Starting phenix.real_space_refine on Sun May 18 19:34:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dd2_27332/05_2025/8dd2_27332.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dd2_27332/05_2025/8dd2_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_27332/05_2025/8dd2_27332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dd2_27332/05_2025/8dd2_27332.map" model { file = "/net/cci-nas-00/data/ceres_data/8dd2_27332/05_2025/8dd2_27332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dd2_27332/05_2025/8dd2_27332.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.45, per 1000 atoms: 0.60 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: 4.87 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.79 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: 6.03 Time building geometry restraints manager: 5.58 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 41.390 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.990 ------------------------------------------------------------------------------- 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 : 5.80 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP C 237 HIS 0.006 0.001 HIS D 102 PHE 0.019 0.001 PHE D 226 TYR 0.017 0.001 TYR C 157 ARG 0.003 0.000 ARG C 321 Details of bonding type rmsd link_NAG-ASN : bond 0.09623 ( 7) link_NAG-ASN : angle 8.49500 ( 21) 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_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) hydrogen bonds : bond 0.16155 ( 862) hydrogen bonds : angle 7.16835 ( 2760) SS BOND : bond 0.00399 ( 9) SS BOND : angle 0.74672 ( 18) covalent geometry : bond 0.00446 (17899) covalent geometry : angle 0.61144 (24346) Misc. bond : bond 0.00064 ( 1) *********************** 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 : 2.063 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: 1.2637 time to fit residues: 544.3073 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 : 2.011 ------------------------------------------------------------------------------- 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 174 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 162 optimal weight: 0.0970 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 187 optimal weight: 0.0870 overall best weight: 1.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** I 53 ASN K 28 ASN K 43 GLN K 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.089808 restraints weight = 24217.772| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.99 r_work: 0.2917 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17932 Z= 0.171 Angle : 0.637 9.397 24433 Z= 0.324 Chirality : 0.045 0.269 2807 Planarity : 0.004 0.049 2991 Dihedral : 9.858 86.881 2847 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.81 % Allowed : 10.99 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2103 helix: 2.08 (0.21), residues: 578 sheet: 0.40 (0.20), residues: 626 loop : -0.32 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 237 HIS 0.006 0.001 HIS D 102 PHE 0.019 0.002 PHE E 299 TYR 0.016 0.001 TYR E 314 ARG 0.005 0.000 ARG E 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 7) link_NAG-ASN : angle 2.56453 ( 21) link_ALPHA1-6 : bond 0.00438 ( 2) link_ALPHA1-6 : angle 1.61222 ( 6) link_BETA1-4 : bond 0.00379 ( 9) link_BETA1-4 : angle 2.35385 ( 27) link_ALPHA1-2 : bond 0.00574 ( 3) link_ALPHA1-2 : angle 1.55703 ( 9) link_ALPHA1-3 : bond 0.00912 ( 2) link_ALPHA1-3 : angle 1.85185 ( 6) hydrogen bonds : bond 0.04557 ( 862) hydrogen bonds : angle 5.25879 ( 2760) SS BOND : bond 0.01183 ( 9) SS BOND : angle 2.29915 ( 18) covalent geometry : bond 0.00385 (17899) covalent geometry : angle 0.62356 (24346) Misc. bond : bond 0.00000 ( 1) *********************** 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 370 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 336 time to evaluate : 1.967 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8469 (ttt90) REVERT: A 294 MET cc_start: 0.7860 (mmm) cc_final: 0.7589 (mmt) REVERT: A 304 TYR cc_start: 0.6783 (t80) cc_final: 0.6560 (t80) REVERT: B 93 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8577 (mptp) REVERT: B 98 ASP cc_start: 0.8748 (p0) cc_final: 0.8470 (p0) REVERT: B 112 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8606 (tpp) REVERT: B 232 LEU cc_start: 0.8732 (mm) cc_final: 0.8433 (mm) REVERT: C 321 ARG cc_start: 0.6648 (ttm-80) cc_final: 0.5879 (ttm110) REVERT: D 304 PHE cc_start: 0.8850 (t80) cc_final: 0.8634 (t80) REVERT: E 244 CYS cc_start: 