0170 chunk 100 optimal weight: 0.1980 overall best weight: 2.0424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 267 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN J 28 ASN K 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.128067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.093745 restraints weight = 24295.285| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.23 r_work: 0.2903 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17932 Z= 0.182 Angle : 0.621 16.944 24433 Z= 0.311 Chirality : 0.044 0.207 2807 Planarity : 0.004 0.049 2991 Dihedral : 6.882 84.137 2847 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.40 % Allowed : 18.37 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.18), residues: 2103 helix: 1.92 (0.22), residues: 575 sheet: 0.34 (0.20), residues: 620 loop : -0.37 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 194 TYR 0.026 0.002 TYR L 49 PHE 0.030 0.002 PHE D 304 TRP 0.016 0.001 TRP C 237 HIS 0.004 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00421 (17899) covalent geometry : angle 0.60983 (24346) SS BOND : bond 0.00332 ( 9) SS BOND : angle 2.54936 ( 18) hydrogen bonds : bond 0.03635 ( 862) hydrogen bonds : angle 4.63323 ( 2760) Misc. bond : bond 0.01006 ( 1) link_ALPHA1-2 : bond 0.00476 ( 3) link_ALPHA1-2 : angle 1.66848 ( 9) link_ALPHA1-3 : bond 0.00929 ( 2) link_ALPHA1-3 : angle 1.26589 ( 6) link_ALPHA1-6 : bond 0.00141 ( 2) link_ALPHA1-6 : angle 1.91867 ( 6) link_BETA1-4 : bond 0.00253 ( 9) link_BETA1-4 : angle 2.09617 ( 27) link_NAG-ASN : bond 0.00390 ( 7) link_NAG-ASN : angle 1.85090 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 306 time to evaluate : 0.678 Fit side-chains REVERT: A 52 GLU cc_start: 0.8237 (mp0) cc_final: 0.7960 (mp0) REVERT: A 68 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8482 (ttt90) REVERT: A 103 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8540 (tttp) REVERT: A 286 MET cc_start: 0.8053 (mpp) cc_final: 0.7832 (mmp) REVERT: A 297 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7307 (tm) REVERT: A 304 TYR cc_start: 0.6806 (t80) cc_final: 0.6522 (t80) REVERT: B 93 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8658 (mptp) REVERT: C 40 MET cc_start: 0.9024 (mmm) cc_final: 0.8461 (mtm) REVERT: C 207 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8371 (ttp80) REVERT: C 231 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8089 (mp) REVERT: C 286 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7941 (mtp) REVERT: C 321 ARG cc_start: 0.6722 (ttm-80) cc_final: 0.5917 (ttm110) REVERT: C 333 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8480 (mm) REVERT: E 239 GLN cc_start: 0.7680 (mt0) cc_final: 0.7469 (mt0) REVERT: E 244 CYS cc_start: 0.8902 (m) cc_final: 0.8575 (m) REVERT: E 247 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8709 (mp) REVERT: E 299 PHE cc_start: 0.8414 (t80) cc_final: 0.8162 (t80) REVERT: E 347 ASN cc_start: 0.5808 (OUTLIER) cc_final: 0.5578 (t0) REVERT: E 348 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6643 (tm) REVERT: J 90 ASP cc_start: 0.8035 (m-30) cc_final: 0.7634 (m-30) outliers start: 64 outliers final: 38 residues processed: 343 average time/residue: 0.5786 time to fit residues: 222.9717 Evaluate side-chains 350 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 301 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 21 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 113 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 267 HIS D 308 ASN E 152 GLN J 28 ASN K 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.129613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.090817 restraints weight = 24263.031| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.98 r_work: 0.2941 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17932 Z= 0.132 Angle : 0.589 17.403 24433 Z= 0.294 Chirality : 0.043 0.186 2807 Planarity : 0.004 0.048 2991 Dihedral : 6.818 83.098 2847 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.92 % Allowed : 19.54 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.75 (0.18), residues: 2103 helix: 1.92 (0.21), residues: 579 sheet: 0.38 (0.20), residues: 633 loop : -0.29 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 18 TYR 0.029 0.001 TYR L 49 PHE 0.017 0.001 PHE A 306 TRP 0.022 0.001 TRP C 237 HIS 0.005 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00296 (17899) covalent geometry : angle 0.57948 (24346) SS BOND : bond 0.00270 ( 9) SS BOND : angle 2.25268 ( 18) hydrogen bonds : bond 0.03369 ( 862) hydrogen bonds : angle 4.50974 ( 2760) Misc. bond : bond 0.00793 ( 1) link_ALPHA1-2 : bond 0.00520 ( 3) link_ALPHA1-2 : angle 1.60104 ( 9) link_ALPHA1-3 : bond 0.01031 ( 2) link_ALPHA1-3 : angle 1.17792 ( 6) link_ALPHA1-6 : bond 0.00202 ( 2) link_ALPHA1-6 : angle 1.79763 ( 6) link_BETA1-4 : bond 0.00320 ( 9) link_BETA1-4 : angle 1.85596 ( 27) link_NAG-ASN : bond 0.00306 ( 7) link_NAG-ASN : angle 1.70326 