Starting phenix.real_space_refine on Thu Jul 2 10:35:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dzg_47329/07_2026/9dzg_47329.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dzg_47329/07_2026/9dzg_47329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dzg_47329/07_2026/9dzg_47329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dzg_47329/07_2026/9dzg_47329.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dzg_47329/07_2026/9dzg_47329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dzg_47329/07_2026/9dzg_47329.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.125 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 32 5.16 5 Cl 2 4.86 5 C 5242 2.51 5 N 1403 2.21 5 O 1431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8110 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3135 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 27, 'TRANS': 397} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 15, 'ASP:plan': 18, 'ARG:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 154 Chain: "B" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3133 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 27, 'TRANS': 397} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 16, 'ARG:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 156 Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 940 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 121} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "L" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 775 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" 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: "D" 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: "E" 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: "F" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.73, per 1000 atoms: 0.21 Number of scatterers: 8110 At special positions: 0 Unit cell: (77.976, 102.885, 115.881, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 32 16.00 O 1431 8.00 N 1403 7.00 C 5242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 213 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 213 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 13 " " NAG D 1 " - " ASN A 395 " " NAG E 1 " - " ASN B 13 " " NAG F 1 " - " ASN B 395 " Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 368.2 milliseconds 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 13 sheets defined 32.8% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 19 through 35 Proline residue: A 25 - end of helix removed outlier: 3.734A pdb=" N LEU A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.178A pdb=" N LEU A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A 75 " --> pdb=" O ASP A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 101 removed outlier: 3.964A pdb=" N ALA A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.694A pdb=" N PHE A 114 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 116 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 145 removed outlier: 4.177A pdb=" N GLY A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASP A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 179 Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.721A pdb=" N THR A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 215 through 229 removed outlier: 3.688A pdb=" N ARG A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 227 " --> pdb=" O MET A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 236 removed outlier: 3.535A pdb=" N ASP A 235 " --> pdb=" O CYS A 232 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A 236 " --> pdb=" O GLY A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 236' Processing helix chain 'A' and resid 266 through 274 removed outlier: 3.932A pdb=" N GLN A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 306 removed outlier: 3.688A pdb=" N LEU A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.828A pdb=" N ASN A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 336 removed outlier: 3.832A pdb=" N TYR A 328 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 344 through 349 removed outlier: 3.510A pdb=" N THR A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 32 Proline residue: B 25 - end of helix Processing helix chain 'B' and resid 64 through 76 removed outlier: 3.809A pdb=" N ASP B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 72 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 111 through 116 removed