0.8957 (m) cc_final: 0.8737 (m) REVERT: E 348 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6443 (tm) REVERT: K 90 ASP cc_start: 0.8110 (m-30) cc_final: 0.7898 (m-30) outliers start: 34 outliers final: 16 residues processed: 349 average time/residue: 1.2007 time to fit residues: 470.0541 Evaluate side-chains 328 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 308 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 243 VAL 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 275 ILE 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 J residue 21 SER Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain L residue 21 LEU 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 19 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 171 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 K 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.127363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.087993 restraints weight = 24115.202| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.98 r_work: 0.2892 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1542 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= 0.219 Angle : 0.645 9.950 24433 Z= 0.327 Chirality : 0.046 0.279 2807 Planarity : 0.004 0.048 2991 Dihedral : 8.290 85.345 2847 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.87 % Allowed : 14.02 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 2103 helix: 1.96 (0.22), residues: 577 sheet: 0.33 (0.20), residues: 630 loop : -0.41 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 103 HIS 0.005 0.001 HIS D 102 PHE 0.016 0.002 PHE E 113 TYR 0.021 0.002 TYR L 49 ARG 0.007 0.000 ARG I 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 7) link_NAG-ASN : angle 2.29030 ( 21) link_ALPHA1-6 : bond 0.00150 ( 2) link_ALPHA1-6 : angle 1.85987 ( 6) link_BETA1-4 : bond 0.00216 ( 9) link_BETA1-4 : angle 2.57037 ( 27) link_ALPHA1-2 : bond 0.00488 ( 3) link_ALPHA1-2 : angle 1.67781 ( 9) link_ALPHA1-3 : bond 0.00714 ( 2) link_ALPHA1-3 : angle 1.56605 ( 6) hydrogen bonds : bond 0.04264 ( 862) hydrogen bonds : angle 5.03015 ( 2760) SS BOND : bond 0.00497 ( 9) SS BOND : angle 2.33166 ( 18) covalent geometry : bond 0.00510 (17899) covalent geometry : angle 0.63202 (24346) Misc. bond : bond 0.00069 ( 1) *********************** 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 365 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 311 time to evaluate : 1.950 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8539 (ttt90) REVERT: A 103 LYS cc_start: 0.8880 (ptmm) cc_final: 0.8522 (tttp) REVERT: A 286 MET cc_start: 0.8068 (mpp) cc_final: 0.7862 (mmp) REVERT: A 294 MET cc_start: 0.7888 (mmm) cc_final: 0.7625 (mmt) REVERT: B 93 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8602 (mptp) REVERT: B 232 LEU cc_start: 0.8733 (mm) cc_final: 0.8401 (mm) REVERT: C 138 MET cc_start: 0.9100 (mtt) cc_final: 0.8737 (mtt) REVERT: C 286 MET cc_start: 0.8197 (mtp) cc_final: 0.7594 (mpp) REVERT: C 321 ARG cc_start: 0.6768 (ttm-80) cc_final: 0.5960 (ttm110) REVERT: E 244 CYS cc_start: 0.8942 (m) cc_final: 0.8697 (m) REVERT: E 348 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6442 (tm) REVERT: J 90 ASP cc_start: 0.7975 (m-30) cc_final: 0.7566 (m-30) REVERT: L 70 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8062 (m-30) outliers start: 54 outliers final: 27 residues processed: 338 average time/residue: 1.1536 time to fit residues: 438.9180 Evaluate side-chains 329 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 298 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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 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 262 THR Chi-restraints excluded: chain C residue 275 ILE 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 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 L residue 15 VAL 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 Chi-restraints excluded: chain K residue 21 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 195 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 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 = 0.3604 r_free = 0.3604 target = 0.128809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.089675 restraints weight = 24136.607| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.98 r_work: 0.2922 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17932 Z= 0.151 Angle : 0.593 12.677 24433 Z= 0.300 Chirality : 0.044 0.247 2807 Planarity : 0.004 0.047 2991 Dihedral : 7.225 82.479 