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 312 time to evaluate : 0.917 Fit side-chains REVERT: A 68 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8467 (ttt90) REVERT: A 103 LYS cc_start: 0.8822 (ptmm) cc_final: 0.8473 (tttp) REVERT: A 286 MET cc_start: 0.8023 (mpp) cc_final: 0.7810 (mmp) REVERT: A 297 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7279 (tm) REVERT: A 304 TYR cc_start: 0.6760 (t80) cc_final: 0.6518 (t80) REVERT: B 93 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8628 (mptp) REVERT: C 40 MET cc_start: 0.9005 (mmm) cc_final: 0.8411 (mtm) REVERT: C 231 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8000 (mp) REVERT: C 286 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7855 (mtp) REVERT: C 333 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8415 (mm) REVERT: E 239 GLN cc_start: 0.7631 (mt0) cc_final: 0.7415 (mt0) REVERT: E 244 CYS cc_start: 0.8922 (m) cc_final: 0.8568 (m) REVERT: E 247 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8660 (mp) REVERT: E 299 PHE cc_start: 0.8376 (t80) cc_final: 0.8117 (t80) REVERT: E 348 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6640 (tm) REVERT: I 79 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.6890 (mm-40) REVERT: J 90 ASP cc_start: 0.7982 (m-30) cc_final: 0.7571 (m-30) REVERT: L 70 ASP cc_start: 0.8380 (m-30) cc_final: 0.8013 (m-30) REVERT: L 79 GLN cc_start: 0.6617 (OUTLIER) cc_final: 0.6332 (mm110) outliers start: 55 outliers final: 36 residues processed: 342 average time/residue: 0.5713 time to fit residues: 219.9943 Evaluate side-chains 344 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 298 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain K residue 21 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 105 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 267 HIS E 152 GLN J 28 ASN K 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.127146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.092698 restraints weight = 24308.613| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.27 r_work: 0.2871 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 17932 Z= 0.252 Angle : 0.683 13.864 24433 Z= 0.343 Chirality : 0.047 0.236 2807 Planarity : 0.005 0.050 2991 Dihedral : 7.141 83.494 2847 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.19 % Allowed : 19.97 % Favored : 76.85 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.54 (0.18), residues: 2103 helix: 1.76 (0.22), residues: 577 sheet: 0.26 (0.20), residues: 634 loop : -0.42 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 18 TYR 0.027 0.002 TYR C 299 PHE 0.031 0.002 PHE D 304 TRP 0.024 0.002 TRP C 237 HIS 0.004 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00591 (17899) covalent geometry : angle 0.67040 (24346) SS BOND : bond 0.00410 ( 9) SS BOND : angle 2.77802 ( 18) hydrogen bonds : bond 0.03946 ( 862) hydrogen bonds : angle 4.77812 ( 2760) Misc. bond : bond 0.00746 ( 1) link_ALPHA1-2 : bond 0.00447 ( 3) link_ALPHA1-2 : angle 1.80697 ( 9) link_ALPHA1-3 : bond 0.00907 ( 2) link_ALPHA1-3 : angle 1.18611 ( 6) link_ALPHA1-6 : bond 0.00110 ( 2) link_ALPHA1-6 : angle 2.01920 ( 6) link_BETA1-4 : bond 0.00211 ( 9) link_BETA1-4 : angle 2.38825 ( 27) link_NAG-ASN : bond 0.00450 ( 7) link_NAG-ASN : angle 2.04110 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 300 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8529 (ttt90) REVERT: A 103 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8568 (tttp) REVERT: A 286 MET cc_start: 0.8103 (mpp) cc_final: 0.7878 (mmp) REVERT: A 297 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7335 (tm) REVERT: A 304 TYR cc_start: 0.6869 (t80) cc_final: 0.6636 (t80) REVERT: B 93 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8655 (mptp) REVERT: C 231 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8167 (mp) REVERT: C 286 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7936 (mtp) REVERT: C 321 ARG cc_start: 0.6753 (ttm-80) cc_final: 0.5877 (ttm110) REVERT: C 333 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8454 (mm) REVERT: E 239 GLN cc_start: 0.7586 (mt0) cc_final: 0.7346 (mt0) REVERT: E 244 CYS cc_start: 0.8915 (m) cc_final: 0.8653 (m) REVERT: E 247 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8704 (mp) REVERT: I 79 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.6816 (mm-40) REVERT: J 90 ASP cc_start: 0.8037 (m-30) cc_final: 0.7633 (m-30) REVERT: L 79 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6409 (mm110) outliers start: 60 outliers final: 40 residues processed: 334 average time/residue: 0.5660 time to fit residues: 212.2661 Evaluate side-chains 347 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 297 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain K residue 21 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 15 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 191 optimal weight: 0.0770 chunk 149 