outlier: 4.173A pdb=" N VAL B 116 " --> pdb=" O GLY B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 145 removed outlier: 4.003A pdb=" N GLY B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 177 Processing helix chain 'B' and resid 193 through 203 removed outlier: 3.583A pdb=" N THR B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 215 through 229 removed outlier: 3.734A pdb=" N ARG B 220 " --> pdb=" O PRO B 216 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR B 221 " --> pdb=" O ASP B 217 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 274 removed outlier: 4.049A pdb=" N GLN B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 304 removed outlier: 3.581A pdb=" N LEU B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR B 302 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 303 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 315 through 327 removed outlier: 3.589A pdb=" N ALA B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 326 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 338 removed outlier: 3.623A pdb=" N GLU B 334 " --> pdb=" O GLN B 330 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR B 335 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 350 removed outlier: 3.624A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.904A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.736A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 51 removed outlier: 9.140A pdb=" N VAL A 80 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A 4 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU A 82 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA A 6 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU A 104 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 187 removed outlier: 6.669A pdb=" N MET A 152 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 210 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU A 241 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE A 212 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE A 238 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE A 280 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N HIS A 240 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N TYR A 282 " --> pdb=" O HIS A 240 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ALA A 277 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N MET A 381 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE A 376 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ASN A 393 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 378 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 355 through 358 Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 51 removed outlier: 9.364A pdb=" N VAL B 80 " --> pdb=" O ASN B 2 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR B 4 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU B 82 " --> pdb=" O THR B 4 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA B 6 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 106 Processing sheet with id=AA6, first strand: chain 'B' and resid 182 through 187 removed outlier: 6.717A pdb=" N ALA B 150 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LEU B 186 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N MET B 152 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL B 209 " --> pdb=" O GLN B 149 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N ALA B 277 " --> pdb=" O MET B 381 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N MET B 381 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 392 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP B 380 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL B 390 " --> pdb=" O ASP B 380 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 355 through 358 Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.796A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 18 through 21 Processing sheet with id=AB2, first strand: chain 'H' and resid 98 through 99 removed outlier: 6.961A pdb=" N ARG H 98 " --> pdb=" O ASP H 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.542A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.354A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 759 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: 1.02 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2588 1.34 - 1.46: 2115 1.46 - 1.58: 3580 1.58 - 1.70: 0 1.70 - 1.81: 50 Bond restraints: 8333 Sorted by residual: bond pdb=" N GLY B 1 " pdb=" CA GLY B 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.19e+00 bond pdb=" N GLY A 1 " pdb=" CA GLY A 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.17e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.42e+00 ... (remaining 8328 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 11339 3.21 - 6.41: 58 6.41 - 9.62: 3 9.62 - 12.82: 0 12.82 - 16.03: 1 Bond angle restraints: 11401 Sorted by residual: angle pdb=" C GLN L 55 " pdb=" CA GLN L 55 " pdb=" CB GLN L 55 " ideal model delta sigma weight residual 111.71 127.74 -16.03 2.23e+00 2.01e-01 5.16e+01 angle pdb=" C SER L 14 " pdb=" CA SER L 14 " pdb=" CB SER L 14 " ideal model delta sigma weight residual 109.50 118.28 -8.78 1.69e+00 3.50e-01 2.70e+01 angle pdb=" N SER L 14 " pdb=" CA SER L 14 " pdb=" CB SER L 14 " ideal model delta sigma weight residual 110.63 118.97 -8.34 1.63e+00 3.76e-01 2.62e+01 angle pdb=" N SER L 14 " pdb=" CA SER L 14 " pdb=" C SER L 14 " ideal model delta sigma weight residual 110.17 117.18 -7.01 1.61e+00 3.86e-01 1.90e+01 angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" CB ALA L 51 " ideal model delta sigma weight residual 114.17 110.05 4.12 1.14e+00 7.69e-01 1.31e+01 ... (remaining 11396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.08: 4548 21.08 - 42.16: 298 42.16 - 63.24: 57 63.24 - 84.32: 13 84.32 - 105.41: 5 Dihedral angle restraints: 4921 sinusoidal: 1833 harmonic: 3088 Sorted by residual: dihedral pdb=" C GLN L 55 " pdb=" N GLN L 55 " pdb=" CA GLN L 55 " pdb=" CB GLN L 55 " ideal model delta harmonic sigma weight residual -122.60 -158.54 35.94 0 2.50e+00 1.60e-01 2.07e+02 dihedral pdb=" N GLN L 55 " pdb=" C GLN L 55 " pdb=" CA GLN L 55 " pdb=" CB GLN L 55 " ideal model delta harmonic sigma weight residual 122.80 155.09 -32.29 0 2.50e+00 1.60e-01 1.67e+02 dihedral pdb=" C SER L 14 " pdb=" N SER L 14 " pdb=" CA SER L 14 " pdb=" CB SER L 14 " ideal model delta harmonic sigma weight residual -122.60 -153.28 30.68 0 2.50e+00 1.60e-01 1.51e+02 ... (remaining 4918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.291: 1298 0.291 - 0.582: 0 0.582 - 0.874: 0 0.874 - 1.165: 0 1.165 - 1.456: 2 Chirality restraints: 1300 Sorted by residual: chirality pdb=" CA GLN L 55 " pdb=" N GLN L 55 " pdb=" C GLN L 55 " pdb=" CB GLN L 55 " both_signs ideal model delta sigma weight residual False 2.51 1.05 1.46 2.00e-01 2.50e+01 5.30e+01 chirality pdb=" CA SER L 14 " pdb=" N SER L 14 " pdb=" C SER L 14 " pdb=" CB SER L 14 " both_signs ideal model delta sigma weight residual False 2.51 1.20 1.31 2.00e-01 2.50e+01 4.31e+01 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1297 not shown) Planarity restraints: 1455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 317 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO A 318 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 318 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 318 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 317 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO B 318 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 318 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 318 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 24 " 0.026 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 25 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " 0.023 5.00e-02 4.00e+02 ... (remaining 1452 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 52 2.62 - 3.19: 6679 3.19 - 3.76: 11279 3.76 - 4.33: 16549 4.33 - 4.90: 28965 Nonbonded interactions: 63524 Sorted by model distance: nonbonded pdb=" OH TYR H 105 " pdb=" O HOH H 301 " model vdw 2.045 3.040 nonbonded pdb=" O GLU H 52 " pdb=" NH1 ARG H 72 " model vdw 2.173 3.120 nonbonded pdb=" OD1 ASN B 385 " pdb=" N GLY B 386 " model vdw 2.248 3.120 nonbonded pdb=" NH1 ARG B 271 " pdb=" O ASN B 385 " model vdw 2.278 3.120 nonbonded pdb=" O SER A 53 " pdb=" OG SER A 53 " model vdw 2.287 3.040 ... (remaining 63519 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' and (resid 1 through 34 or (resid 35 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 61 or (resid 62 and (nam \ e N or name CA or name C or name O or name CB )) or resid 63 through 74 or (resi \ d 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throug \ h 189 or (resid 190 through 194 and (name N or name CA or name C or name O or na \ me CB )) or resid 195 through 271 or (resid 272 through 273 and (name N or name \ CA or name C or name