2847 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.03 % Allowed : 15.88 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 2103 helix: 1.98 (0.22), residues: 579 sheet: 0.35 (0.20), residues: 626 loop : -0.37 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 237 HIS 0.004 0.001 HIS C 267 PHE 0.016 0.001 PHE B 258 TYR 0.021 0.001 TYR C 299 ARG 0.006 0.000 ARG E 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 7) link_NAG-ASN : angle 1.94739 ( 21) link_ALPHA1-6 : bond 0.00247 ( 2) link_ALPHA1-6 : angle 1.82571 ( 6) link_BETA1-4 : bond 0.00286 ( 9) link_BETA1-4 : angle 2.25299 ( 27) link_ALPHA1-2 : bond 0.00512 ( 3) link_ALPHA1-2 : angle 1.58957 ( 9) link_ALPHA1-3 : bond 0.01023 ( 2) link_ALPHA1-3 : angle 1.36729 ( 6) hydrogen bonds : bond 0.03684 ( 862) hydrogen bonds : angle 4.75651 ( 2760) SS BOND : bond 0.00279 ( 9) SS BOND : angle 2.38137 ( 18) covalent geometry : bond 0.00344 (17899) covalent geometry : angle 0.58129 (24346) Misc. bond : bond 0.00024 ( 1) *********************** 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 371 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 314 time to evaluate : 2.134 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8500 (ttt90) REVERT: A 103 LYS cc_start: 0.8851 (ptmm) cc_final: 0.8508 (tttp) REVERT: A 286 MET cc_start: 0.8079 (mpp) cc_final: 0.7828 (mmp) REVERT: A 294 MET cc_start: 0.7898 (mmm) cc_final: 0.7646 (mmt) REVERT: A 304 TYR cc_start: 0.6815 (t80) cc_final: 0.6557 (t80) REVERT: C 138 MET cc_start: 0.9076 (mtt) cc_final: 0.8704 (mtt) REVERT: C 286 MET cc_start: 0.8201 (mtp) cc_final: 0.7510 (mpp) REVERT: C 321 ARG cc_start: 0.6638 (ttm-80) cc_final: 0.5877 (ttm110) REVERT: C 333 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8432 (mm) REVERT: D 21 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7772 (ttm170) REVERT: E 239 GLN cc_start: 0.7755 (mt0) cc_final: 0.7522 (mt0) REVERT: E 244 CYS cc_start: 0.8888 (m) cc_final: 0.8663 (m) REVERT: E 247 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8672 (mp) REVERT: E 348 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6447 (tm) REVERT: J 90 ASP cc_start: 0.7989 (m-30) cc_final: 0.7552 (m-30) REVERT: K 67 LYS cc_start: 0.7485 (tptm) cc_final: 0.7201 (tptm) outliers start: 57 outliers final: 27 residues processed: 342 average time/residue: 1.2026 time to fit residues: 463.4898 Evaluate side-chains 324 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 292 time to evaluate : 1.919 ------------------------------------------------------------------------------- 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 B residue 63 ASP 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 165 GLU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 275 ILE 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 21 ARG 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 246 LEU 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 J residue 21 SER 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 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 23 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 101 optimal weight: 0.2980 chunk 132 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.129458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.095153 restraints weight = 24471.541| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.26 r_work: 0.2924 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17932 Z= 0.138 Angle : 0.582 15.969 24433 Z= 0.293 Chirality : 0.043 0.219 2807 Planarity : 0.004 0.047 2991 Dihedral : 6.905 86.582 2847 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.24 % Allowed : 16.57 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2103 helix: 2.02 (0.22), residues: 577 sheet: 0.37 (0.20), residues: 619 loop : -0.32 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 237 HIS 0.005 0.001 HIS C 267 PHE 0.015 0.001 PHE B 258 TYR 0.024 0.001 TYR L 49 ARG 0.004 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 7) link_NAG-ASN : angle 1.94939 ( 21) link_ALPHA1-6 : bond 0.00204 ( 2) link_ALPHA1-6 : angle 1.84801 ( 6) link_BETA1-4 : bond 0.00290 ( 9) link_BETA1-4 : angle 2.02373 ( 27) link_ALPHA1-2 : bond 0.00521 ( 3) link_ALPHA1-2 : angle 1.58691 ( 9) link_ALPHA1-3 : bond 0.01018 ( 2) link_ALPHA1-3 : angle 1.30232 ( 6) hydrogen bonds : bond 0.03502 ( 862) hydrogen bonds : angle 4.61459 ( 2760) SS BOND : bond 0.00274 ( 9) SS BOND : angle 2.54620 ( 18) covalent geometry : bond 0.00310 (17899) covalent geometry : angle 0.56991 (24346) Misc. bond : bond 0.00031 ( 1) *********************** 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 366 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 305 time to evaluate : 2.011 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8517 (ttt90) REVERT: A 103 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8560 (tttp) REVERT: A 286 MET cc_start: 0.8046 (mpp) cc_final: 0.7826 (mmp) REVERT: A 294 MET cc_start: 0.7906 (mmm) cc_final: 0.7654 (mmt) REVERT: A 304 TYR cc_start: 0.6860 (t80) cc_final: 0.6577 (t80) REVERT: C 138 MET cc_start: 0.9063 (mtt) cc_final: 0.8701 (mtt) REVERT: C 286 MET cc_start: 0.8242 (mtp) cc_final: 0.7556 (mpp) REVERT: C 321 ARG cc_start: 0.6630 (ttm-80) cc_final: 0.5881 (ttm110) REVERT: C 333 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8473 (mm) REVERT: D 21 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7807 (ttm170) REVERT: D 310 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.6833 (m-10) REVERT: E 155 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8136 (mm) REVERT: E 244 CYS cc_start: 0.8859 (m) cc_final: 0.8548 (m) REVERT: E 247 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8693 (mp) REVERT: E 299 PHE cc_start: 0.8420 (t80) cc_final: 0.8206 (t80) REVERT: I 79 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.6811 (mm-40) REVERT: I 104 GLU cc_start: 0.4905 (OUTLIER) cc_final: 0.4092 (tt0) REVERT: J 90 ASP cc_start: 0.8020 (m-30) cc_final: 0.7607 (m-30) REVERT: L 70 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8018 (m-30) outliers start: 61 outliers final: 31 residues processed: 336 average time/residue: 1.2029 time to fit residues: 455.1272 Evaluate side-chains 332 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 291 time to evaluate : 1.859 ------------------------------------------------------------------------------- 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 B residue 63 ASP 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 323 PHE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 ARG 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 236 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 310 PHE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 112 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 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 89 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 202 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3583 r_free = 0.3583 target = 0.127248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.087902 restraints weight = 24345.503| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.00 r_work: 0.2891 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: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 17932 Z= 0.223 Angle : 0.643 16.206 24433 Z= 0.324 Chirality : 0.045 0.243 2807 Planarity : 0.004 0.049 2991 Dihedral : 7.080 85.550 2847 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.45 % Allowed : 17.31 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2103 helix: 1.87 (0.22), residues: 579 sheet: 0.33 (0.20), residues: 620 loop : -0.43 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 237 HIS 0.004 0.001 HIS C 267 PHE 0.016 0.002 PHE C 289 TYR 0.023 0.002 TYR C 299 ARG 0.008 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 7) link_NAG-ASN : angle 1.99251 ( 21) link_ALPHA1-6 : bond 0.00194 ( 2) link_ALPHA1-6 : angle 1.98680 ( 6) link_BETA1-4 : bond 0.00235 ( 9) link_BETA1-4 : angle 2.30924 ( 27) link_ALPHA1-2 : bond 0.00467 ( 3) link_ALPHA1-2 : angle 1.73814 ( 9) link_ALPHA1-3 : bond 0.00899 ( 2) link_ALPHA1-3 : angle 1.29364 ( 6) hydrogen bonds : bond 0.03850 ( 862) hydrogen bonds : angle 4.76894 ( 2760) SS BOND : bond 0.00415 ( 9) SS BOND : angle 2.76037 ( 18) covalent geometry : bond 0.00520 (17899) covalent geometry : angle 0.63068 (24346) Misc. bond : bond 0.00084 ( 1) *********************** 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 367 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 302 time to evaluate : 2.141 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8473 (ttt90) REVERT: A 103 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8571 (tttp) REVERT: A 286 MET cc_start: 0.8030 (mpp) cc_final: 0.7807 (mmp) REVERT: A 304 TYR cc_start: 0.6830 (t80) cc_final: 0.6561 (t80) REVERT: B 93 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8657 (mptp) REVERT: C 286 MET cc_start: 0.8238 (mtp) cc_final: 0.8028 (mtt) REVERT: C 321 ARG cc_start: 0.6697 (ttm-80) cc_final: 0.5881 (ttm110) REVERT: C 