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 chunk 175 optimal weight: 0.1980 chunk 135 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 202 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 267 HIS E 69 ASN E 152 GLN J 28 ASN K 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.130680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.092056 restraints weight = 24204.991| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.99 r_work: 0.2961 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17932 Z= 0.115 Angle : 0.590 16.561 24433 Z= 0.295 Chirality : 0.043 0.182 2807 Planarity : 0.004 0.048 2991 Dihedral : 6.759 82.879 2847 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.50 % Allowed : 20.82 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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 (0.18), residues: 2103 helix: 1.83 (0.21), residues: 580 sheet: 0.35 (0.20), residues: 633 loop : -0.26 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 18 TYR 0.029 0.001 TYR C 299 PHE 0.025 0.001 PHE D 304 TRP 0.028 0.001 TRP C 237 HIS 0.005 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00253 (17899) covalent geometry : angle 0.58187 (24346) SS BOND : bond 0.00194 ( 9) SS BOND : angle 2.05925 ( 18) hydrogen bonds : bond 0.03280 ( 862) hydrogen bonds : angle 4.46135 ( 2760) Misc. bond : bond 0.00462 ( 1) link_ALPHA1-2 : bond 0.00532 ( 3) link_ALPHA1-2 : angle 1.56010 ( 9) link_ALPHA1-3 : bond 0.01083 ( 2) link_ALPHA1-3 : angle 1.11783 ( 6) link_ALPHA1-6 : bond 0.00323 ( 2) link_ALPHA1-6 : angle 1.71216 ( 6) link_BETA1-4 : bond 0.00374 ( 9) link_BETA1-4 : angle 1.66523 ( 27) link_NAG-ASN : bond 0.00276 ( 7) link_NAG-ASN : angle 1.62431 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 315 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8491 (ttt90) REVERT: A 103 LYS cc_start: 0.8793 (ptmm) cc_final: 0.8438 (tttp) REVERT: A 286 MET cc_start: 0.8044 (mpp) cc_final: 0.7816 (mmp) REVERT: A 297 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7301 (tm) REVERT: A 304 TYR cc_start: 0.6824 (t80) cc_final: 0.6540 (t80) REVERT: B 93 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8636 (mptp) REVERT: C 231 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8043 (mp) REVERT: C 286 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7894 (mtp) REVERT: C 321 ARG cc_start: 0.6686 (ttm-80) cc_final: 0.5870 (ttm110) REVERT: E 239 GLN cc_start: 0.7502 (mt0) cc_final: 0.7279 (mt0) REVERT: E 244 CYS cc_start: 0.8872 (m) cc_final: 0.8530 (m) REVERT: E 247 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8677 (mp) REVERT: E 255 PHE cc_start: 0.7435 (m-80) cc_final: 0.7014 (m-80) REVERT: E 299 PHE cc_start: 0.8361 (t80) cc_final: 0.8140 (t80) REVERT: I 79 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6874 (mm-40) REVERT: I 104 GLU cc_start: 0.4793 (tm-30) cc_final: 0.4515 (tm-30) REVERT: J 90 ASP cc_start: 0.7932 (m-30) cc_final: 0.7516 (m-30) REVERT: L 70 ASP cc_start: 0.8361 (m-30) cc_final: 0.8015 (m-30) outliers start: 47 outliers final: 32 residues processed: 344 average time/residue: 0.5812 time to fit residues: 224.3025 Evaluate side-chains 338 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 299 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 167 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 195 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 267 HIS E 152 GLN K 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.127167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.087946 restraints weight = 24446.623| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.99 r_work: 0.2892 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 17932 Z= 0.233 Angle : 0.677 16.979 24433 Z= 0.339 Chirality : 0.046 0.215 2807 Planarity : 0.005 0.050 2991 Dihedral : 7.079 82.702 2847 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.66 % Allowed : 21.24 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.55 (0.18), residues: 2103 helix: 1.72 (0.22), residues: 577 sheet: 0.27 (0.20), residues: 629 loop : -0.39 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 18 TYR 0.043 0.002 TYR C 299 PHE 0.039 0.002 PHE D 304 TRP 0.030 0.002 TRP C 237 HIS 0.007 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00548 (17899) covalent geometry : angle 0.66619 (24346) SS BOND : bond 0.00354 ( 9) SS BOND : angle 2.63035 ( 18) hydrogen bonds : bond 0.03828 ( 862) hydrogen bonds : angle 4.72363 ( 2760) Misc. bond : bond 0.00653 ( 1) link_ALPHA1-2 : bond 0.00369 ( 3) link_ALPHA1-2 : angle 1.72095 ( 9) link_ALPHA1-3 : bond 0.01029 ( 2) link_ALPHA1-3 : angle 1.18237 ( 6) link_ALPHA1-6 : bond 0.00197 ( 2) link_ALPHA1-6 : angle 2.01755 ( 6) link_BETA1-4 : bond 0.00225 ( 9) link_BETA1-4 : angle 2.27826 ( 27) link_NAG-ASN : bond 0.00411 ( 7) link_NAG-ASN : angle 1.94325 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6897.10 seconds wall clock time: 118 minutes 3.99 seconds (7083.99 seconds total)