O or name CB )) or resid 274 through 294 or (resid 295 and \ (name N or name CA or name C or name O or name CB )) or resid 296 through 305 or \ (resid 306 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 7 through 345 or (resid 346 and (name N or name CA or name C or name O or name C \ B )) or resid 347 through 349 or (resid 350 and (name N or name CA or name C or \ name O or name CB )) or resid 351 through 1101)) selection = (chain 'B' and (resid 1 through 115 or (resid 116 and (name N or name CA or name \ C or name O or name CB )) or resid 117 through 134 or (resid 135 and (name N or \ name CA or name C or name O or name CB )) or resid 136 through 168 or (resid 16 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 170 through \ 196 or (resid 197 through 198 and (name N or name CA or name C or name O or name \ CB )) or resid 199 through 213 or (resid 214 and (name N or name CA or name C o \ r name O or name CB )) or resid 215 through 231 or (resid 232 and (name N or nam \ e CA or name C or name O or name CB )) or resid 233 through 260 or (resid 261 an \ d (name N or name CA or name C or name O or name CB )) or resid 262 through 266 \ or (resid 267 through 268 and (name N or name CA or name C or name O or name CB \ )) or resid 269 through 303 or (resid 304 and (name N or name CA or name C or na \ me O or name CB )) or resid 305 through 310 or (resid 311 and (name N or name CA \ or name C or name O or name CB )) or resid 312 through 367 or (resid 368 and (n \ ame N or name CA or name C or name O or name CB )) or resid 369 through 384 or ( \ resid 385 and (name N or name CA or name C or name O or name CB )) or resid 386 \ through 422 or (resid 423 and (name N or name CA or name C or name O or name CB \ )) or resid 424 through 1101)) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } 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: 1.030 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.220 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 : 0.003 0.048 8348 Z= 0.139 Angle : 0.626 16.026 11440 Z= 0.313 Chirality : 0.068 1.456 1300 Planarity : 0.004 0.049 1451 Dihedral : 15.036 105.405 2939 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.25), residues: 1073 helix: -1.68 (0.28), residues: 298 sheet: -1.04 (0.31), residues: 302 loop : -1.42 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.010 0.001 TYR H 80 PHE 0.012 0.001 PHE B 172 TRP 0.008 0.001 TRP A 260 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 8333) covalent geometry : angle 0.59599 / 0.31 (11401) SS BOND : bond 0.00253 / 0.18 ( 6) SS BOND : angle 0.51493 / 0.36 ( 12) hydrogen bonds : bond 0.19332 / 13.66 ( 278) hydrogen bonds : angle 7.18891 / 5.02 ( 759) link_BETA1-4 : bond 0.00519 / 0.33 ( 5) link_BETA1-4 : angle 2.09688 / 1.29 ( 15) link_NAG-ASN : bond 0.00485 / 0.32 ( 4) link_NAG-ASN : angle 5.54526 / 2.49 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.206 Fit side-chains REVERT: A 252 GLN cc_start: 0.7467 (tm-30) cc_final: 0.6752 (tp40) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.0639 time to fit residues: 9.0046 Evaluate side-chains 90 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.0870 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.123893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.097915 restraints weight = 9477.019| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.93 r_work: 0.2841 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8348 Z= 0.145 Angle : 0.597 8.804 11440 Z= 0.293 Chirality : 0.044 0.282 1300 Planarity : 0.004 0.049 1451 Dihedral : 8.467 62.546 1364 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.62 % Allowed : 11.73 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.25), residues: 1073 helix: -1.10 (0.29), residues: 318 sheet: -1.05 (0.30), residues: 302 loop : -1.32 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 72 TYR 0.011 0.001 TYR H 80 PHE 0.014 0.001 PHE B 219 TRP 0.009 0.001 TRP H 47 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.14 ( 8333) covalent geometry : angle 0.59237 / 0.29 (11401) SS BOND : bond 0.00285 / 0.21 ( 6) SS BOND : angle 0.76941 / 0.55 ( 12) hydrogen bonds : bond 0.04415 / 3.08 ( 278) hydrogen bonds : angle 5.11325 / 3.48 ( 759) link_BETA1-4 : bond 0.00501 / 0.32 ( 5) link_BETA1-4 : angle 1.89812 / 1.47 ( 15) link_NAG-ASN : bond 0.00315 / 0.21 ( 4) link_NAG-ASN : angle 1.14328 / 0.