333 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8420 (mm) REVERT: D 304 PHE cc_start: 0.8809 (t80) cc_final: 0.8608 (t80) REVERT: E 244 CYS cc_start: 0.8878 (m) cc_final: 0.8646 (m) REVERT: E 247 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8690 (mp) REVERT: E 348 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6425 (tm) REVERT: I 104 GLU cc_start: 0.4671 (OUTLIER) cc_final: 0.3856 (tt0) REVERT: J 28 ASN cc_start: 0.7853 (t0) cc_final: 0.7526 (t0) REVERT: J 90 ASP cc_start: 0.7993 (m-30) cc_final: 0.7600 (m-30) REVERT: L 79 GLN cc_start: 0.6610 (OUTLIER) cc_final: 0.6325 (mm110) outliers start: 65 outliers final: 36 residues processed: 337 average time/residue: 1.1936 time to fit residues: 452.1452 Evaluate side-chains 340 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 296 time to evaluate : 2.081 ------------------------------------------------------------------------------- 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 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 227 MET Chi-restraints excluded: chain C residue 275 ILE 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 21 ARG 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 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 348 LEU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 104 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 145 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 163 optimal weight: 10.0000 chunk 192 optimal weight: 6.9990 chunk 69 optimal weight: 0.0980 chunk 63 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 176 optimal weight: 0.0070 chunk 9 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- 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 E 239 GLN K 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.130294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.091497 restraints weight = 24170.992| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.98 r_work: 0.2952 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2114 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= 0.116 Angle : 0.571 17.252 24433 Z= 0.287 Chirality : 0.042 0.181 2807 Planarity : 0.004 0.048 2991 Dihedral : 6.730 84.491 2847 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.76 % Allowed : 18.53 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2103 helix: 2.07 (0.22), residues: 564 sheet: 0.40 (0.20), residues: 628 loop : -0.31 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 237 HIS 0.005 0.001 HIS C 267 PHE 0.015 0.001 PHE B 258 TYR 0.030 0.001 TYR L 49 ARG 0.005 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 7) link_NAG-ASN : angle 1.60931 ( 21) link_ALPHA1-6 : bond 0.00316 ( 2) link_ALPHA1-6 : angle 1.73990 ( 6) link_BETA1-4 : bond 0.00370 ( 9) link_BETA1-4 : angle 1.74706 ( 27) link_ALPHA1-2 : bond 0.00542 ( 3) link_ALPHA1-2 : angle 1.53122 ( 9) link_ALPHA1-3 : bond 0.01123 ( 2) link_ALPHA1-3 : angle 1.18917 ( 6) hydrogen bonds : bond 0.03286 ( 862) hydrogen bonds : angle 4.50421 ( 2760) SS BOND : bond 0.00208 ( 9) SS BOND : angle 2.13692 ( 18) covalent geometry : bond 0.00257 (17899) covalent geometry : angle 0.56239 (24346) Misc. bond : bond 0.00007 ( 1) *********************** 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 367 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 315 time to evaluate : 2.126 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8480 (ttt90) REVERT: A 103 LYS cc_start: 0.8808 (ptmm) cc_final: 0.8458 (tttp) REVERT: A 286 MET cc_start: 0.8023 (mpp) cc_final: 0.7795 (mmp) REVERT: A 297 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7288 (tm) REVERT: A 304 TYR cc_start: 0.6858 (t80) cc_final: 0.6557 (t80) REVERT: B 93 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8639 (mptp) REVERT: C 265 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8436 (t160) REVERT: C 286 MET cc_start: 0.8216 (mtp) cc_final: 0.7454 (mpp) REVERT: C 321 ARG cc_start: 0.6678 (ttm-80) cc_final: 0.5882 (ttm110) REVERT: C 333 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8401 (mm) REVERT: D 21 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7757 (ttm170) REVERT: E 244 CYS cc_start: 0.8875 (m) cc_final: 0.8516 (m) REVERT: E 247 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8679 (mp) REVERT: E 299 PHE cc_start: 0.8382 (t80) cc_final: 0.8163 (t80) REVERT: E 348 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6450 (tm) REVERT: I 79 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6779 (mm-40) REVERT: J 90 ASP cc_start: 