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.245 Fit side-chains REVERT: A 252 GLN cc_start: 0.7676 (tm-30) cc_final: 0.6973 (tp40) REVERT: B 323 ASP cc_start: 0.7944 (m-30) cc_final: 0.7648 (m-30) REVERT: B 389 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.6165 (mtm180) outliers start: 12 outliers final: 8 residues processed: 101 average time/residue: 0.0734 time to fit residues: 10.5064 Evaluate side-chains 100 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 57 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 35 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.122427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.097386 restraints weight = 9450.281| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.95 r_work: 0.2746 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8348 Z= 0.160 Angle : 0.584 9.876 11440 Z= 0.288 Chirality : 0.044 0.271 1300 Planarity : 0.004 0.051 1451 Dihedral : 7.180 58.858 1364 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.89 % Allowed : 13.75 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.25), residues: 1073 helix: -0.93 (0.29), residues: 324 sheet: -0.99 (0.30), residues: 302 loop : -1.41 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 72 TYR 0.012 0.001 TYR B 290 PHE 0.017 0.001 PHE A 136 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.16 ( 8333) covalent geometry : angle 0.57977 / 0.29 (11401) SS BOND : bond 0.00319 / 0.25 ( 6) SS BOND : angle 0.82757 / 0.59 ( 12) hydrogen bonds : bond 0.04017 / 2.74 ( 278) hydrogen bonds : angle 4.85487 / 3.34 ( 759) link_BETA1-4 : bond 0.00469 / 0.30 ( 5) link_BETA1-4 : angle 1.92671 / 1.31 ( 15) link_NAG-ASN : bond 0.00329 / 0.22 ( 4) link_NAG-ASN : angle 0.96977 / 0.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.342 Fit side-chains REVERT: A 252 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7035 (tp40) REVERT: B 274 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.7384 (t80) REVERT: B 371 ASP cc_start: 0.8151 (m-30) cc_final: 0.7835 (m-30) REVERT: B 389 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.6241 (mtm180) REVERT: L 55 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7297 (tt0) outliers start: 14 outliers final: 8 residues processed: 102 average time/residue: 0.0753 time to fit residues: 11.1101 Evaluate side-chains 100 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 35 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 330 GLN B 338 HIS ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.122529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.097479 restraints weight = 9607.408| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.93 r_work: 0.2820 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8348 Z= 0.156 Angle : 0.578 9.866 11440 Z= 0.285 Chirality : 0.044 0.275 1300 Planarity : 0.004 0.050 1451 Dihedral : 6.621 59.245 1364 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.43 % Allowed : 15.23 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.25), residues: 1073 helix: -0.73 (0.29), residues: 312 sheet: -0.99 (0.30), residues: 301 loop : -1.41 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 72 TYR 0.011 0.001 TYR H 80 PHE 0.017 0.001 PHE A 136 TRP 0.010 0.001 TRP H 47 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 ( 8333) covalent geometry : angle 0.57330 / 0.28 (11401) SS BOND : bond 0.00310 / 0.24 ( 6) SS BOND : angle 0.79733 / 0.56 ( 12) hydrogen bonds : bond 0.03682 / 2.49 ( 278) hydrogen bonds : angle 4.65439 / 3.23 ( 759) link_BETA1-4 : bond 0.00418 / 0.26 ( 5) link_BETA1-4 : angle 1.90706 / 1.29 ( 15) link_NAG-ASN : bond 0.00321 / 0.21 ( 4) link_NAG-ASN : angle 0.90950 / 0.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.273 Fit side-chains REVERT: A 252 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7024 (tp40) REVERT: A 389 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7488 (ppt170) REVERT: B 274 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7426 (t80) REVERT: B 389 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.6245 (mtm180) REVERT: L 55 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7299 (tt0) outliers start: 18 outliers final: 13 residues processed: 100 average time/residue: 0.0782 time to fit residues: 10.9085 Evaluate side-chains 102 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 52 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 338 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.123497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.098704 restraints weight = 9465.869| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.85 r_work: 0.2784 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8348 Z= 0.129 Angle : 0.547 9.825 11440 Z= 0.269 Chirality : 0.042 0.267 1300 Planarity : 0.004 0.048 1451 Dihedral : 6.223 58.250 1364 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.56 % Allowed : 16.04 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.25), residues: 1073 helix: -0.62 (0.29), residues: 312 sheet: -0.93 (0.29), residues: 301 loop : -1.37 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 72 TYR 0.015 0.001 TYR H 80 PHE 0.014 0.001 PHE A 136 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 8333) covalent geometry : angle 0.54265 / 0.27 (11401) SS BOND : bond 0.00274 / 0.21 ( 6) SS BOND : angle 0.70048 / 0.49 ( 12) hydrogen bonds : bond 0.03331 / 2.24 ( 278) hydrogen bonds : angle 4.51445 / 3.15 ( 759) link_BETA1-4 : bond 0.00452 / 0.28 ( 5) link_BETA1-4 : angle 1.77173 / 1.17 ( 15) link_NAG-ASN : bond 0.00329 / 0.21 ( 4) link_NAG-ASN : angle 0.82906 / 0.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.261 Fit side-chains REVERT: A 252 GLN cc_start: 0.7696 (tm-30) cc_final: 0.6900 (tp40) REVERT: A 371 ASP cc_start: 0.7904 (m-30) cc_final: 0.7518 (m-30) REVERT: A 389 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7497 (ppt170) REVERT: B 274 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.7517 (t80) REVERT: B 323 ASP cc_start: 0.7852 (m-30) cc_final: 0.7605 (m-30) REVERT: B 389 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.6238 (mtm180) REVERT: L 55 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7258 (tt0) outliers start: 19 outliers final: 10 residues processed: 101 average time/residue: 0.0764 time to fit residues: 10.9496 Evaluate side-chains 102 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 59 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 0.0980 chunk 55 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.124270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.098722 restraints weight = 9340.002| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.01 r_work: 0.2850 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8348 Z= 0.111 Angle : 0.526 9.778 11440 Z= 0.257 Chirality : 0.042 0.261 1300 Planarity : 0.004 0.046 1451 Dihedral : 6.018 57.758 1364 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.10 % Allowed : 15.36 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.25), residues: 1073 helix: -0.49 (0.29), residues: 312 sheet: -0.86 (0.29), residues: 301 loop : -1.32 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.012 0.001 TYR H 80 PHE 0.011 0.001 PHE A 136 TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.11 ( 8333) covalent geometry : angle 0.52131 / 0.26 (11401) SS BOND : bond 0.00249 / 0.18 ( 6) SS BOND : angle 0.66140 / 0.46 ( 12) hydrogen bonds : bond 0.03069 / 2.06 ( 278) hydrogen bonds : angle 4.37662 / 3.07 ( 759) link_BETA1-4 : bond 0.00472 / 0.29 ( 5) link_BETA1-4 : angle 1.81044 / 1.26 ( 15) link_NAG-ASN : bond 0.00340 / 0.21 ( 4) link_NAG-ASN : angle 0.76188 / 0.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.296 Fit side-chains REVERT: A 252 GLN cc_start: 0.7715 (tm-30) cc_final: 0.6953 (tp40) REVERT: A 295 LYS cc_start: 0.7321 (mtpt) cc_final: 0.7114 (mtpt) REVERT: A 389 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7471 (ppt170) REVERT: B 274 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.7499 (t80) REVERT: B 323 ASP cc_start: 0.7913 (m-30) cc_final: 0.7654 (m-30) REVERT: B 389 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.6331 (mtm180) REVERT: L 55 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7272 (tt0) outliers start: 23 outliers final: 18 residues processed: 106 average time/residue: 0.0818 time to fit residues: 12.4636 Evaluate side-chains 104 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.124727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.098516 restraints weight = 9477.670| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.10 r_work: 0.2843 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8348 Z= 0.114 Angle : 0.526 9.794 11440 Z= 0.256 Chirality : 0.042 0.261 1300 Planarity : 0.004 0.046 1451 Dihedral : 5.956 58.503 1364 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.64 % Allowed : 15.77 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.25), residues: 1073 helix: -0.34 (0.29), residues: 312 sheet: -0.84 (0.30), residues: 303 loop : -1.28 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.012 0.001 TYR H 80 PHE 0.011 0.001 PHE A 136 TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.11 ( 8333) covalent geometry : angle 0.52178 / 0.26 (11401) SS BOND : bond 0.00256 / 0.19 ( 6) SS BOND : angle 0.67154 / 0.47 ( 12) hydrogen bonds : bond 0.03050 / 2.05 ( 278) hydrogen bonds : angle 4.30767 / 3.02 ( 759) link_BETA1-4 : bond 0.00461 / 0.29 ( 5) link_BETA1-4 : angle 1.79008 / 1.24 ( 15) link_NAG-ASN : bond 0.00325 / 0.21 ( 4) link_NAG-ASN : angle 0.78179 / 0.