0.8011 (m-30) cc_final: 0.7585 (m-30) REVERT: L 22 SER cc_start: 0.8272 (OUTLIER) cc_final: 0.8013 (p) REVERT: L 70 ASP cc_start: 0.8393 (m-30) cc_final: 0.8029 (m-30) outliers start: 52 outliers final: 28 residues processed: 341 average time/residue: 1.1865 time to fit residues: 455.2605 Evaluate side-chains 328 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 290 time to evaluate : 1.993 ------------------------------------------------------------------------------- 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 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 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 265 ASN Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 ARG 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 236 MET 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 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 88 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 113 SER 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 194 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3583 r_free = 0.3583 target = 0.127382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.093163 restraints weight = 24191.822| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.32 r_work: 0.2877 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17932 Z= 0.233 Angle : 0.659 16.829 24433 Z= 0.331 Chirality : 0.046 0.221 2807 Planarity : 0.005 0.049 2991 Dihedral : 7.018 83.355 2847 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.08 % Allowed : 19.12 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2103 helix: 1.91 (0.22), residues: 565 sheet: 0.29 (0.20), residues: 630 loop : -0.39 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 237 HIS 0.011 0.001 HIS C 267 PHE 0.018 0.002 PHE A 306 TYR 0.020 0.002 TYR A 157 ARG 0.007 0.000 ARG E 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 7) link_NAG-ASN : angle 1.92276 ( 21) link_ALPHA1-6 : bond 0.00195 ( 2) link_ALPHA1-6 : angle 2.00349 ( 6) link_BETA1-4 : bond 0.00192 ( 9) link_BETA1-4 : angle 2.27263 ( 27) link_ALPHA1-2 : bond 0.00439 ( 3) link_ALPHA1-2 : angle 1.75435 ( 9) link_ALPHA1-3 : bond 0.00915 ( 2) link_ALPHA1-3 : angle 1.24830 ( 6) hydrogen bonds : bond 0.03824 ( 862) hydrogen bonds : angle 4.73836 ( 2760) SS BOND : bond 0.00318 ( 9) SS BOND : angle 2.51311 ( 18) covalent geometry : bond 0.00545 (17899) covalent geometry : angle 0.64767 (24346) Misc. bond : bond 0.00094 ( 1) *********************** 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 360 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 302 time to evaluate : 2.061 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8533 (ttt90) REVERT: A 103 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8569 (tttp) REVERT: A 171 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6438 (t0) REVERT: A 286 MET cc_start: 0.8061 (mpp) cc_final: 0.7837 (mmp) REVERT: A 297 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7317 (tm) REVERT: A 304 TYR cc_start: 0.6848 (t80) cc_final: 0.6578 (t80) REVERT: B 93 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8666 (mptp) REVERT: C 231 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8095 (mp) REVERT: C 286 MET cc_start: 0.8281 (mtp) cc_final: 0.8077 (mtt) REVERT: C 321 ARG cc_start: 0.6758 (ttm-80) cc_final: 0.5931 (ttm110) REVERT: C 333 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8462 (mm) REVERT: E 244 CYS cc_start: 0.8899 (m) cc_final: 0.8629 (m) REVERT: E 247 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8684 (mp) REVERT: E 348 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6409 (tm) REVERT: J 90 ASP cc_start: 0.8030 (m-30) cc_final: 0.7617 (m-30) outliers start: 58 outliers final: 31 residues processed: 331 average time/residue: 1.1889 time to fit residues: 444.9797 Evaluate side-chains 335 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 295 time to evaluate : 2.127 ------------------------------------------------------------------------------- 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 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 275 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 21 ARG 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 D residue 302 ILE 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 348 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 65 SER 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 160 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 69 ASN E 152 GLN E 239 GLN J 28 ASN K 28 ASN K 43 