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.371 Fit side-chains REVERT: A 252 GLN cc_start: 0.7705 (tm-30) cc_final: 0.6950 (tp40) REVERT: A 295 LYS cc_start: 0.7295 (mtpt) cc_final: 0.7089 (mtpt) REVERT: A 389 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7434 (ppt170) REVERT: B 274 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7393 (t80) REVERT: B 323 ASP cc_start: 0.7901 (m-30) cc_final: 0.7622 (m-30) REVERT: B 389 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.6274 (mtm180) REVERT: L 55 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7258 (tt0) outliers start: 27 outliers final: 19 residues processed: 108 average time/residue: 0.0814 time to fit residues: 12.5888 Evaluate side-chains 107 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 0.0970 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.124196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.098432 restraints weight = 9391.006| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.98 r_work: 0.2787 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8348 Z= 0.121 Angle : 0.534 9.807 11440 Z= 0.260 Chirality : 0.042 0.262 1300 Planarity : 0.004 0.046 1451 Dihedral : 5.898 58.184 1364 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.50 % Allowed : 16.31 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.25), residues: 1073 helix: -0.23 (0.29), residues: 312 sheet: -0.85 (0.29), residues: 303 loop : -1.26 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.012 0.001 TYR H 80 PHE 0.011 0.001 PHE A 136 TRP 0.007 0.001 TRP A 379 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.12 ( 8333) covalent geometry : angle 0.53000 / 0.26 (11401) SS BOND : bond 0.00267 / 0.20 ( 6) SS BOND : angle 0.69000 / 0.48 ( 12) hydrogen bonds : bond 0.03071 / 2.06 ( 278) hydrogen bonds : angle 4.29876 / 3.02 ( 759) link_BETA1-4 : bond 0.00448 / 0.28 ( 5) link_BETA1-4 : angle 1.74104 / 1.18 ( 15) link_NAG-ASN : bond 0.00326 / 0.21 ( 4) link_NAG-ASN : angle 0.82198 / 0.57 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.241 Fit side-chains REVERT: A 252 GLN cc_start: 0.7661 (tm-30) cc_final: 0.6889 (tp40) REVERT: A 271 ARG cc_start: 0.7597 (ttt-90) cc_final: 0.7095 (ttt-90) REVERT: A 295 LYS cc_start: 0.7183 (mtpt) cc_final: 0.6978 (mtpt) REVERT: A 389 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7364 (ppt170) REVERT: B 274 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.7369 (t80) REVERT: B 323 ASP cc_start: 0.7807 (m-30) cc_final: 0.7526 (m-30) REVERT: B 389 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.6163 (mtm180) REVERT: L 55 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7185 (tt0) outliers start: 26 outliers final: 19 residues processed: 107 average time/residue: 0.0916 time to fit residues: 13.6294 Evaluate side-chains 107 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 6 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 49 optimal weight: 0.0870 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.125590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.099253 restraints weight = 9373.799| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.09 r_work: 0.2861 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8348 Z= 0.103 Angle : 0.518 9.753 11440 Z= 0.251 Chirality : 0.041 0.256 1300 Planarity : 0.004 0.071 1451 Dihedral : 5.733 57.583 1364 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.10 % Allowed : 16.71 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.25), residues: 1073 helix: -0.05 (0.30), residues: 312 sheet: -0.82 (0.30), residues: 303 loop : -1.20 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.011 0.001 TYR H 80 PHE 0.010 0.001 PHE A 172 TRP 0.008 0.001 TRP A 379 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.10 ( 8333) covalent geometry : angle 0.51409 / 0.25 (11401) SS BOND : bond 0.00230 / 0.17 ( 6) SS BOND : angle 0.64505 / 0.44 ( 12) hydrogen bonds : bond 0.02866 / 1.93 ( 278) hydrogen bonds : angle 4.23177 / 2.98 ( 759) link_BETA1-4 : bond 0.00465 / 0.29 ( 5) link_BETA1-4 : angle 1.66309 / 1.14 ( 15) link_NAG-ASN : bond 0.00339 / 0.21 ( 4) link_NAG-ASN : angle 0.77512 / 0.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.337 Fit side-chains REVERT: A 252 GLN cc_start: 0.7698 (tm-30) cc_final: 0.6966 (tp40) REVERT: A 271 ARG cc_start: 0.7624 (ttt-90) cc_final: 0.7137 (ttt-90) REVERT: A 389 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7408 (ppt170) REVERT: B 274 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7488 (t80) REVERT: B 323 ASP cc_start: 0.7938 (m-30) cc_final: 0.7671 (m-30) REVERT: B 389 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.6273 (mtm180) REVERT: L 55 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7254 (tt0) outliers start: 23 outliers final: 19 residues processed: 102 average time/residue: 0.0903 time to fit residues: 13.0232 Evaluate side-chains 105 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.0030 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.123855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.097491 restraints weight = 9467.800| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.09 r_work: 0.2859 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8348 Z= 0.142 Angle : 0.555 9.856 11440 Z= 0.268 Chirality : 0.043 0.266 1300 Planarity : 0.004 0.065 1451 Dihedral : 5.861 58.324 1364 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.23 % Allowed : 16.71 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.25), residues: 1073 helix: -0.06 (0.30), residues: 312 sheet: -0.89 (0.29), residues: 307 loop : -1.22 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.013 0.001 TYR H 80 PHE 0.015 0.001 PHE A 136 TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.14 ( 8333) covalent geometry : angle 0.55135 / 0.27 (11401) SS BOND : bond 0.00289 / 0.22 ( 6) SS BOND : angle 0.75089 / 0.52 ( 12) hydrogen bonds : bond 0.03240 / 2.17 ( 278) hydrogen bonds : angle 4.27032 / 3.00 ( 759) link_BETA1-4 : bond 0.00424 / 0.27 ( 5) link_BETA1-4 : angle 1.76586 / 1.18 ( 15) link_NAG-ASN : bond 0.00314 / 0.20 ( 4) link_NAG-ASN : angle 0.92716 / 0.65 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.281 Fit side-chains REVERT: A 252 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7032 (tp40) REVERT: A 271 ARG cc_start: 0.7593 (ttt-90) cc_final: 0.7072 (ttt-90) REVERT: A 389 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7432 (ppt170) REVERT: B 274 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7434 (t80) REVERT: B 323 ASP cc_start: 0.7888 (m-30) cc_final: 0.7617 (m-30) REVERT: B 389 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.6237 (mtm180) REVERT: L 55 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7224 (tt0) outliers start: 24 outliers final: 20 residues processed: 102 average time/residue: 0.0873 time to fit residues: 12.5257 Evaluate side-chains 108 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 18 optimal weight: 0.0570 chunk 3 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 0.0670 chunk 86 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.123047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.097445 restraints weight = 9469.449| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.92 r_work: 0.2777 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8348 Z= 0.145 Angle : 0.562 9.858 11440 Z= 0.272 Chirality : 0.043 0.269 1300 Planarity : 0.004 0.059 1451 Dihedral : 5.914 58.451 1364 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.37 % Allowed : 16.71 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.25), residues: 1073 helix: -0.07 (0.29), residues: 312 sheet: -0.89 (0.29), residues: 307 loop : -1.24 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.013 0.001 TYR H 80 PHE 0.015 0.001 PHE A 136 TRP 0.007 0.001 TRP L 92 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.14 ( 8333) covalent geometry : angle 0.55744 / 0.27 (11401) SS BOND : bond 0.00313 / 0.24 ( 6) SS BOND : angle 0.75401 / 0.52 ( 12) hydrogen bonds : bond 0.03325 / 2.24 ( 278) hydrogen bonds : angle 4.30152 / 3.01 ( 759) link_BETA1-4 : bond 0.00434 / 0.27 ( 5) link_BETA1-4 : angle 1.78719 / 1.18 ( 15) link_NAG-ASN : bond 0.00346 / 0.22 ( 4) link_NAG-ASN : angle 0.95253 / 0.66 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2013.16 seconds wall clock time: 35 minutes 6.52 seconds (2106.52 seconds total)