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.130150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.096154 restraints weight = 24406.132| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.31 r_work: 0.2937 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17932 Z= 0.119 Angle : 0.585 17.730 24433 Z= 0.293 Chirality : 0.042 0.183 2807 Planarity : 0.004 0.048 2991 Dihedral : 6.735 82.983 2847 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.23 % Allowed : 19.97 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2103 helix: 1.95 (0.22), residues: 568 sheet: 0.34 (0.20), residues: 637 loop : -0.27 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 237 HIS 0.006 0.001 HIS C 267 PHE 0.033 0.001 PHE D 304 TYR 0.032 0.001 TYR L 49 ARG 0.009 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 7) link_NAG-ASN : angle 1.61776 ( 21) link_ALPHA1-6 : bond 0.00302 ( 2) link_ALPHA1-6 : angle 1.73280 ( 6) link_BETA1-4 : bond 0.00350 ( 9) link_BETA1-4 : angle 1.72920 ( 27) link_ALPHA1-2 : bond 0.00533 ( 3) link_ALPHA1-2 : angle 1.55494 ( 9) link_ALPHA1-3 : bond 0.01060 ( 2) link_ALPHA1-3 : angle 1.15853 ( 6) hydrogen bonds : bond 0.03319 ( 862) hydrogen bonds : angle 4.51341 ( 2760) SS BOND : bond 0.00179 ( 9) SS BOND : angle 2.12717 ( 18) covalent geometry : bond 0.00265 (17899) covalent geometry : angle 0.57671 (24346) Misc. bond : bond 0.00005 ( 1) *********************** 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 355 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 313 time to evaluate : 1.953 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8509 (ttt90) REVERT: A 103 LYS cc_start: 0.8842 (ptmm) cc_final: 0.8480 (tttp) REVERT: A 171 ASP cc_start: 0.6758 (OUTLIER) cc_final: 0.6326 (t0) REVERT: A 286 MET cc_start: 0.8048 (mpp) cc_final: 0.7814 (mmp) REVERT: A 297 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7312 (tm) REVERT: A 304 TYR cc_start: 0.6895 (t80) cc_final: 0.6601 (t80) REVERT: B 93 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8661 (mptp) REVERT: C 286 MET cc_start: 0.8266 (mtp) cc_final: 0.7508 (mpp) REVERT: C 321 ARG cc_start: 0.6722 (ttm-80) cc_final: 0.5904 (ttm110) REVERT: C 333 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8417 (mm) REVERT: D 21 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7778 (ttm170) REVERT: E 244 CYS cc_start: 0.8890 (m) cc_final: 0.8544 (m) REVERT: E 247 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8688 (mp) REVERT: E 299 PHE cc_start: 0.8404 (t80) cc_final: 0.8184 (t80) REVERT: E 348 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6437 (tm) REVERT: I 79 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.6839 (mm-40) REVERT: I 104 GLU cc_start: 0.4842 (OUTLIER) cc_final: 0.4518 (tm-30) REVERT: J 90 ASP cc_start: 0.8003 (m-30) cc_final: 0.7599 (m-30) REVERT: L 22 SER cc_start: 0.8297 (OUTLIER) cc_final: 0.8054 (p) REVERT: L 70 ASP cc_start: 0.8383 (m-30) cc_final: 0.8019 (m-30) outliers start: 42 outliers final: 29 residues processed: 334 average time/residue: 1.1423 time to fit residues: 430.4931 Evaluate side-chains 341 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 301 time to evaluate : 2.005 ------------------------------------------------------------------------------- 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 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 323 PHE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 ARG 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 236 MET 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 E residue 348 LEU Chi-restraints excluded: chain I residue 79 GLN 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 65 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 E 239 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 = 0.3606 r_free = 0.3606 target = 0.129144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.094864 restraints weight = 24255.826| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.28 r_work: 0.2911 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17932 Z= 0.165 Angle : 0.614 14.173 24433 Z= 0.308 Chirality : 0.044 0.197 2807 Planarity : 0.004 0.048 2991 Dihedral : 6.817 83.373 2847 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.66 % Allowed : 20.02 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2103 helix: 1.87 (0.22), residues: 568 sheet: 0.33 (0.20), residues: 641 loop : -0.29 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 237 HIS 0.007 0.001 HIS C 267 PHE 0.024 0.002 PHE D 304 TYR 0.018 0.002 TYR C 299 ARG 0.009 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 7) link_NAG-ASN : angle 1.72465 ( 21) link_ALPHA1-6 : bond 0.00148 ( 2) link_ALPHA1-6 : angle 1.90033 ( 6) link_BETA1-4 : bond 0.00258 ( 9) link_BETA1-4 : angle 1.98353 ( 27) link_ALPHA1-2 : bond 0.00470 ( 3) link_ALPHA1-2 : angle 1.62741 ( 9) link_ALPHA1-3 : bond 0.01060 ( 2) link_ALPHA1-3 : angle 1.17218 ( 6) hydrogen bonds : bond 0.03527 ( 862) hydrogen bonds : angle 4.59051 ( 2760) SS BOND : bond 0.00247 ( 9) SS BOND : angle 2.23397 ( 18) covalent geometry : bond 0.00381 (17899) covalent geometry : angle 0.60482 (24346) Misc. bond : bond 0.00054 ( 1) ********************** 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 349 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 299 time to evaluate : 1.975 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8498 (ttt90) REVERT: A 103 LYS cc_start: 0.8869 (ptmm) cc_final: 0.8521 (tttp) REVERT: A 171 ASP cc_start: 0.6811 (OUTLIER) cc_final: 0.6380 (t0) REVERT: A 286 MET cc_start: 0.8046 (mpp) cc_final: 0.7829 (mmp) REVERT: A 297 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7330 (tm) REVERT: A 304 TYR cc_start: 0.6892 (t80) cc_final: 0.6593 (t80) REVERT: B 93 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8644 (mptp) REVERT: C 231 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8039 (mp) REVERT: C 286 MET cc_start: 0.8250 (mtp) cc_final: 0.7484 (mpp) REVERT: C 321 ARG cc_start: 0.6761 (ttm-80) cc_final: 0.5926 (ttm110) REVERT: C 333 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8446 (mm) REVERT: E 244 CYS cc_start: 0.8889 (m) cc_final: 0.8507 (m) REVERT: E 247 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8671 (mp) REVERT: E 299 PHE cc_start: 0.8375 (t80) cc_final: 0.8159 (t80) REVERT: E 348 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6419 (tm) REVERT: I 79 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.6931 (mm-40) REVERT: J 90 ASP cc_start: 0.7986 (m-30) cc_final: 0.7568 (m-30) REVERT: L 22 SER cc_start: 0.8303 (OUTLIER) cc_final: 0.8049 (p) REVERT: L 70 ASP cc_start: 0.8359 (m-30) cc_final: 0.8078 (m-30) outliers start: 50 outliers final: 35 residues processed: 327 average time/residue: 1.1550 time to fit residues: 425.6639 Evaluate side-chains 341 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 296 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 150 CYS 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 294 MET 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 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 231 LEU Chi-restraints excluded: chain C residue 275 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 21 ARG 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 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 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 100 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 170 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 K 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 = 0.3599 r_free = 0.3599 target = 0.128594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.094046 restraints weight = 24150.111| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.28 r_work: 0.2898 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17932 Z= 0.194 Angle : 0.642 17.154 24433 Z= 0.323 Chirality : 0.045 0.200 2807 Planarity : 0.004 0.048 2991 Dihedral : 6.969 82.924 2847 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.66 % Allowed : 20.13 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2103 helix: 1.77 (0.22), residues: 568 sheet: 0.32 (0.20), residues: 629 loop : -0.35 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 237 HIS 0.007 0.001 HIS C 267 PHE 0.035 0.002 PHE D 304 TYR 0.028 0.002 TYR L 49 ARG 0.009 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 7) link_NAG-ASN : angle 1.81667 ( 21) link_ALPHA1-6 : bond 0.00149 ( 2) link_ALPHA1-6 : angle 1.92287 ( 6) link_BETA1-4 : bond 0.00244 ( 9) link_BETA1-4 : angle 2.13467 ( 27) link_ALPHA1-2 : bond 0.00464 ( 3) link_ALPHA1-2 : angle 1.70923 ( 9) link_ALPHA1-3 : bond 0.01096 ( 2) link_ALPHA1-3 : angle 1.18733 ( 6) hydrogen bonds : bond 0.03689 ( 862) hydrogen bonds : angle 4.69031 ( 2760) SS BOND : bond 0.00284 ( 9) SS BOND : angle 2.39749 ( 18) covalent geometry : bond 0.00452 (17899) covalent geometry : angle 0.63185 (24346) Misc. bond : bond 0.00063 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14194.14 seconds wall clock time: 245 minutes 4.56 seconds (14704.56 seconds total)